# 21_3dRNA_1_rpr.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Sun Feb 25 09:32:27 2024 File name: 21_3dRNA_1_rpr.pdb no. of DNA/RNA chains: 1 [A=39] no. of nucleotides: 39 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 5 base pair(s) 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W -155.3(anti) C3'-endo lambda=54.9; -153.9(anti) C2'-endo lambda=53.5 d(C1'-C1')=10.80 d(N1-N9)=9.06 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=5.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.94]; N3-N1(imino)[2.95]; N4(amino)-O6(carbonyl)[2.83]" bp_pars: [0.30 -0.10 -0.30 7.77 -11.12 -1.79] 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W -151.8(anti) C3'-endo lambda=50.9; -161.2(anti) C3'-endo lambda=50.6 d(C1'-C1')=11.02 d(N1-N9)=9.14 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-9.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.11]; N3-N1(imino)[3.00]; N4(amino)-O6(carbonyl)[2.75]" bp_pars: [0.31 -0.10 -0.54 11.74 -8.29 -6.71] 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W -161.1(anti) C3'-endo lambda=56.7; -149.4(anti) C3'-endo lambda=53.2 d(C1'-C1')=10.75 d(N1-N9)=9.04 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=-11.6 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.81]; N1(imino)-N3[2.88]; N2(amino)-O2(carbonyl)[2.88]" bp_pars: [0.16 -0.11 -0.33 -4.55 -18.44 -0.13] 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W -154.4(anti) C3'-endo lambda=55.6; -151.1(anti) C3'-endo lambda=65.2 d(C1'-C1')=10.46 d(N1-N9)=8.99 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-6.5 H-bonds[4]: "O6(carbonyl)-N4(amino)[3.25]; N1(imino)-O2(carbonyl)[3.25]; N1(imino)-N3[3.07]; N2(amino)-O2(carbonyl)[2.72]" bp_pars: [-0.88 0.01 -0.15 0.15 -6.82 8.03] 5 A.A5 A.C20 [A-C] 00-n/a tWH tW-M -133.9(anti) C2'-endo lambda=66.4; -170.5(anti) C1'-exo lambda=10.5 d(C1'-C1')=10.94 d(N1-N9)=9.02 d(C6-C8)=8.74 tor(N1-C1'-C1'-N9)=152.0 H-bonds[1]: "N3-N4(amino)[3.40]" bp_pars: [6.37 -2.96 -1.83 8.61 -13.19 -54.48] **************************************************************************** List of 1 helix helix=1[1] bps=5 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W 5 A.A5 A.C20 [A-C] 00-n/a tWH tW-M **************************************************************************** List of 1 stem stem=1[#1] bps=4 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W **************************************************************************** >chain-A #1 RNA* with 39 nts CCGGACGAGGUGCGCGUACCCGGUACGACAAGACGGCGC ((((...............))))................ # 21_Adamiak_1_rpr.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Sun Feb 25 09:32:27 2024 File name: 21_Adamiak_1_rpr.pdb no. of DNA/RNA chains: 1 [A=41] no. of nucleotides: 41 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 17 base pair(s) 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 174.7(anti) C2'-exo lambda=59.4; -163.7(anti) C3'-endo lambda=50.6 d(C1'-C1')=10.42 d(N1-N9)=8.75 d(C6-C8)=9.72 tor(N1-C1'-C1'-N9)=1.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.69]; N3-N1(imino)[2.89]; N4(amino)-O6(carbonyl)[2.96]" bp_pars: [0.92 -0.34 -0.09 -3.48 1.20 2.01] 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W -158.6(anti) C2'-exo lambda=57.8; -171.4(anti) C3'-endo lambda=50.2 d(C1'-C1')=10.38 d(N1-N9)=8.66 d(C6-C8)=9.59 tor(N1-C1'-C1'-N9)=-4.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.68]; N3-N1(imino)[2.77]; N4(amino)-O6(carbonyl)[2.76]" bp_pars: [0.79 -0.45 0.07 -6.55 -5.27 -0.27] 3 A.G3 A.C21 [G-C] 00-n/a c.W c.-W 178.0(anti) C2'-exo lambda=24.1; 175.2(anti) C2'-exo lambda=29.2 d(C1'-C1')=12.79 d(N1-N9)=10.17 d(C6-C8)=9.74 tor(N1-C1'-C1'-N9)=24.5 H-bonds[1]: "O6(carbonyl)-N4(amino)[2.89]" bp_pars: [-0.84 0.76 -2.08 9.02 -13.49 -55.99] 4 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 178.0(anti) C2'-exo lambda=46.0; -173.0(anti) C2'-exo lambda=54.9 d(C1'-C1')=10.51 d(N1-N9)=8.66 d(C6-C8)=9.45 tor(N1-C1'-C1'-N9)=-15.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.71]; N1(imino)-N3[2.78]; N2(amino)-O2(carbonyl)[2.92]" bp_pars: [-0.92 -0.61 0.41 1.48 -16.99 -6.33] 5 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W -161.1(anti) C2'-exo lambda=45.5; 175.2(anti) C2'-exo lambda=54.9 d(C1'-C1')=10.62 d(N1-N9)=8.76 d(C6-C8)=9.53 tor(N1-C1'-C1'-N9)=-17.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.83]; N1(imino)-N3[2.90]; N2(amino)-O2(carbonyl)[3.00]" bp_pars: [-0.88 -0.55 0.83 5.31 -14.59 -7.70] 6 A.G7 A.A35 [G+A] 09-IX cWH cW+M -145.5(anti) C3'-endo lambda=56.5; -164.4(anti) C3'-endo lambda=42.2 d(C1'-C1')=10.56 d(N1-N9)=8.68 d(C6-C8)=7.91 tor(N1-C1'-C1'-N9)=11.1 H-bonds[3]: "O6(carbonyl)-N6(amino)[3.21]; N1(imino)-N7[3.15]; N2(amino)-OP2[3.12]" bp_pars: [-0.15 4.57 -2.10 15.40 -11.00 -83.31] 7 A.A8 A.A35 [A+A] 00-n/a cWH cW+M -136.6(anti) C3'-endo lambda=94.7; -164.4(anti) C3'-endo lambda=54.6 d(C1'-C1')=8.03 d(N1-N9)=7.31 d(C6-C8)=7.39 tor(N1-C1'-C1'-N9)=-12.1 H-bonds[1]: "N1-N6(amino)[3.06]" bp_pars: [3.50 2.81 0.51 25.61 -20.04 -34.38] 8 A.G10 A.G38 [G-G] 00-n/a tWH tW-M 106.7(...) C2'-exo lambda=28.8; -153.5(anti) C2'-exo lambda=70.4 d(C1'-C1')=9.18 d(N1-N9)=7.63 d(C6-C8)=6.89 tor(N1-C1'-C1'-N9)=116.2 H-bonds[2]: "N1(imino)-N7[3.21]; N2(amino)-N7[3.25]" bp_pars: [6.12 -0.09 1.13 -24.65 -20.93 -165.48] 9 A.G12 A.C41 [G-C] WC 19-XIX cWW cW-W -175.1(anti) C2'-exo lambda=46.7; -158.6(anti) C3'-endo lambda=58.1 d(C1'-C1')=10.55 d(N1-N9)=8.77 d(C6-C8)=9.63 tor(N1-C1'-C1'-N9)=-1.4 H-bonds[4]: "O6(carbonyl)-N4(amino)[2.85]; N1(imino)-O2(carbonyl)[3.08]; N1(imino)-N3[2.96]; N2(amino)-O2(carbonyl)[2.95]" bp_pars: [-1.12 -0.45 0.04 -2.65 -1.37 -2.92] 10 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W -166.7(anti) C3'-endo lambda=58.7; -176.9(anti) C2'-exo lambda=49.0 d(C1'-C1')=10.45 d(N1-N9)=8.73 d(C6-C8)=9.66 tor(N1-C1'-C1'-N9)=-7.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.77]; N3-N1(imino)[2.87]; N4(amino)-O6(carbonyl)[2.90]" bp_pars: [0.97 -0.41 0.12 0.48 -8.67 -0.06] 11 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W -150.9(anti) C2'-exo lambda=49.8; -142.1(anti) C3'-endo lambda=61.1 d(C1'-C1')=10.33 d(N1-N9)=8.68 d(C6-C8)=9.67 tor(N1-C1'-C1'-N9)=-3.5 H-bonds[4]: "O6(carbonyl)-N4(amino)[3.00]; N1(imino)-O2(carbonyl)[3.01]; N1(imino)-N3[2.88]; N2(amino)-O2(carbonyl)[2.67]" bp_pars: [-1.07 -0.40 -0.10 -1.16 -6.28 3.29] 12 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W -163.4(anti) C3'-endo lambda=61.4; -153.5(anti) C2'-exo lambda=48.8 d(C1'-C1')=10.31 d(N1-N9)=8.65 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=-8.6 H-bonds[4]: "O2(carbonyl)-N1(imino)[2.91]; O2(carbonyl)-N2(amino)[2.72]; N3-N1(imino)[2.91]; N4(amino)-O6(carbonyl)[3.02]" bp_pars: [1.21 -0.47 0.15 4.03 -9.14 2.33] 13 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W -159.4(anti) C3'-endo lambda=61.5; -161.8(anti) C3'-endo lambda=47.9 d(C1'-C1')=10.36 d(N1-N9)=8.68 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=5.1 H-bonds[5]: "O2(carbonyl)-N1(imino)[2.92]; O2(carbonyl)-N2(amino)[2.82]; N3*O6(carbonyl)[2.92]; N3-N1(imino)[2.96]; N4(amino)-O6(carbonyl)[3.01]" bp_pars: [1.28 -0.46 -0.19 7.78 5.02 1.04] 14 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W -165.7(anti) C3'-endo lambda=52.2; -161.4(anti) C3'-endo lambda=58.3 d(C1'-C1')=10.52 d(N1-N9)=8.85 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=2.6 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.00]; N1(imino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.70]" bp_pars: [-0.65 -0.20 -0.18 -5.98 2.17 2.29] 15 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W -150.0(anti) C3'-endo lambda=60.4; -164.4(anti) C3'-endo lambda=58.9 d(C1'-C1')=9.99 d(N1-N9)=8.51 d(C6-C8)=9.67 tor(N1-C1'-C1'-N9)=5.7 H-bonds[2]: "N3(imino)-N1[2.62]; O4(carbonyl)-N6(amino)[3.06]" bp_pars: [0.08 -0.24 -0.32 5.00 4.54 9.40] 16 A.C20 A.G34 [C-G] 00-n/a cWW cW-W -179.7(anti) C2'-exo lambda=74.0; 172.8(anti) C2'-exo lambda=51.7 d(C1'-C1')=9.15 d(N1-N9)=7.87 d(C6-C8)=9.10 tor(N1-C1'-C1'-N9)=32.5 H-bonds[2]: "O2(carbonyl)-N2(amino)[2.87]; N3-N1(imino)[2.68]" bp_pars: [0.76 -0.04 -0.89 48.12 42.72 20.23] 17 A.C20 A.A35 [C-A] 00-n/a cWS cW-m -179.7(anti) C2'-exo lambda=56.6; -164.4(anti) C3'-endo lambda=79.6 d(C1'-C1')=8.44 d(N1-N9)=7.39 d(C6-C8)=8.65 tor(N1-C1'-C1'-N9)=25.5 H-bonds[1]: "N4(amino)-N1[3.05]" bp_pars: [-2.03 -1.03 1.86 23.96 46.63 54.56] **************************************************************************** List of 4 multiplet(s) 1 nts=3 A.G7+A.C20+A.G34 [GCG] 2 nts=3 A.G7+A.C20+A.A35 [GCA] 3 nts=3 A.A8+A.U18+A.A35 [AUA] 4 nts=3 A.G10+A.C15+A.G38 [GCG] **************************************************************************** List of 2 helices helix=1[1] bps=4 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W helix=2[1] bps=8 1 A.G12 A.C41 [G-C] WC 19-XIX cWW cW-W 2 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W 3 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W 4 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W 5 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W 6 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W 7 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W 8 A.C20 A.G34 [C-G] 00-n/a cWW cW-W **************************************************************************** List of 2 stems stem=1[#1] bps=4 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W stem=2[#2] bps=7 1 A.G12 A.C41 [G-C] WC 19-XIX cWW cW-W 2 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W 3 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W 4 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W 5 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W 6 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W 7 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W **************************************************************************** List of 2 hairpin loop(s) 1 nts=16 ACGAGGUGCGCCGUAC closed by pair {A.G4+A.C21 [GC], #1} A.G4+A.A5+A.C6+A.G7+A.A8+A.G9+A.G10+A.U11+A.G12+A.C13+A.G14+A.C15+A.C16+A.G17+A.U18+A.A19+A.C20+A.C21 [GACGAGGUGCGCCGUACC] 2 nts=16 ACCCGGUCACGACAAG closed by pair {A.U18+A.A35 [UA], #2} A.U18+A.A19+A.C20+A.C21+A.C22+A.G23+A.G24+A.U25+A.C26+A.A27+A.C28+A.G29+A.A30+A.C31+A.A32+A.A33+A.G34+A.A35 [UACCCGGUCACGACAAGA] This structure contains pseudo-knot(s). **************************************************************************** >chain-A #1 RNA with 41 nts CCGGACGAGGUGCGCCGUACCCGGUCACGACAAGACGGCGC ((((.......[[[[[[[..))))..........]]]]]]] # 21_ChenHighLig_1_rpr.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Sun Feb 25 09:32:28 2024 File name: 21_ChenHighLig_1_rpr.pdb no. of DNA/RNA chains: 1 [A=41] no. of nucleotides: 41 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 23 base pair(s) 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W -162.3(anti) C3'-endo lambda=60.2; -168.8(anti) C3'-endo lambda=59.5 d(C1'-C1')=10.47 d(N1-N9)=8.98 d(C6-C8)=10.11 tor(N1-C1'-C1'-N9)=-1.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.56]; N3-N1(imino)[3.06]; N4(amino)-O6(carbonyl)[3.43]" bp_pars: [0.06 0.13 0.26 1.89 2.56 9.52] 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W -165.9(anti) C3'-endo lambda=52.6; -170.2(anti) C3'-endo lambda=51.1 d(C1'-C1')=10.89 d(N1-N9)=9.06 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=-3.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.13]; N3-N1(imino)[2.98]; N4(amino)-O6(carbonyl)[2.74]" bp_pars: [0.25 -0.16 0.23 -4.70 9.19 -6.31] 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W -155.8(anti) C3'-endo lambda=52.7; -171.7(anti) C3'-endo lambda=56.8 d(C1'-C1')=10.72 d(N1-N9)=9.01 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=5.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.09]; N1(imino)-N3[3.04]; N2(amino)-O2(carbonyl)[2.88]" bp_pars: [-0.51 -0.01 -0.04 17.56 6.84 0.35] 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W -172.5(anti) C3'-endo lambda=58.2; -162.3(anti) C3'-endo lambda=56.5 d(C1'-C1')=10.68 d(N1-N9)=9.08 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-7.0 H-bonds[4]: "O6(carbonyl)-N4(amino)[3.27]; N1(imino)-N3[3.07]; N2(amino)-O2(carbonyl)[2.71]; N2(amino)-N3[3.35]" bp_pars: [0.18 0.10 0.07 -1.40 -4.76 5.04] 5 A.A5 A.C20 [A-C] 00-n/a ... c... -147.2(anti) C3'-endo lambda=57.5; -165.9(anti) C3'-endo lambda=50.0 d(C1'-C1')=10.66 d(N1-N9)=8.92 d(C6-C8)=9.76 tor(N1-C1'-C1'-N9)=-4.4 H-bonds[2]: "N6(amino)*N4(amino)[2.73]; N1*N3[2.92]" bp_pars: [0.54 -0.19 -0.78 11.52 -13.35 -1.93] 6 A.A5 A.A32 [A+A] 00-n/a tSW tm+W -147.2(anti) C3'-endo lambda=108.7; -163.1(anti) C3'-endo lambda=7.4 d(C1'-C1')=10.11 d(N1-N9)=9.20 d(C6-C8)=9.95 tor(N1-C1'-C1'-N9)=-105.6 H-bonds[1]: "N3-N6(amino)[2.94]" bp_pars: [3.37 -3.30 0.76 0.51 -0.85 -75.57] 7 A.C6 A.A19 [C-A] 00-n/a cW. cW-. -162.3(anti) C3'-endo lambda=61.6; -165.1(anti) C3'-endo lambda=27.6 d(C1'-C1')=11.28 d(N1-N9)=9.27 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=4.3 H-bonds[2]: "O2(carbonyl)-N6(amino)[3.29]; N3-N6(amino)[2.96]" bp_pars: [3.32 -0.81 -1.23 -4.43 -12.15 -19.87] 8 A.C6 A.G34 [C-G] 00-n/a tSH cm-M -162.3(anti) C3'-endo lambda=106.0; 69.4(syn) C1'-exo lambda=22.5 d(C1'-C1')=7.75 d(N1-N9)=6.86 d(C6-C8)=7.72 tor(N1-C1'-C1'-N9)=9.0 H-bonds[3]: "O2'(hydroxyl)-O6(carbonyl)[2.71]; O2'(hydroxyl)-N2(amino)[2.49]; O2(carbonyl)-N1(imino)[3.30]" bp_pars: [4.94 -3.98 -1.84 21.71 2.74 19.61] 9 A.G7 A.C16 [G-C] 00-n/a cW. cW-. -154.4(anti) C3'-endo lambda=38.2; -159.7(anti) C3'-endo lambda=20.3 d(C1'-C1')=12.65 d(N1-N9)=10.10 d(C6-C8)=9.00 tor(N1-C1'-C1'-N9)=41.1 H-bonds[1]: "O6(carbonyl)-N4(amino)[2.37]" bp_pars: [2.73 1.73 0.22 -42.80 -1.84 -84.73] 10 A.G7 A.G17 [G-G] 00-n/a cWH cW-M -154.4(anti) C3'-endo lambda=62.0; -167.8(anti) C3'-endo lambda=19.6 d(C1'-C1')=12.25 d(N1-N9)=10.21 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=4.5 H-bonds[2]: "N1(imino)-O6(carbonyl)[2.80]; N2(amino)-O6(carbonyl)[2.72]" bp_pars: [3.68 0.79 1.76 -48.59 -0.57 -46.73] 11 A.G7 A.C36 [G+C] 00-n/a ... c... -154.4(anti) C3'-endo lambda=95.0; -143.9(anti) C3'-endo lambda=24.9 d(C1'-C1')=8.75 d(N1-N9)=7.59 d(C6-C8)=8.05 tor(N1-C1'-C1'-N9)=-3.4 H-bonds[1]: "N1(imino)*N4(amino)[2.50]" bp_pars: [2.88 0.17 2.39 -58.03 3.51 -59.29] 12 A.G10 A.G12 [G-G] 00-n/a tWH tW-M -171.9(anti) C3'-endo lambda=61.5; -170.2(anti) C3'-endo lambda=36.1 d(C1'-C1')=8.78 d(N1-N9)=7.09 d(C6-C8)=6.64 tor(N1-C1'-C1'-N9)=-105.7 H-bonds[1]: "N2(amino)-O6(carbonyl)[2.74]" bp_pars: [5.14 -3.23 -1.42 56.48 28.46 -107.95] 13 A.U11 A.G12 [U+G] 00-n/a cWH cW+M -166.2(anti) C3'-endo lambda=92.5; -170.2(anti) C3'-endo lambda=61.2 d(C1'-C1')=5.39 d(N1-N9)=4.76 d(C6-C8)=4.57 tor(N1-C1'-C1'-N9)=-17.9 H-bonds[2]: "O3'*O5'[2.29]; N3(imino)-N7[2.53]" bp_pars: [2.74 1.97 -0.46 -21.12 -25.37 -7.43] 14 A.G12 A.C41 [G-C] WC 19-XIX cWW cW-W -170.2(anti) C3'-endo lambda=54.9; -175.3(anti) C3'-endo lambda=58.6 d(C1'-C1')=10.25 d(N1-N9)=8.63 d(C6-C8)=9.66 tor(N1-C1'-C1'-N9)=-18.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.11]; N1(imino)-N3[2.79]; N2(amino)-O2(carbonyl)[2.45]" bp_pars: [-0.52 -0.39 0.79 -3.39 -14.62 3.40] 15 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W -147.2(anti) C3'-endo lambda=56.9; -154.1(anti) C3'-endo lambda=52.0 d(C1'-C1')=10.56 d(N1-N9)=8.82 d(C6-C8)=9.71 tor(N1-C1'-C1'-N9)=-1.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.68]; N3-N1(imino)[2.87]; N4(amino)-O6(carbonyl)[2.96]" bp_pars: [0.60 -0.23 0.05 -12.11 -7.58 1.86] 16 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W -170.1(anti) C3'-endo lambda=56.8; -162.3(anti) C3'-endo lambda=61.5 d(C1'-C1')=10.23 d(N1-N9)=8.72 d(C6-C8)=9.81 tor(N1-C1'-C1'-N9)=-16.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.25]; N1(imino)-N3[2.87]; N2(amino)-O2(carbonyl)[2.40]" bp_pars: [-0.41 -0.17 0.56 3.72 -9.36 7.67] 17 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W -172.8(anti) C3'-endo lambda=54.8; -168.5(anti) C3'-endo lambda=55.5 d(C1'-C1')=10.67 d(N1-N9)=8.99 d(C6-C8)=9.96 tor(N1-C1'-C1'-N9)=-8.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.74]; N3-N1(imino)[2.90]; N4(amino)-O6(carbonyl)[2.96]" bp_pars: [0.02 -0.08 0.22 0.56 -10.85 1.35] 18 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W -159.7(anti) C3'-endo lambda=55.4; -171.5(anti) C3'-endo lambda=47.0 d(C1'-C1')=10.88 d(N1-N9)=9.04 d(C6-C8)=9.99 tor(N1-C1'-C1'-N9)=-27.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.76]; N3-N1(imino)[3.02]; N4(amino)-O6(carbonyl)[3.25]" bp_pars: [0.38 -0.04 0.53 -7.33 -22.25 2.41] 19 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W -167.8(anti) C3'-endo lambda=55.8; -143.9(anti) C3'-endo lambda=64.7 d(C1'-C1')=10.03 d(N1-N9)=8.58 d(C6-C8)=9.75 tor(N1-C1'-C1'-N9)=1.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.25]; N1(imino)-N3[2.84]; N2(amino)-O2(carbonyl)[2.29]" bp_pars: [-0.79 -0.25 -0.76 -9.24 -2.94 11.70] 20 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W -176.0(anti) C2'-exo lambda=62.0; -165.4(anti) C3'-endo lambda=70.8 d(C1'-C1')=9.60 d(N1-N9)=8.42 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-14.0 H-bonds[1]: "N3(imino)-N1[2.89]" bp_pars: [-0.39 0.11 0.52 20.25 -20.54 20.03] 21 A.A19 A.G34 [A+G] 00-n/a ... c... -165.1(anti) C3'-endo lambda=69.0; 69.4(syn) C1'-exo lambda=69.8 d(C1'-C1')=8.27 d(N1-N9)=7.23 d(C6-C8)=6.74 tor(N1-C1'-C1'-N9)=1.2 H-bonds[1]: "N1*N7[2.23]" bp_pars: [0.88 4.89 0.07 24.06 -11.53 -41.98] 22 A.C20 A.A33 [C-A] 00-n/a ... c... -165.9(anti) C3'-endo lambda=114.1; 177.3(anti) C3'-endo lambda=100.8 d(C1'-C1')=5.51 d(N1-N9)=6.42 d(C6-C8)=9.01 tor(N1-C1'-C1'-N9)=-20.4 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.31]; O2(carbonyl)*N1[3.23]" bp_pars: [0.83 3.08 1.44 9.16 -13.93 107.22] 23 A.C21 A.A32 [C-A] 00-n/a cSW cm-W -162.3(anti) C3'-endo lambda=163.9; -163.1(anti) C3'-endo lambda=54.5 d(C1'-C1')=5.68 d(N1-N9)=6.30 d(C6-C8)=8.15 tor(N1-C1'-C1'-N9)=-24.6 H-bonds[2]: "O4'*N3[2.84]; O2(carbonyl)-N6(amino)[2.86]" bp_pars: [4.42 1.18 1.73 -8.78 -12.47 109.61] **************************************************************************** List of 6 multiplet(s) 1 nts=3 A.G4+A.C21+A.A32 [GCA] 2 nts=3* A.A5+A.C20+A.A33 [ACA] 3 nts=3 A.C6+A.A19+A.G34 [CAG] 4 nts=3 A.G7+A.C16+A.G37 [GCG] 5 nts=3* A.G7+A.G17+A.C36 [GGC] 6 nts=3 A.U11+A.G12+A.C41 [UGC] **************************************************************************** List of 1 helix helix=1[2] bps=13 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W 5 A.A5 A.C20 [A-C] 00-n/a ... c... 6 A.C6 A.A19 [C-A] 00-n/a cW. cW-. 7 A.A35 A.U18 [A-U] WC 20-XX cWW cW-W 8 A.C36 A.G17 [C-G] WC 19-XIX cWW cW-W 9 A.G37 A.C16 [G-C] WC 19-XIX cWW cW-W 10 A.G38 A.C15 [G-C] WC 19-XIX cWW cW-W 11 A.C39 A.G14 [C-G] WC 19-XIX cWW cW-W 12 A.G40 A.C13 [G-C] WC 19-XIX cWW cW-W 13 A.C41 A.G12 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems stem=1[#1] bps=4 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W stem=2[#1] bps=7 1 A.G12 A.C41 [G-C] WC 19-XIX cWW cW-W 2 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W 3 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W 4 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W 5 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W 6 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W 7 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 2 stems: [#1, #2] **************************************************************************** >chain-A #1 RNA* with 41 nts CCGGACGAGGUGCGCCGUACCCGGUCACGACAAGACGGCGC ((((.......(((((((..))))..........))))))) # 21_Das_1_rpr.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Sun Feb 25 09:32:28 2024 File name: 21_Das_1_rpr.pdb no. of DNA/RNA chains: 1 [A=41] no. of nucleotides: 41 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 31 base pair(s) 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W -164.1(anti) C3'-endo lambda=55.2; -159.6(anti) C3'-endo lambda=53.8 d(C1'-C1')=10.60 d(N1-N9)=8.89 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=5.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.71]; N3-N1(imino)[2.86]; N4(amino)-O6(carbonyl)[2.87]" bp_pars: [0.19 -0.21 -0.48 -4.97 2.96 -0.08] 2 A.C1 A.U25 [C-U] 00-n/a cWW cW-W -164.1(anti) C3'-endo lambda=46.1; -115.4(anti) C2'-endo lambda=90.0 d(C1'-C1')=8.95 d(N1-N9)=7.94 d(C6-C8)=9.30 tor(N1-C1'-C1'-N9)=16.8 H-bonds[1]: "N4(amino)-O2(carbonyl)[3.62]" bp_pars: [-2.81 -0.61 1.10 -39.28 35.45 35.96] 3 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W -163.3(anti) C3'-endo lambda=54.6; -169.1(anti) C3'-endo lambda=53.3 d(C1'-C1')=10.73 d(N1-N9)=8.99 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=0.0 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.80]; N3-N1(imino)[2.91]; N4(amino)-O6(carbonyl)[2.86]" bp_pars: [0.16 -0.13 -0.05 -1.00 -0.53 -0.89] 4 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W -165.3(anti) C3'-endo lambda=53.1; -163.4(anti) C3'-endo lambda=53.8 d(C1'-C1')=10.78 d(N1-N9)=9.01 d(C6-C8)=9.89 tor(N1-C1'-C1'-N9)=-1.0 H-bonds[3]: "N1(imino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.86]; O6(carbonyl)-N4(amino)[2.83]" bp_pars: [-0.10 -0.12 -0.15 -5.66 -3.14 -2.07] 5 A.G3 A.C31 [G+C] 29-XXIX* tSW tm+W -165.3(anti) C3'-endo lambda=97.2; -125.4(anti) C2'-endo lambda=6.1 d(C1'-C1')=9.09 d(N1-N9)=7.94 d(C6-C8)=8.83 tor(N1-C1'-C1'-N9)=-107.7 H-bonds[3]: "O2'(hydroxyl)-N4(amino)[2.86]; N2(amino)-N3[2.84]; N3-N4(amino)[2.69]" bp_pars: [2.21 -2.54 1.02 -17.36 -28.00 -79.54] 6 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W -150.9(anti) C3'-endo lambda=53.4; -169.8(anti) C3'-endo lambda=53.7 d(C1'-C1')=10.53 d(N1-N9)=8.78 d(C6-C8)=9.70 tor(N1-C1'-C1'-N9)=-17.7 H-bonds[3]: "N1(imino)-N3[2.69]; N2(amino)-O2(carbonyl)[2.74]; O6(carbonyl)-N4(amino)[2.84]" bp_pars: [-0.13 -0.32 0.11 -4.91 -25.40 0.16] 7 A.G4 A.A32 [G+A] 00-n/a tSW cm+W -150.9(anti) C3'-endo lambda=115.6; -150.1(anti) C3'-endo lambda=12.1 d(C1'-C1')=8.96 d(N1-N9)=8.26 d(C6-C8)=9.04 tor(N1-C1'-C1'-N9)=74.1 H-bonds[3]: "O2'(hydroxyl)-N6(amino)[3.01]; N2(amino)-N1[2.52]; N3-N6(amino)[2.57]" bp_pars: [3.26 -3.14 -0.86 -12.73 1.76 -61.49] 8 A.A5 A.A19 [A-A] 00-n/a tWH cW-M -153.5(anti) C3'-endo lambda=38.3; -158.3(anti) C3'-endo lambda=3.6 d(C1'-C1')=12.43 d(N1-N9)=9.84 d(C6-C8)=9.04 tor(N1-C1'-C1'-N9)=56.9 H-bonds[1]: "N1-N6(amino)[2.72]" bp_pars: [3.88 -0.02 -2.33 -4.09 -38.19 -66.94] 9 A.A5 A.C20 [A-C] 00-n/a cWW cW-W -153.5(anti) C3'-endo lambda=59.8; -162.7(anti) C3'-endo lambda=35.2 d(C1'-C1')=11.48 d(N1-N9)=9.55 d(C6-C8)=10.16 tor(N1-C1'-C1'-N9)=-25.1 H-bonds[1]: "N1-N4(amino)[2.58]" bp_pars: [2.48 -0.10 0.92 0.89 -20.86 -14.77] 10 A.A5 A.A33 [A+A] 00-n/a cSH cm+M -153.5(anti) C3'-endo lambda=126.6; -159.5(anti) C3'-endo lambda=29.2 d(C1'-C1')=7.89 d(N1-N9)=7.51 d(C6-C8)=7.71 tor(N1-C1'-C1'-N9)=-29.6 H-bonds[2]: "O2'(hydroxyl)-N7[3.86]; N3-N6(amino)[3.02]" bp_pars: [5.46 -0.40 1.99 -12.07 -11.69 -25.90] 11 A.C6 A.G17 [C-G] 00-n/a tWH cW-M -138.3(anti) C3'-endo lambda=24.5; -165.3(anti) C3'-endo lambda=13.4 d(C1'-C1')=11.94 d(N1-N9)=9.17 d(C6-C8)=8.06 tor(N1-C1'-C1'-N9)=37.0 H-bonds[1]: "N4(amino)-O6(carbonyl)[2.76]" bp_pars: [1.67 1.10 -0.18 -31.83 -12.42 -91.47] 12 A.C6 A.A35 [C+A] 00-n/a cWH cW+M -138.3(anti) C3'-endo lambda=95.0; -172.4(anti) C3'-endo lambda=22.6 d(C1'-C1')=8.43 d(N1-N9)=7.29 d(C6-C8)=7.69 tor(N1-C1'-C1'-N9)=-46.9 H-bonds[2]: "O2(carbonyl)-N6(amino)[2.45]; N3-N6(amino)[3.24]" bp_pars: [2.30 -0.41 2.38 -15.21 -19.46 -65.54] 13 A.C6 A.C36 [C+C] 00-n/a cW. cW+. -138.3(anti) C3'-endo lambda=68.4; -163.8(anti) C3'-endo lambda=20.9 d(C1'-C1')=10.62 d(N1-N9)=8.74 d(C6-C8)=8.98 tor(N1-C1'-C1'-N9)=19.2 H-bonds[1]: "N3-N4(amino)[3.28]" bp_pars: [1.50 1.11 -0.09 -37.42 -14.17 -89.08] 14 A.G7 A.C15 [G-C] 00-n/a t.. t.-. -157.2(anti) C3'-endo lambda=1.8; -162.1(anti) C3'-endo lambda=21.2 d(C1'-C1')=13.19 d(N1-N9)=10.35 d(C6-C8)=8.59 tor(N1-C1'-C1'-N9)=-117.3 H-bonds[1]: "O6(carbonyl)-N4(amino)[2.71]" bp_pars: [1.64 3.63 -1.58 -12.62 5.75 -125.40] 15 A.G7 A.C16 [G-C] 00-n/a cW. cW-. -157.2(anti) C3'-endo lambda=22.3; -162.1(anti) C3'-endo lambda=6.1 d(C1'-C1')=13.39 d(N1-N9)=10.57 d(C6-C8)=9.38 tor(N1-C1'-C1'-N9)=51.8 H-bonds[1]: "O6(carbonyl)-N4(amino)[2.47]" bp_pars: [1.89 2.40 1.30 -21.34 4.63 -93.70] 16 A.G7 A.G37 [G+G] 06-VI cWH cW+M -157.2(anti) C3'-endo lambda=67.6; -167.8(anti) C3'-endo lambda=22.3 d(C1'-C1')=11.40 d(N1-N9)=9.51 d(C6-C8)=9.38 tor(N1-C1'-C1'-N9)=-0.6 H-bonds[3]: "N1(imino)-O6(carbonyl)[2.47]; N2(amino)-O6(carbonyl)[3.18]; N2(amino)-N7[2.71]" bp_pars: [1.88 2.62 1.36 -22.10 5.02 -92.32] 17 A.A8 A.G14 [A-G] 00-n/a cHH cM-M -155.0(anti) C3'-endo lambda=17.6; -165.3(anti) C3'-endo lambda=20.1 d(C1'-C1')=13.80 d(N1-N9)=11.01 d(C6-C8)=8.77 tor(N1-C1'-C1'-N9)=-38.7 H-bonds[1]: "N6(amino)-O6(carbonyl)[3.66]" bp_pars: [0.11 5.72 -1.77 -5.66 -5.04 -144.59] 18 A.A8 A.G38 [A+G] 00-n/a cWH cW+M -155.0(anti) C3'-endo lambda=46.3; -168.0(anti) C3'-endo lambda=25.0 d(C1'-C1')=12.28 d(N1-N9)=9.94 d(C6-C8)=9.24 tor(N1-C1'-C1'-N9)=-14.1 H-bonds[1]: "N6(amino)-O6(carbonyl)[2.69]" bp_pars: [0.06 4.51 0.97 -10.73 -6.95 -109.18] 19 A.G9 A.C13 [G-C] 00-n/a cH. cM-. -150.3(anti) C3'-endo lambda=14.5; -157.7(anti) C3'-endo lambda=19.8 d(C1'-C1')=13.87 d(N1-N9)=11.04 d(C6-C8)=8.91 tor(N1-C1'-C1'-N9)=-11.9 H-bonds[1]: "O6(carbonyl)-N4(amino)[3.50]" bp_pars: [0.60 5.76 -1.65 -3.82 -30.48 -144.04] 20 A.G12 A.C41 [G-C] WC 19-XIX cWW cW-W -171.8(anti) C3'-endo lambda=52.0; -164.1(anti) C3'-endo lambda=52.9 d(C1'-C1')=10.91 d(N1-N9)=9.10 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=-0.8 H-bonds[3]: "N1(imino)-N3[2.99]; N2(amino)-O2(carbonyl)[3.01]; O6(carbonyl)-N4(amino)[2.82]" bp_pars: [-0.12 -0.08 -0.21 -3.22 -3.51 -3.95] 21 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W -157.7(anti) C3'-endo lambda=54.2; -168.1(anti) C3'-endo lambda=52.7 d(C1'-C1')=10.75 d(N1-N9)=8.99 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=-2.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.88]; N3-N1(imino)[2.91]; N4(amino)-O6(carbonyl)[2.82]" bp_pars: [0.19 -0.15 -0.34 5.66 -8.38 -1.67] 22 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W -165.3(anti) C3'-endo lambda=53.2; -163.4(anti) C3'-endo lambda=53.7 d(C1'-C1')=10.78 d(N1-N9)=9.01 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-1.5 H-bonds[3]: "N1(imino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.86]; O6(carbonyl)-N4(amino)[2.83]" bp_pars: [-0.09 -0.12 -0.12 -5.24 -3.55 -2.04] 23 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W -162.1(anti) C3'-endo lambda=54.5; -168.0(anti) C3'-endo lambda=53.1 d(C1'-C1')=10.75 d(N1-N9)=9.00 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=-0.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.83]; N3-N1(imino)[2.92]; N4(amino)-O6(carbonyl)[2.86]" bp_pars: [0.16 -0.12 -0.04 0.32 -1.85 -1.23] 24 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W -162.1(anti) C3'-endo lambda=54.5; -167.8(anti) C3'-endo lambda=53.1 d(C1'-C1')=10.75 d(N1-N9)=9.00 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-0.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.83]; N3-N1(imino)[2.92]; N4(amino)-O6(carbonyl)[2.86]" bp_pars: [0.16 -0.12 -0.05 -0.02 -0.96 -1.29] 25 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W -165.3(anti) C3'-endo lambda=53.1; -163.8(anti) C3'-endo lambda=53.7 d(C1'-C1')=10.78 d(N1-N9)=9.02 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-1.4 H-bonds[3]: "N1(imino)-N3[2.92]; N2(amino)-O2(carbonyl)[2.86]; O6(carbonyl)-N4(amino)[2.83]" bp_pars: [-0.10 -0.12 -0.11 -4.90 -3.36 -2.03] 26 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W -168.4(anti) C3'-endo lambda=56.4; -172.4(anti) C3'-endo lambda=56.9 d(C1'-C1')=9.98 d(N1-N9)=8.36 d(C6-C8)=9.34 tor(N1-C1'-C1'-N9)=-6.5 H-bonds[2]: "N3(imino)-N1[2.55]; O4(carbonyl)-N6(amino)[2.65]" bp_pars: [-0.06 -0.63 0.99 7.64 1.66 2.38] 27 A.A19 A.G34 [A-G] 00-n/a cWW cW-W -158.3(anti) C3'-endo lambda=51.5; -163.5(anti) C3'-endo lambda=52.7 d(C1'-C1')=11.61 d(N1-N9)=9.80 d(C6-C8)=10.43 tor(N1-C1'-C1'-N9)=1.0 H-bonds[1]: "N6(amino)-O6(carbonyl)[2.54]" bp_pars: [-0.14 0.45 -1.73 3.43 -17.56 -3.44] 28 A.C20 A.G34 [C-G] 00-n/a cWW cW-W -162.7(anti) C3'-endo lambda=93.7; -163.5(anti) C3'-endo lambda=61.8 d(C1'-C1')=8.50 d(N1-N9)=7.90 d(C6-C8)=9.61 tor(N1-C1'-C1'-N9)=-4.8 H-bonds[1]: "O2(carbonyl)-N2(amino)[2.62]" bp_pars: [2.36 -0.10 1.94 -2.25 1.92 46.23] 29 A.C21 A.A33 [C-A] 00-n/a cSW cm-W -169.8(anti) C3'-endo lambda=128.6; -159.5(anti) C3'-endo lambda=38.2 d(C1'-C1')=8.41 d(N1-N9)=8.18 d(C6-C8)=9.58 tor(N1-C1'-C1'-N9)=0.6 H-bonds[1]: "O2(carbonyl)-N6(amino)[2.42]" bp_pars: [6.02 -1.29 1.28 1.28 4.11 58.37] 30 A.G23 A.G29 [G-G] 00-n/a cSW cm-W -169.1(anti) C3'-endo lambda=113.0; -162.3(anti) C3'-endo lambda=44.8 d(C1'-C1')=9.87 d(N1-N9)=9.41 d(C6-C8)=10.91 tor(N1-C1'-C1'-N9)=17.0 H-bonds[2]: "O2'(hydroxyl)-N2(amino)[3.21]; N2(amino)-O6(carbonyl)[2.43]" bp_pars: [5.63 0.15 -1.78 -6.29 10.94 46.98] 31 A.G23 A.A30 [G-A] 00-n/a cSW cm-W -169.1(anti) C3'-endo lambda=130.3; -156.3(anti) C3'-endo lambda=38.1 d(C1'-C1')=8.35 d(N1-N9)=8.15 d(C6-C8)=9.52 tor(N1-C1'-C1'-N9)=18.3 H-bonds[2]: "O2'(hydroxyl)-N1[2.93]; N3-N6(amino)[2.72]" bp_pars: [6.21 -1.08 0.65 -18.92 15.81 63.71] **************************************************************************** List of 7 multiplet(s) 1 nts=3 A.G3+A.C22+A.C31 [GCC] 2 nts=3 A.C6+A.G17+A.C36 [CGC] 3 nts=3 A.G7+A.C16+A.G37 [GCG] 4 nts=3 A.A8+A.C15+A.G38 [ACG] 5 nts=4* A.C2+A.G23+A.G29+A.A30 [CGGA] 6 nts=4 A.G4+A.C21+A.A32+A.A33 [GCAA] 7 nts=4* A.A5+A.A19+A.C20+A.G34 [AACG] **************************************************************************** List of 1 helix helix=1[2] bps=13 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W 5 A.A5 A.C20 [A-C] 00-n/a cWW cW-W 6 A.G34 A.A19 [G-A] 00-n/a cWW cW-W 7 A.A35 A.U18 [A-U] WC 20-XX cWW cW-W 8 A.C36 A.G17 [C-G] WC 19-XIX cWW cW-W 9 A.G37 A.C16 [G-C] WC 19-XIX cWW cW-W 10 A.G38 A.C15 [G-C] WC 19-XIX cWW cW-W 11 A.C39 A.G14 [C-G] WC 19-XIX cWW cW-W 12 A.G40 A.C13 [G-C] WC 19-XIX cWW cW-W 13 A.C41 A.G12 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems stem=1[#1] bps=4 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W stem=2[#1] bps=7 1 A.G12 A.C41 [G-C] WC 19-XIX cWW cW-W 2 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W 3 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W 4 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W 5 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W 6 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W 7 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 2 stems: [#1, #2] **************************************************************************** List of 2 hairpin loop(s) 1 nts=16 ACGAGGUGCGCCGUAC closed by pair {A.G4+A.C21 [GC], #1} A.G4+A.A5+A.C6+A.G7+A.A8+A.G9+A.G10+A.U11+A.G12+A.C13+A.G14+A.C15+A.C16+A.G17+A.U18+A.A19+A.C20+A.C21 [GACGAGGUGCGCCGUACC] 2 nts=16 ACCCGGUCACGACAAG closed by pair {A.U18+A.A35 [UA], #2} A.U18+A.A19+A.C20+A.C21+A.C22+A.G23+A.G24+A.U25+A.C26+A.A27+A.C28+A.G29+A.A30+A.C31+A.A32+A.A33+A.G34+A.A35 [UACCCGGUCACGACAAGA] This structure contains pseudo-knot(s). **************************************************************************** >chain-A #1 RNA with 41 nts CCGGACGAGGUGCGCCGUACCCGGUCACGACAAGACGGCGC ((((.......[[[[[[[..))))..........]]]]]]] # 21_solution_2_rpr.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Sun Feb 25 09:32:30 2024 File name: 21_solution_2_rpr.pdb no. of DNA/RNA chains: 1 [A=41] no. of nucleotides: 41 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 29 base pair(s) 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 170.9(anti) C3'-endo lambda=52.5; -140.7(anti) C2'-endo lambda=51.6 d(C1'-C1')=10.59 d(N1-N9)=8.79 d(C6-C8)=9.66 tor(N1-C1'-C1'-N9)=1.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.66]; N3-N1(imino)[2.75]; N4(amino)-O6(carbonyl)[2.75]" bp_pars: [0.22 -0.34 0.02 0.18 -0.53 -2.37] 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 175.9(anti) C3'-exo lambda=44.2; 175.0(anti) C3'-endo lambda=52.8 d(C1'-C1')=11.07 d(N1-N9)=9.13 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-13.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.95]; N3-N1(imino)[2.84]; N4(amino)-O6(carbonyl)[2.58]" bp_pars: [-0.64 -0.23 0.65 2.04 -9.70 -7.92] 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W -169.9(anti) C3'-endo lambda=60.7; -155.7(anti) C3'-endo lambda=55.2 d(C1'-C1')=10.23 d(N1-N9)=8.67 d(C6-C8)=9.74 tor(N1-C1'-C1'-N9)=-4.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.84]; N1(imino)-N3[2.74]; N2(amino)-O2(carbonyl)[2.58]" bp_pars: [-0.11 -0.28 -0.01 -1.66 -1.87 3.36] 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W -173.4(anti) C3'-endo lambda=57.9; -175.0(anti) C3'-endo lambda=53.0 d(C1'-C1')=10.37 d(N1-N9)=8.71 d(C6-C8)=9.65 tor(N1-C1'-C1'-N9)=3.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.68]; N1(imino)-N3[2.72]; N2(amino)-O2(carbonyl)[2.69]" bp_pars: [-0.16 -0.36 -0.06 4.09 -1.49 -2.40] 5 A.A5 A.A19 [A-A] 00-n/a tWH tW-M -121.6(anti) C2'-exo lambda=27.1; -170.1(anti) C3'-endo lambda=14.4 d(C1'-C1')=12.22 d(N1-N9)=9.53 d(C6-C8)=8.24 tor(N1-C1'-C1'-N9)=151.7 H-bonds[1]: "N1-N6(amino)[3.29]" bp_pars: [4.75 0.57 -0.86 -7.98 -13.12 -101.16] 6 A.C6 A.U18 [C-U] 00-n/a tWH tW-M -113.6(anti) C2'-endo lambda=10.3; -164.5(anti) C3'-endo lambda=21.0 d(C1'-C1')=12.41 d(N1-N9)=9.62 d(C6-C8)=8.06 tor(N1-C1'-C1'-N9)=-150.1 H-bonds[1]: "N4(amino)-O4(carbonyl)[3.20]" bp_pars: [3.06 2.37 -1.89 1.83 -24.70 -120.22] 7 A.C6 A.G34 [C+G] rWC 22-XXII tWW tW+W -113.6(anti) C2'-endo lambda=67.8; -169.7(anti) C3'-endo lambda=37.4 d(C1'-C1')=10.04 d(N1-N9)=8.61 d(C6-C8)=10.35 tor(N1-C1'-C1'-N9)=-177.7 H-bonds[3]: "O2(carbonyl)-N1(imino)[2.56]; O2(carbonyl)-N2(amino)[2.71]; N3-N2(amino)[2.74]" bp_pars: [-0.56 -4.81 -0.59 2.68 -0.57 -151.91] 8 A.G7 A.A35 [G+A] 09-IX cWH cW+M -160.1(anti) C3'-endo lambda=47.7; -113.1(anti) C2'-endo lambda=31.4 d(C1'-C1')=11.31 d(N1-N9)=9.09 d(C6-C8)=8.22 tor(N1-C1'-C1'-N9)=-29.5 H-bonds[3]: "O6(carbonyl)-N6(amino)[2.77]; N1(imino)-N7[3.01]; N2(amino)-OP2[2.82]" bp_pars: [-0.87 4.58 1.44 -14.84 -22.76 -103.92] 9 A.G7 A.C36 [G+C] 00-n/a cWH cW+M -160.1(anti) C3'-endo lambda=30.2; -172.5(anti) C3'-endo lambda=17.8 d(C1'-C1')=14.32 d(N1-N9)=11.65 d(C6-C8)=10.77 tor(N1-C1'-C1'-N9)=39.2 H-bonds[1]: "O6(carbonyl)-N4(amino)[3.65]" bp_pars: [-0.75 6.01 -1.73 -14.16 -6.54 -139.68] 10 A.A8 A.C36 [A+C] 00-n/a cWH cW+M -157.6(anti) C3'-endo lambda=58.7; -172.5(anti) C3'-endo lambda=28.6 d(C1'-C1')=11.93 d(N1-N9)=9.89 d(C6-C8)=9.51 tor(N1-C1'-C1'-N9)=-13.3 H-bonds[1]: "N1-N4(amino)[2.88]" bp_pars: [1.43 4.14 1.23 -9.67 -2.39 -92.01] 11 A.A8 A.G37 [A+G] 00-n/a cWH cW+M -157.6(anti) C3'-endo lambda=38.9; -169.1(anti) C3'-endo lambda=23.6 d(C1'-C1')=14.11 d(N1-N9)=11.63 d(C6-C8)=10.86 tor(N1-C1'-C1'-N9)=27.4 H-bonds[1]: "N6(amino)-O6(carbonyl)[3.89]" bp_pars: [0.65 5.31 -1.62 -12.03 -1.00 -123.52] 12 A.G9 A.C16 [G-C] 00-n/a c.. c.-. -156.3(anti) C3'-endo lambda=14.3; -175.7(anti) C3'-endo lambda=5.3 d(C1'-C1')=14.21 d(N1-N9)=11.33 d(C6-C8)=10.12 tor(N1-C1'-C1'-N9)=-63.4 H-bonds[1]: "O6(carbonyl)-N4(amino)[2.83]" bp_pars: [1.20 3.19 0.58 1.24 -2.84 -94.00] 13 A.G9 A.G37 [G+G] 06-VI cWH cW+M -156.3(anti) C3'-endo lambda=60.7; -169.1(anti) C3'-endo lambda=31.1 d(C1'-C1')=11.66 d(N1-N9)=9.69 d(C6-C8)=9.24 tor(N1-C1'-C1'-N9)=-7.8 H-bonds[2]: "N1(imino)-O6(carbonyl)[3.04]; N2(amino)-N7[3.16]" bp_pars: [1.19 3.75 0.62 0.96 -1.83 -94.04] 14 A.G10 A.C15 [G-C] 00-n/a cW. cW-. -153.8(anti) C3'-endo lambda=23.2; -160.5(anti) C3'-endo lambda=10.1 d(C1'-C1')=14.05 d(N1-N9)=11.26 d(C6-C8)=10.33 tor(N1-C1'-C1'-N9)=-67.8 H-bonds[1]: "O6(carbonyl)-N4(amino)[3.04]" bp_pars: [2.60 2.52 -0.26 16.34 -8.75 -81.79] 15 A.G10 A.G38 [G+G] 06-VI cWH cW+M -153.8(anti) C3'-endo lambda=69.8; -175.4(anti) C3'-endo lambda=31.5 d(C1'-C1')=10.97 d(N1-N9)=9.25 d(C6-C8)=9.08 tor(N1-C1'-C1'-N9)=-6.1 H-bonds[3]: "N1(imino)-O6(carbonyl)[2.81]; N2(amino)-N7[2.42]; N2(amino)-O6(carbonyl)[3.32]" bp_pars: [2.35 3.11 -0.36 17.91 -7.82 -77.16] 16 A.U11 A.G14 [U+G] 00-n/a cWH cW+M -150.5(anti) C2'-endo lambda=66.7; -169.8(anti) C2'-exo lambda=25.7 d(C1'-C1')=9.89 d(N1-N9)=8.04 d(C6-C8)=8.11 tor(N1-C1'-C1'-N9)=24.9 H-bonds[1]: "N3(imino)-O6(carbonyl)[2.73]" bp_pars: [0.58 2.02 1.16 -26.66 26.73 -98.07] 17 A.U11 A.C39 [U-C] 00-n/a c.. c.-. -150.5(anti) C2'-endo lambda=16.7; 168.9(anti) C3'-endo lambda=9.7 d(C1'-C1')=12.91 d(N1-N9)=10.05 d(C6-C8)=8.83 tor(N1-C1'-C1'-N9)=39.6 H-bonds[1]: "O4(carbonyl)-N4(amino)[2.23]" bp_pars: [0.99 2.30 1.34 -23.86 21.76 -99.39] 18 A.G12 A.C41 [G-C] 00-n/a cWW cW-W -159.9(anti) C3'-endo lambda=46.3; -173.5(anti) C4'-exo lambda=45.6 d(C1'-C1')=10.18 d(N1-N9)=8.13 d(C6-C8)=8.81 tor(N1-C1'-C1'-N9)=-14.2 H-bonds[1]: "N2(amino)-O2(carbonyl)[2.26]" bp_pars: [0.57 -1.17 0.06 2.25 -13.40 -10.11] 19 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W -165.1(anti) C3'-endo lambda=55.2; -165.1(anti) C3'-endo lambda=52.2 d(C1'-C1')=10.44 d(N1-N9)=8.70 d(C6-C8)=9.61 tor(N1-C1'-C1'-N9)=-13.0 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.61]; N3-N1(imino)[2.72]; N4(amino)-O6(carbonyl)[2.78]" bp_pars: [0.22 -0.39 0.32 0.87 -8.97 -0.74] 20 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W -169.8(anti) C2'-exo lambda=57.9; 168.9(anti) C3'-endo lambda=50.1 d(C1'-C1')=10.72 d(N1-N9)=9.00 d(C6-C8)=9.97 tor(N1-C1'-C1'-N9)=-5.5 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.78]; N1(imino)-N3[2.81]; N2(amino)-O2(carbonyl)[2.75]" bp_pars: [0.53 -0.14 -0.06 -2.23 -5.35 -0.71] 21 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W -160.5(anti) C3'-endo lambda=51.6; -175.4(anti) C3'-endo lambda=51.3 d(C1'-C1')=10.52 d(N1-N9)=8.70 d(C6-C8)=9.57 tor(N1-C1'-C1'-N9)=-3.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.67]; N3-N1(imino)[2.67]; N4(amino)-O6(carbonyl)[2.56]" bp_pars: [0.22 -0.46 0.05 1.09 0.61 -4.75] 22 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W -175.7(anti) C3'-endo lambda=57.0; -169.1(anti) C3'-endo lambda=48.8 d(C1'-C1')=10.49 d(N1-N9)=8.72 d(C6-C8)=9.64 tor(N1-C1'-C1'-N9)=-1.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.60]; N3-N1(imino)[2.70]; N4(amino)-O6(carbonyl)[2.76]" bp_pars: [0.41 -0.39 -0.06 0.54 -0.89 0.04] 23 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W -165.6(anti) C3'-endo lambda=47.3; -172.5(anti) C3'-endo lambda=56.9 d(C1'-C1')=10.57 d(N1-N9)=8.77 d(C6-C8)=9.69 tor(N1-C1'-C1'-N9)=-9.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.90]; N1(imino)-N3[2.80]; N2(amino)-O2(carbonyl)[2.69]" bp_pars: [-0.38 -0.34 0.56 1.84 -5.12 -0.58] 24 A.U18 A.G34 [U-G] 00-n/a c.S c.-m -164.5(anti) C3'-endo lambda=30.2; -169.7(anti) C3'-endo lambda=107.1 d(C1'-C1')=11.54 d(N1-N9)=10.72 d(C6-C8)=11.94 tor(N1-C1'-C1'-N9)=9.7 H-bonds[1]: "O4(carbonyl)-N2(amino)[3.72]" bp_pars: [-7.52 -0.36 -1.35 24.34 -5.20 31.08] 25 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W -164.5(anti) C3'-endo lambda=50.6; -113.1(anti) C2'-endo lambda=54.3 d(C1'-C1')=10.60 d(N1-N9)=8.81 d(C6-C8)=9.65 tor(N1-C1'-C1'-N9)=-2.0 H-bonds[2]: "N3(imino)-N1[2.77]; O4(carbonyl)-N6(amino)[2.72]" bp_pars: [-0.11 -0.23 0.27 -10.93 -1.18 -5.86] 26 A.A19 A.G34 [A-G] 00-n/a cWS cW-m -170.1(anti) C3'-endo lambda=39.3; -169.7(anti) C3'-endo lambda=129.1 d(C1'-C1')=8.94 d(N1-N9)=8.74 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=-19.1 H-bonds[2]: "N6(amino)-N3[3.12]; N1-O2'(hydroxyl)[2.60]" bp_pars: [-6.71 -1.09 1.31 25.81 -10.53 55.64] 27 A.C20 A.G29 [C-G] WC 19-XIX cWW cW-W -174.7(anti) C3'-endo lambda=52.2; -131.7(anti) C3'-endo lambda=58.0 d(C1'-C1')=10.45 d(N1-N9)=8.76 d(C6-C8)=9.73 tor(N1-C1'-C1'-N9)=-7.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.63]; N3-N1(imino)[2.78]; N4(amino)-O6(carbonyl)[2.89]" bp_pars: [-0.02 -0.20 0.09 11.63 -4.46 2.89] 28 A.G23 A.A27 [G-A] 00-n/a c.S c.-m 175.0(anti) C3'-endo lambda=105.5; -146.9(anti) C3'-endo lambda=142.9 d(C1'-C1')=5.59 d(N1-N9)=7.24 d(C6-C8)=9.76 tor(N1-C1'-C1'-N9)=-45.2 H-bonds[4]: "O2'(hydroxyl)-O3'[2.63]; O2'(hydroxyl)-O2'(hydroxyl)[2.38]; N2(amino)-N3[2.95]; N3-O2'(hydroxyl)[2.67]" bp_pars: [-2.07 7.15 -1.19 -30.57 -0.93 152.56] 29 A.G24 A.U25 [G+U] Platform 00-n/a cSH cm+M -140.7(anti) C2'-endo lambda=136.2; -154.9(anti) C2'-endo lambda=65.4 d(C1'-C1')=6.36 d(N1-N9)=6.86 d(C6-C8)=6.86 tor(N1-C1'-C1'-N9)=41.8 H-bonds[1]: "N2(amino)-O4(carbonyl)[3.60]" bp_pars: [8.68 2.74 -0.37 1.49 27.34 28.63] **************************************************************************** List of 7 multiplet(s) 1 nts=3 A.C2+A.G23+A.A27 [CGA] 2 nts=3 A.C6+A.A19+A.G34 [CAG] 3 nts=3 A.G7+A.U18+A.A35 [GUA] 4 nts=3 A.A8+A.G17+A.C36 [AGC] 5 nts=3 A.G9+A.C16+A.G37 [GCG] 6 nts=3 A.G10+A.C15+A.G38 [GCG] 7 nts=3 A.U11+A.G14+A.C39 [UGC] **************************************************************************** List of 2 helices helix=1[2] bps=6 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W 5 A.G29 A.C20 [G-C] WC 19-XIX cWW cW-W 6 A.A5 A.A19 [A-A] 00-n/a tWH tW-M helix=2[1] bps=7 1 A.G12 A.C41 [G-C] 00-n/a cWW cW-W 2 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W 3 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W 4 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W 5 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W 6 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W 7 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W **************************************************************************** List of 3 stems stem=1[#1] bps=2 1 A.C1 A.G24 [C-G] WC 19-XIX cWW cW-W 2 A.C2 A.G23 [C-G] WC 19-XIX cWW cW-W stem=2[#1] bps=2 1 A.G3 A.C22 [G-C] WC 19-XIX cWW cW-W 2 A.G4 A.C21 [G-C] WC 19-XIX cWW cW-W stem=3[#2] bps=6 1 A.C13 A.G40 [C-G] WC 19-XIX cWW cW-W 2 A.G14 A.C39 [G-C] WC 19-XIX cWW cW-W 3 A.C15 A.G38 [C-G] WC 19-XIX cWW cW-W 4 A.C16 A.G37 [C-G] WC 19-XIX cWW cW-W 5 A.G17 A.C36 [G-C] WC 19-XIX cWW cW-W 6 A.U18 A.A35 [U-A] WC 20-XX cWW cW-W **************************************************************************** List of 1 lone WC/wobble pair(s) -1 A.C20 A.G29 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 2 stems: [#1, #2] **************************************************************************** List of 2 hairpin loop(s) 1 nts=16 ACGAGGUGCGCCGUAC closed by pair {A.G4+A.C21 [GC], #2} A.G4+A.A5+A.C6+A.G7+A.A8+A.G9+A.G10+A.U11+A.G12+A.C13+A.G14+A.C15+A.C16+A.G17+A.U18+A.A19+A.C20+A.C21 [GACGAGGUGCGCCGUACC] 2 nts=8 CCGGUCAC closed by pair {A.C20+A.G29 [CG], #-1} A.C20+A.C21+A.C22+A.G23+A.G24+A.U25+A.C26+A.A27+A.C28+A.G29 [CCCGGUCACG] **************************************************************************** List of 1 internal loop(s) 1 asymmetric internal loop: 10 nts; [1x5]; linked by [#3, #-1] A.U18+A.A19+A.C20+A.G29+A.A30+A.C31+A.A32+A.A33+A.G34+A.A35 [UACGACAAGA] This structure contains pseudo-knot(s). **************************************************************************** List of 1 A-minor motif(s) 1 type=I A/C-G A.A27 vs A.C2+A.G23 [WC] +A.C2 H-bonds[1]: "N1-O2'(hydroxyl)[2.42]" -A.G23 H-bonds[4]: "O3'-O2'(hydroxyl)[2.63]; O2'(hydroxyl)-O2'(hydroxyl)[2.38]; O2'(hydroxyl)-N3[2.67]; N3-N2(amino)[2.95]" **************************************************************************** >chain-A #1 RNA* with 41 nts CCGGACGAGGUGCGCCGUACCCGGUCACGACAAGACGGCGC [[((........[[[[[[.[))]]....].....]]]]]]. DONE!