# 1.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: Tue Sep 5 05:38:18 2023 File name: 1.pdb no. of DNA/RNA chains: 1 [A=41] no. of nucleotides: 41 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 21 base pair(s) 1 A.G1 A.C41 [G-C] WC 19-XIX cWW cW-W -174.9(anti) C3'-endo lambda=52.9; -163.1(anti) C3'-endo lambda=55.8 d(C1'-C1')=10.71 d(N1-N9)=8.98 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-10.4 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.03]; N1(imino)-N3[2.99]; N2(amino)-O2(carbonyl)[2.83]" bp_pars: [-0.33 -0.09 0.67 10.39 -2.19 0.90] 2 A.G2 A.C40 [G-C] WC 19-XIX cWW cW-W -158.7(anti) C3'-endo lambda=54.6; -170.5(anti) C3'-endo lambda=58.4 d(C1'-C1')=10.45 d(N1-N9)=8.82 d(C6-C8)=9.78 tor(N1-C1'-C1'-N9)=-11.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.94]; N1(imino)-N3[2.92]; N2(amino)-O2(carbonyl)[2.76]" bp_pars: [-0.44 -0.14 0.55 19.45 -8.89 0.52] 3 A.C3 A.G39 [C-G] WC 19-XIX cWW cW-W -142.2(anti) C3'-endo lambda=52.3; -158.4(anti) C3'-endo lambda=58.9 d(C1'-C1')=10.62 d(N1-N9)=8.94 d(C6-C8)=9.89 tor(N1-C1'-C1'-N9)=-13.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.90]; N3-N1(imino)[2.97]; N4(amino)-O6(carbonyl)[3.15]" bp_pars: [0.09 0.04 -0.55 23.39 -33.76 6.03] 4 A.C4 A.G38 [C-G] WC 19-XIX cWW cW-W -152.0(anti) C3'-endo lambda=56.3; -146.1(anti) C3'-endo lambda=56.2 d(C1'-C1')=10.50 d(N1-N9)=8.87 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=-19.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.81]; N3-N1(imino)[2.94]; N4(amino)-O6(carbonyl)[3.34]" bp_pars: [0.32 -0.05 -0.45 8.64 -31.94 9.93] 5 A.A6 A.G35 [A-G] 08-VIII cWW cW-W -155.5(anti) C3'-endo lambda=37.9; -147.5(anti) C3'-endo lambda=47.6 d(C1'-C1')=12.97 d(N1-N9)=10.86 d(C6-C8)=11.10 tor(N1-C1'-C1'-N9)=-35.0 H-bonds[3]: "N6(amino)-O6(carbonyl)[3.16]; N6(amino)*N1(imino)[2.99]; N1-N2(amino)[3.34]" bp_pars: [-1.76 1.42 -0.86 -17.10 -41.19 -20.93] 6 A.A6 A.U36 [A-U] 00-n/a cWW cW-W -155.5(anti) C3'-endo lambda=60.5; -145.3(anti) C4'-exo lambda=50.2 d(C1'-C1')=10.02 d(N1-N9)=8.40 d(C6-C8)=9.39 tor(N1-C1'-C1'-N9)=-41.2 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.31]; N1-N3(imino)[2.87]" bp_pars: [0.25 -0.54 1.53 -21.69 -32.24 -2.73] 7 A.G8 A.G31 [G-G] 00-n/a tHW tM-W -136.1(anti) C3'-endo lambda=19.5; 166.8(anti) C2'-endo lambda=33.8 d(C1'-C1')=13.43 d(N1-N9)=10.90 d(C6-C8)=10.19 tor(N1-C1'-C1'-N9)=159.7 H-bonds[1]: "O6(carbonyl)-N2(amino)[3.23]" bp_pars: [-5.68 0.51 -0.62 -4.28 51.41 -87.70] 8 A.G8 A.A34 [G-A] 08-VIII cWW cW-W -136.1(anti) C3'-endo lambda=49.9; -151.7(anti) C3'-endo lambda=41.5 d(C1'-C1')=12.83 d(N1-N9)=10.80 d(C6-C8)=11.20 tor(N1-C1'-C1'-N9)=-23.4 H-bonds[3]: "O6(carbonyl)-N6(amino)[3.00]; N1(imino)-N1[3.02]; N2(amino)-N1[3.15]" bp_pars: [0.95 1.40 -0.45 0.62 -33.72 -16.32] 9 A.G9 A.A32 [G-A] 00-n/a cWW cW-W -154.0(anti) C3'-endo lambda=36.1; -141.6(anti) C3'-endo lambda=25.1 d(C1'-C1')=14.32 d(N1-N9)=11.80 d(C6-C8)=11.40 tor(N1-C1'-C1'-N9)=-10.0 H-bonds[1]: "O6(carbonyl)-N6(amino)[3.37]" bp_pars: [1.16 2.24 -2.46 9.64 -39.65 -44.61] 10 A.G9 A.G33 [G-G] 00-n/a cWW cW-W -154.0(anti) C3'-endo lambda=52.1; -155.6(anti) C3'-endo lambda=35.9 d(C1'-C1')=13.11 d(N1-N9)=11.03 d(C6-C8)=11.28 tor(N1-C1'-C1'-N9)=-7.5 H-bonds[2]: "N1(imino)-O6(carbonyl)[2.82]; N2(amino)*N1(imino)[3.08]" bp_pars: [2.16 1.42 0.42 8.73 -12.23 -25.80] 11 A.U10 A.A32 [U-A] WC 20-XX cWW cW-W -148.2(anti) C3'-endo lambda=45.6; -141.6(anti) C3'-endo lambda=44.9 d(C1'-C1')=11.11 d(N1-N9)=9.05 d(C6-C8)=9.68 tor(N1-C1'-C1'-N9)=-37.7 H-bonds[2]: "N3(imino)-N1[2.96]; O4(carbonyl)-N6(amino)[2.85]" bp_pars: [0.42 -0.14 0.02 13.94 -40.43 -13.41] 12 A.G12 A.C30 [G-C] WC 19-XIX cWW cW-W -146.2(anti) C3'-endo lambda=51.4; -159.6(anti) C4'-exo lambda=57.2 d(C1'-C1')=10.59 d(N1-N9)=8.87 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=-21.5 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.14]; N1(imino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.91]" bp_pars: [-0.60 -0.19 0.18 0.67 -30.97 2.84] 13 A.U13 A.G29 [U-G] Wobble 28-XXVIII cWW cW-W -156.5(anti) C3'-endo lambda=70.0; 165.3(anti) C4'-exo lambda=34.4 d(C1'-C1')=10.56 d(N1-N9)=8.85 d(C6-C8)=9.76 tor(N1-C1'-C1'-N9)=-19.0 H-bonds[2]: "O2(carbonyl)-N1(imino)[2.76]; N3(imino)-O6(carbonyl)[2.91]" bp_pars: [2.66 -0.60 0.35 -7.14 -18.96 1.26] 14 A.G14 A.A27 [G-A] 00-n/a cWW cW-W -162.6(anti) C3'-endo lambda=31.5; -149.9(anti) C3'-endo lambda=39.6 d(C1'-C1')=13.48 d(N1-N9)=11.10 d(C6-C8)=10.94 tor(N1-C1'-C1'-N9)=-2.6 H-bonds[1]: "O6(carbonyl)-N6(amino)[2.87]" bp_pars: [-1.12 1.37 -2.48 -4.39 -33.21 -34.84] 15 A.G14 A.U28 [G-U] Wobble 28-XXVIII cWW cW-W -162.6(anti) C3'-endo lambda=46.3; -136.0(anti) C3'-endo lambda=67.6 d(C1'-C1')=10.34 d(N1-N9)=8.78 d(C6-C8)=9.81 tor(N1-C1'-C1'-N9)=-29.1 H-bonds[2]: "O6(carbonyl)-N3(imino)[3.21]; N1(imino)-O2(carbonyl)[2.79]" bp_pars: [-2.45 -0.36 0.43 -16.22 -31.86 5.49] 16 A.U15 A.A27 [U-A] WC 20-XX cWW cW-W -153.3(anti) C3'-endo lambda=61.3; -149.9(anti) C3'-endo lambda=56.3 d(C1'-C1')=10.41 d(N1-N9)=8.89 d(C6-C8)=10.06 tor(N1-C1'-C1'-N9)=-20.0 H-bonds[2]: "N3(imino)-N1[3.05]; O4(carbonyl)-N6(amino)[3.93]" bp_pars: [0.30 0.13 0.97 -7.59 -27.83 9.46] 17 A.G16 A.C26 [G-C] WC 19-XIX cWW cW-W -157.3(anti) C3'-endo lambda=56.1; -154.6(anti) C3'-endo lambda=53.7 d(C1'-C1')=10.65 d(N1-N9)=8.95 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-19.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.07]; N1(imino)-N3[2.92]; N2(amino)-O2(carbonyl)[2.81]" bp_pars: [-0.15 -0.17 0.76 4.58 -21.36 -1.56] 18 A.G17 A.C25 [G-C] WC 19-XIX cWW cW-W -163.4(anti) C3'-endo lambda=49.1; -160.9(anti) C3'-endo lambda=55.2 d(C1'-C1')=10.68 d(N1-N9)=8.87 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-23.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.19]; N1(imino)-N3[2.93]; N2(amino)-O2(carbonyl)[2.88]" bp_pars: [-0.70 -0.28 0.51 -1.39 -29.25 -1.46] 19 A.G18 A.C24 [G-C] WC 19-XIX cWW cW-W -159.8(anti) C3'-endo lambda=52.0; -159.0(anti) C3'-endo lambda=66.8 d(C1'-C1')=10.33 d(N1-N9)=8.85 d(C6-C8)=10.04 tor(N1-C1'-C1'-N9)=-16.7 H-bonds[3]: "N1(imino)-O2(carbonyl)[3.02]; N1(imino)-N3[3.21]; N2(amino)-O2(carbonyl)[2.75]" bp_pars: [-1.42 -0.04 0.42 2.45 -25.20 12.16] 20 A.G19 A.C23 [G-C] WC 19-XIX cWW cW-W -161.4(anti) C3'-endo lambda=57.7; -170.9(anti) C2'-exo lambda=63.1 d(C1'-C1')=10.23 d(N1-N9)=8.76 d(C6-C8)=9.80 tor(N1-C1'-C1'-N9)=0.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.19]; N1(imino)-N3[2.99]; N2(amino)-O2(carbonyl)[2.69]" bp_pars: [-0.87 -0.14 0.61 18.52 6.19 5.65] 21 A.U20 A.U22 [U-U] 00-n/a ... t... -173.0(anti) C3'-endo lambda=79.4; -167.0(anti) C3'-endo lambda=38.2 d(C1'-C1')=8.78 d(N1-N9)=7.70 d(C6-C8)=7.59 tor(N1-C1'-C1'-N9)=-155.4 H-bonds[1]: "N3(imino)-OP2[2.69]" bp_pars: [7.41 -6.80 -0.88 22.54 1.36 -71.32] **************************************************************************** List of 1 multiplet(s) 1 nts=3 A.G8+A.G31+A.A34 [GGA] **************************************************************************** List of 3 helices helix=1[1] bps=4 1 A.G1 A.C41 [G-C] WC 19-XIX cWW cW-W 2 A.G2 A.C40 [G-C] WC 19-XIX cWW cW-W 3 A.C3 A.G39 [C-G] WC 19-XIX cWW cW-W 4 A.C4 A.G38 [C-G] WC 19-XIX cWW cW-W helix=2[0] bps=4 1 A.A6 A.G35 [A-G] 08-VIII cWW cW-W 2 A.G8 A.A34 [G-A] 08-VIII cWW cW-W 3 A.G9 A.G33 [G-G] 00-n/a cWW cW-W 4 A.U10 A.A32 [U-A] WC 20-XX cWW cW-W helix=3[1] bps=9 1 A.G12 A.C30 [G-C] WC 19-XIX cWW cW-W 2 A.U13 A.G29 [U-G] Wobble 28-XXVIII cWW cW-W 3 A.G14 A.U28 [G-U] Wobble 28-XXVIII cWW cW-W 4 A.U15 A.A27 [U-A] WC 20-XX cWW cW-W 5 A.G16 A.C26 [G-C] WC 19-XIX cWW cW-W 6 A.G17 A.C25 [G-C] WC 19-XIX cWW cW-W 7 A.G18 A.C24 [G-C] WC 19-XIX cWW cW-W 8 A.G19 A.C23 [G-C] WC 19-XIX cWW cW-W 9 A.U20 A.U22 [U-U] 00-n/a ... t... **************************************************************************** List of 2 stems stem=1[#1] bps=4 1 A.G1 A.C41 [G-C] WC 19-XIX cWW cW-W 2 A.G2 A.C40 [G-C] WC 19-XIX cWW cW-W 3 A.C3 A.G39 [C-G] WC 19-XIX cWW cW-W 4 A.C4 A.G38 [C-G] WC 19-XIX cWW cW-W stem=2[#3] bps=8 1 A.G12 A.C30 [G-C] WC 19-XIX cWW cW-W 2 A.U13 A.G29 [U-G] Wobble 28-XXVIII cWW cW-W 3 A.G14 A.U28 [G-U] Wobble 28-XXVIII cWW cW-W 4 A.U15 A.A27 [U-A] WC 20-XX cWW cW-W 5 A.G16 A.C26 [G-C] WC 19-XIX cWW cW-W 6 A.G17 A.C25 [G-C] WC 19-XIX cWW cW-W 7 A.G18 A.C24 [G-C] WC 19-XIX cWW cW-W 8 A.G19 A.C23 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 1 lone WC/wobble pair(s) -1 A.U10 A.A32 [U-A] WC 20-XX cWW cW-W **************************************************************************** List of 1 hairpin loop(s) 1 nts=3 UCU closed by pair {A.G19+A.C23 [GC], #2} A.G19+A.U20+A.C21+A.U22+A.C23 [GUCUC] **************************************************************************** List of 2 internal loop(s) 1 symmetric internal loop: 14 nts; [5x5]; linked by [#1, #-1] A.C4+A.G5+A.A6+A.U7+A.G8+A.G9+A.U10+A.A32+A.G33+A.A34+A.G35+A.U36+A.A37+A.G38 [CGAUGGUAGAGUAG] 2 symmetric internal loop: 6 nts; [1x1]; linked by [#-1, #2] A.U10+A.A11+A.G12+A.C30+A.G31+A.A32 [UAGCGA] **************************************************************************** >chain-A #1 RNA with 41 nts GGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGCC ((((.....(.((((((((...)))))))).).....)))) # 1A51.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: Tue Sep 5 05:38:18 2023 File name: 1A51.pdb no. of DNA/RNA chains: 1 [A=41] no. of nucleotides: 41 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 19 base pair(s) 1 1:A.G68 1:A.C108 [G-C] WC 19-XIX cWW cW-W -171.0(anti) C3'-endo lambda=52.4; -160.0(anti) C3'-endo lambda=55.6 d(C1'-C1')=10.56 d(N1-N9)=8.84 d(C6-C8)=9.78 tor(N1-C1'-C1'-N9)=-3.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.84]; N1(imino)-N3[2.82]; N2(amino)-O2(carbonyl)[2.68]" bp_pars: [-0.39 -0.25 0.04 -0.60 -3.48 0.41] 2 1:A.G69 1:A.C107 [G-C] WC 19-XIX cWW cW-W -150.9(anti) C3'-endo lambda=50.3; -169.5(anti) C3'-endo lambda=58.8 d(C1'-C1')=10.37 d(N1-N9)=8.68 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=-0.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.83]; N1(imino)-N3[2.80]; N2(amino)-O2(carbonyl)[2.66]" bp_pars: [-0.89 -0.45 -0.12 -2.02 0.24 0.79] 3 1:A.C70 1:A.G106 [C-G] WC 19-XIX cWW cW-W -168.0(anti) C3'-endo lambda=57.0; -153.6(anti) C3'-endo lambda=50.2 d(C1'-C1')=10.50 d(N1-N9)=8.77 d(C6-C8)=9.68 tor(N1-C1'-C1'-N9)=-0.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.72]; N3-N1(imino)[2.83]; N4(amino)-O6(carbonyl)[2.82]" bp_pars: [0.74 -0.37 -0.22 3.12 -0.03 -0.45] 4 1:A.C71 1:A.G105 [C-G] WC 19-XIX cWW cW-W -158.2(anti) C3'-endo lambda=55.8; -166.3(anti) C3'-endo lambda=54.3 d(C1'-C1')=10.48 d(N1-N9)=8.79 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-3.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.63]; N3-N1(imino)[2.79]; N4(amino)-O6(carbonyl)[2.86]" bp_pars: [0.24 -0.25 -0.28 -5.04 -5.76 2.35] 5 1:A.G72 1:A.A104 [G-A] Sheared 11-XI tSH cm-M -161.5(anti) C3'-endo lambda=96.9; -169.2(anti) C3'-endo lambda=8.5 d(C1'-C1')=9.83 d(N1-N9)=8.65 d(C6-C8)=9.09 tor(N1-C1'-C1'-N9)=-24.1 H-bonds[2]: "N2(amino)-N7[2.96]; N3-N6(amino)[3.09]" bp_pars: [6.91 -3.93 0.19 4.08 -1.33 -4.16] 6 1:A.A73 1:A.U103 [A-U] 00-n/a tHW tM-W 166.9(anti) C2'-exo lambda=21.4; -166.7(anti) C3'-endo lambda=22.2 d(C1'-C1')=9.96 d(N1-N9)=7.32 d(C6-C8)=6.11 tor(N1-C1'-C1'-N9)=176.0 H-bonds[3]: "N7-N3(imino)[2.82]; N7*O4(carbonyl)[2.80]; N6(amino)-O2(carbonyl)[3.06]" bp_pars: [-3.55 -1.00 -0.02 2.88 -10.18 -108.00] 7 1:A.U74 1:A.G102 [U-G] 00-n/a tHW tM-W -166.5(anti) C3'-endo lambda=11.8; 176.7(anti) C3'-endo lambda=27.1 d(C1'-C1')=12.68 d(N1-N9)=9.98 d(C6-C8)=8.85 tor(N1-C1'-C1'-N9)=-162.5 H-bonds[2]: "O4(carbonyl)-N1(imino)[2.39]; O4(carbonyl)-N2(amino)[3.32]" bp_pars: [-4.20 0.99 -0.43 -4.94 -7.96 -93.93] 8 1:A.G75 1:A.A101 [G-A] 00-n/a c.W c.-W -173.7(anti) C3'-endo lambda=11.3; -164.3(anti) C2'-exo lambda=27.4 d(C1'-C1')=13.97 d(N1-N9)=11.24 d(C6-C8)=10.40 tor(N1-C1'-C1'-N9)=-1.6 H-bonds[1]: "O6(carbonyl)-N6(amino)[2.77]" bp_pars: [-2.01 2.18 -0.09 -1.29 -2.04 -70.26] 9 1:A.G76 1:A.G100 [G-G] 00-n/a tWH tW-M 173.4(anti) C3'-endo lambda=27.6; 173.6(anti) C3'-endo lambda=13.4 d(C1'-C1')=12.68 d(N1-N9)=10.01 d(C6-C8)=8.80 tor(N1-C1'-C1'-N9)=-177.8 H-bonds[2]: "N1(imino)-O6(carbonyl)[3.03]; N2(amino)-O6(carbonyl)[2.82]" bp_pars: [4.43 0.93 -0.31 2.72 0.24 -95.07] 10 1:A.U77 1:A.A99 [U-A] rHoogsteen 24-XXIV tWH tW-M -161.7(anti) C3'-endo lambda=31.0; 170.2(anti) C2'-exo lambda=17.2 d(C1'-C1')=10.05 d(N1-N9)=7.49 d(C6-C8)=6.51 tor(N1-C1'-C1'-N9)=-172.4 H-bonds[2]: "O2(carbonyl)-N6(amino)[2.79]; N3(imino)-N7[3.03]" bp_pars: [3.99 -1.67 -0.48 2.90 -6.54 -94.50] 11 1:A.A78 1:A.G98 [A-G] Sheared 11-XI tHS cM-m 177.3(anti) C3'-endo lambda=8.9; -160.4(anti) C3'-endo lambda=101.7 d(C1'-C1')=9.29 d(N1-N9)=8.23 d(C6-C8)=8.73 tor(N1-C1'-C1'-N9)=10.8 H-bonds[3]: "N7-N2(amino)[2.98]; N6(amino)-O2'(hydroxyl)[2.70]; N6(amino)-N3[3.00]" bp_pars: [-6.76 -4.33 -0.15 3.28 -0.22 0.73] 12 1:A.G79 1:A.C97 [G-C] WC 19-XIX cWW cW-W -167.9(anti) C3'-endo lambda=50.5; -172.0(anti) C3'-endo lambda=58.7 d(C1'-C1')=10.36 d(N1-N9)=8.66 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=-4.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.82]; N1(imino)-N3[2.77]; N2(amino)-O2(carbonyl)[2.63]" bp_pars: [-0.82 -0.44 -0.25 -2.53 -6.68 1.70] 13 1:A.U80 1:A.G96 [U-G] Wobble 28-XXVIII cWW cW-W -166.2(anti) C3'-endo lambda=60.7; -176.3(anti) C3'-endo lambda=44.7 d(C1'-C1')=10.65 d(N1-N9)=8.90 d(C6-C8)=9.75 tor(N1-C1'-C1'-N9)=-11.8 H-bonds[3]: "O2(carbonyl)-N1(imino)[3.01]; O2(carbonyl)-N2(amino)[3.27]; N3(imino)-O6(carbonyl)[3.00]" bp_pars: [1.53 -0.38 0.45 3.39 -7.62 -4.52] 14 1:A.G81 1:A.U95 [G-U] 00-n/a cWW cW-W -171.8(anti) C3'-endo lambda=45.8; -153.4(anti) C3'-endo lambda=57.3 d(C1'-C1')=10.36 d(N1-N9)=8.55 d(C6-C8)=9.32 tor(N1-C1'-C1'-N9)=-1.5 H-bonds[4]: "O6(carbonyl)-N3(imino)[2.78]; O6(carbonyl)*O4(carbonyl)[2.72]; N1(imino)-O2(carbonyl)[2.95]; N2(amino)-O2(carbonyl)[3.02]" bp_pars: [-1.09 -0.74 -1.08 -10.73 -8.76 -5.65] 15 1:A.U82 1:A.A94 [U-A] WC 20-XX cWW cW-W -166.2(anti) C3'-endo lambda=54.4; -165.9(anti) C3'-endo lambda=55.3 d(C1'-C1')=10.43 d(N1-N9)=8.74 d(C6-C8)=9.70 tor(N1-C1'-C1'-N9)=-7.9 H-bonds[2]: "N3(imino)-N1[2.71]; O4(carbonyl)-N6(amino)[2.82]" bp_pars: [0.06 -0.24 0.08 1.56 -6.52 0.64] 16 1:A.G83 1:A.C93 [G-C] WC 19-XIX cWW cW-W -171.9(anti) C3'-endo lambda=48.2; -170.7(anti) C3'-endo lambda=52.0 d(C1'-C1')=10.39 d(N1-N9)=8.53 d(C6-C8)=9.29 tor(N1-C1'-C1'-N9)=-21.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.56]; N1(imino)-N3[2.55]; N2(amino)-O2(carbonyl)[2.66]" bp_pars: [-0.40 -0.75 0.89 5.08 -16.72 -8.43] 17 1:A.G84 1:A.C92 [G-C] WC 19-XIX cWW cW-W -172.0(anti) C3'-endo lambda=52.4; -167.9(anti) C3'-endo lambda=54.9 d(C1'-C1')=10.58 d(N1-N9)=8.85 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-7.9 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.81]; N1(imino)-N3[2.81]; N2(amino)-O2(carbonyl)[2.72]" bp_pars: [-0.34 -0.26 -0.07 -0.55 -9.96 -0.04] 18 1:A.G85 1:A.C91 [G-C] WC 19-XIX cWW cW-W 179.9(anti) C3'-endo lambda=50.1; -164.2(anti) C3'-endo lambda=59.4 d(C1'-C1')=10.34 d(N1-N9)=8.65 d(C6-C8)=9.60 tor(N1-C1'-C1'-N9)=-6.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.87]; N1(imino)-N3[2.82]; N2(amino)-O2(carbonyl)[2.65]" bp_pars: [-0.98 -0.45 -0.05 -6.99 -5.11 1.45] 19 1:A.G86 1:A.C90 [G-C] 00-n/a cWW cW-W -146.1(anti) C3'-endo lambda=86.5; -142.1(anti) C2'-exo lambda=74.8 d(C1'-C1')=9.67 d(N1-N9)=9.19 d(C6-C8)=11.17 tor(N1-C1'-C1'-N9)=7.0 H-bonds[2]: "N2(amino)-O2(carbonyl)[2.87]; N2(amino)-N3[3.02]" bp_pars: [0.84 2.20 -1.20 -10.35 6.48 53.78] **************************************************************************** List of 1 helix helix=1[3] bps=19 1 1:A.G68 1:A.C108 [G-C] WC 19-XIX cWW cW-W 2 1:A.G69 1:A.C107 [G-C] WC 19-XIX cWW cW-W 3 1:A.C70 1:A.G106 [C-G] WC 19-XIX cWW cW-W 4 1:A.C71 1:A.G105 [C-G] WC 19-XIX cWW cW-W 5 1:A.G72 1:A.A104 [G-A] Sheared 11-XI tSH cm-M 6 1:A.A73 1:A.U103 [A-U] 00-n/a tHW tM-W 7 1:A.U74 1:A.G102 [U-G] 00-n/a tHW tM-W 8 1:A.G75 1:A.A101 [G-A] 00-n/a c.W c.-W 9 1:A.G76 1:A.G100 [G-G] 00-n/a tWH tW-M 10 1:A.U77 1:A.A99 [U-A] rHoogsteen 24-XXIV tWH tW-M 11 1:A.A78 1:A.G98 [A-G] Sheared 11-XI tHS cM-m 12 1:A.G79 1:A.C97 [G-C] WC 19-XIX cWW cW-W 13 1:A.U80 1:A.G96 [U-G] Wobble 28-XXVIII cWW cW-W 14 1:A.G81 1:A.U95 [G-U] 00-n/a cWW cW-W 15 1:A.U82 1:A.A94 [U-A] WC 20-XX cWW cW-W 16 1:A.G83 1:A.C93 [G-C] WC 19-XIX cWW cW-W 17 1:A.G84 1:A.C92 [G-C] WC 19-XIX cWW cW-W 18 1:A.G85 1:A.C91 [G-C] WC 19-XIX cWW cW-W 19 1:A.G86 1:A.C90 [G-C] 00-n/a cWW cW-W **************************************************************************** List of 3 stems stem=1[#1] bps=4 1 1:A.G68 1:A.C108 [G-C] WC 19-XIX cWW cW-W 2 1:A.G69 1:A.C107 [G-C] WC 19-XIX cWW cW-W 3 1:A.C70 1:A.G106 [C-G] WC 19-XIX cWW cW-W 4 1:A.C71 1:A.G105 [C-G] WC 19-XIX cWW cW-W stem=2[#1] bps=2 1 1:A.G79 1:A.C97 [G-C] WC 19-XIX cWW cW-W 2 1:A.U80 1:A.G96 [U-G] Wobble 28-XXVIII cWW cW-W stem=3[#1] bps=4 1 1:A.U82 1:A.A94 [U-A] WC 20-XX cWW cW-W 2 1:A.G83 1:A.C93 [G-C] WC 19-XIX cWW cW-W 3 1:A.G84 1:A.C92 [G-C] WC 19-XIX cWW cW-W 4 1:A.G85 1:A.C91 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 3 stems: [#1, #2, #3] **************************************************************************** List of 1 hairpin loop(s) 1 nts=5 GUCUC closed by pair {1:A.G85+1:A.C91 [GC], #3} 1:A.G85+1:A.G86+1:A.U87+1:A.C88+1:A.U89+1:A.C90+1:A.C91 [GGUCUCC] **************************************************************************** List of 2 internal loop(s) 1 symmetric internal loop: 18 nts; [7x7]; linked by [#1, #2] 1:A.C71+1:A.G72+1:A.A73+1:A.U74+1:A.G75+1:A.G76+1:A.U77+1:A.A78+1:A.G79+1:A.C97+1:A.G98+1:A.A99+1:A.G100+1:A.A101+1:A.G102+1:A.U103+1:A.A104+1:A.G105 [CGAUGGUAGCGAGAGUAG] 2 symmetric internal loop: 6 nts; [1x1]; linked by [#2, #3] 1:A.U80+1:A.G81+1:A.U82+1:A.A94+1:A.U95+1:A.G96 [UGUAUG] **************************************************************************** >chain-A #1 RNA with 41 nts GGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGCC ((((.......((.((((.....)))).)).......)))) DONE!