# 2LKR_3_A.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: Mon Aug 21 11:29:42 2023 File name: 2LKR_3_A.pdb no. of DNA/RNA chains: 1 [A=111] no. of nucleotides: 111 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 44 base pair(s) 1 A.G1 A.C111 [G-C] WC 19-XIX cWW cW-W 167.3(anti) C2'-exo lambda=47.0; -142.5(anti) C1'-exo lambda=53.6 d(C1'-C1')=10.98 d(N1-N9)=9.10 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=-4.2 H-bonds[3]: "N1(imino)-N3[3.07]; N2(amino)-O2(carbonyl)[3.20]; O6(carbonyl)-N4(amino)[2.80]" bp_pars: [-0.65 -0.18 0.04 -1.30 0.04 -7.71] 2 A.G2 A.U110 [G-U] Wobble 28-XXVIII cWW cW-W 174.7(anti) C2'-endo lambda=35.3; -140.3(anti) C2'-exo lambda=60.4 d(C1'-C1')=10.94 d(N1-N9)=9.02 d(C6-C8)=9.66 tor(N1-C1'-C1'-N9)=26.0 H-bonds[2]: "N1(imino)-O2(carbonyl)[3.12]; O6(carbonyl)-N3(imino)[2.76]" bp_pars: [-2.49 -0.64 -0.32 0.26 26.18 -13.51] 3 A.C3 A.G109 [C-G] WC 19-XIX cWW cW-W -91.9(anti) C1'-exo lambda=66.5; -150.5(anti) C4'-exo lambda=52.0 d(C1'-C1')=10.32 d(N1-N9)=8.83 d(C6-C8)=9.50 tor(N1-C1'-C1'-N9)=4.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.23]; N3-N1(imino)[3.13]; N4(amino)-O6(carbonyl)[2.92]" bp_pars: [0.76 0.07 -0.41 39.50 -20.07 -7.18] 4 A.A4 A.U108 [A-U] WC 20-XX cWW cW-W -162.4(anti) C2'-exo lambda=54.0; -154.2(anti) C3'-endo lambda=48.0 d(C1'-C1')=10.25 d(N1-N9)=8.41 d(C6-C8)=9.02 tor(N1-C1'-C1'-N9)=33.2 H-bonds[2]: "N1-N3(imino)[2.73]; N6(amino)-O4(carbonyl)[2.70]" bp_pars: [-0.31 -0.50 -0.62 32.12 27.09 -14.90] 5 A.U6 A.A105 [U-A] WC 20-XX cWW cW-W -174.7(anti) C3'-endo lambda=54.1; -136.9(anti) C4'-exo lambda=58.0 d(C1'-C1')=10.50 d(N1-N9)=8.86 d(C6-C8)=9.80 tor(N1-C1'-C1'-N9)=3.4 H-bonds[2]: "N3(imino)-N1[2.89]; O4(carbonyl)-N6(amino)[2.91]" bp_pars: [-0.32 -0.05 -0.13 -17.99 -3.27 -0.73] 6 A.A7 A.U104 [A-U] WC 20-XX cWW cW-W -160.6(anti) C4'-exo lambda=55.2; -156.3(anti) O4'-endo lambda=51.0 d(C1'-C1')=10.82 d(N1-N9)=9.05 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=3.2 H-bonds[2]: "N1-N3(imino)[2.97]; N6(amino)-O4(carbonyl)[2.78]" bp_pars: [0.38 0.02 -0.11 -18.70 3.49 -6.96] 7 A.C8 A.U101 [C-U] 00-n/a cWW cW-W -154.6(anti) C4'-exo lambda=26.2; 170.1(anti) C1'-exo lambda=41.8 d(C1'-C1')=10.26 d(N1-N9)=7.88 d(C6-C8)=7.97 tor(N1-C1'-C1'-N9)=40.0 H-bonds[1]: "N4(amino)-O4(carbonyl)[3.08]" bp_pars: [-1.83 -1.54 -1.51 26.53 17.54 -47.93] 8 A.C8 A.G103 [C-G] WC 19-XIX cWW cW-W -154.6(anti) C4'-exo lambda=65.7; -121.6(anti) C3'-endo lambda=52.2 d(C1'-C1')=10.14 d(N1-N9)=8.64 d(C6-C8)=9.57 tor(N1-C1'-C1'-N9)=-6.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.87]; N3-N1(imino)[3.07]; N4(amino)-O6(carbonyl)[3.18]" bp_pars: [1.09 -0.05 0.39 -34.63 4.03 3.30] 9 A.A13 A.A97 [A-A] 00-n/a tWH tW-M 126.0(...) C2'-endo lambda=27.6; -102.7(anti) C1'-exo lambda=25.6 d(C1'-C1')=11.24 d(N1-N9)=8.70 d(C6-C8)=7.38 tor(N1-C1'-C1'-N9)=171.5 H-bonds[2]: "N1-N6(amino)[3.37]; N1*N7[2.71]" bp_pars: [4.94 -0.06 0.89 -2.31 15.50 -110.38] 10 A.U14 A.A96 [U-A] WC 20-XX cWW cW-W -130.1(anti) C4'-exo lambda=55.2; 173.1(anti) C3'-endo lambda=55.3 d(C1'-C1')=10.52 d(N1-N9)=8.84 d(C6-C8)=9.76 tor(N1-C1'-C1'-N9)=15.1 H-bonds[2]: "N3(imino)-N1[2.99]; O4(carbonyl)-N6(amino)[2.96]" bp_pars: [-0.26 -0.04 0.36 21.44 27.90 1.08] 11 A.G15 A.C95 [G-C] WC 19-XIX cWW cW-W -165.0(anti) C4'-exo lambda=55.1; -135.7(anti) O4'-endo lambda=48.1 d(C1'-C1')=11.03 d(N1-N9)=9.20 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=14.1 H-bonds[4]: "N1(imino)-N3[3.08]; N2(amino)-O2(carbonyl)[3.18]; N2(amino)-N3[3.31]; O6(carbonyl)-N4(amino)[2.88]" bp_pars: [0.79 0.01 -0.76 -18.55 9.11 -8.26] 12 A.A16 A.U94 [A-U] WC 20-XX cWW cW-W -145.9(anti) C4'-exo lambda=58.0; -134.1(anti) C4'-exo lambda=55.0 d(C1'-C1')=10.57 d(N1-N9)=8.94 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=0.6 H-bonds[2]: "N1-N3(imino)[2.89]; N6(amino)-O4(carbonyl)[3.00]" bp_pars: [0.26 -0.03 -0.22 -7.16 -2.07 1.04] 13 A.U17 A.A93 [U-A] WC 20-XX cWW cW-W -129.4(anti) O4'-endo lambda=54.5; -139.5(anti) C3'-endo lambda=57.3 d(C1'-C1')=10.67 d(N1-N9)=9.02 d(C6-C8)=9.99 tor(N1-C1'-C1'-N9)=0.9 H-bonds[2]: "N3(imino)-N1[2.95]; O4(carbonyl)-N6(amino)[3.03]" bp_pars: [-0.21 0.02 -0.13 1.56 -1.59 0.33] 14 A.C18 A.G92 [C-G] WC 19-XIX cWW cW-W -162.0(anti) O4'-endo lambda=57.9; -130.4(anti) C3'-endo lambda=52.5 d(C1'-C1')=10.55 d(N1-N9)=8.87 d(C6-C8)=9.80 tor(N1-C1'-C1'-N9)=9.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.83]; N3-N1(imino)[2.96]; N4(amino)-O6(carbonyl)[2.98]" bp_pars: [0.71 -0.18 0.22 -12.84 11.42 0.61] 15 A.A19 A.U89 [A-U] WC 20-XX cWW cW-W -170.5(anti) C4'-exo lambda=53.0; -129.9(anti) O4'-endo lambda=51.0 d(C1'-C1')=11.08 d(N1-N9)=9.26 d(C6-C8)=10.04 tor(N1-C1'-C1'-N9)=8.6 H-bonds[2]: "N1-N3(imino)[3.14]; N6(amino)-O4(carbonyl)[2.92]" bp_pars: [0.26 0.16 -0.00 -13.41 9.06 -7.44] 16 A.A19 A.A91 [A-A] 00-n/a cSW cm-W -170.5(anti) C4'-exo lambda=90.8; -112.7(anti) O4'-endo lambda=56.2 d(C1'-C1')=9.46 d(N1-N9)=8.67 d(C6-C8)=9.95 tor(N1-C1'-C1'-N9)=12.8 H-bonds[2]: "N1-N6(amino)[3.01]; N3*N1[2.97]" bp_pars: [3.24 0.88 0.90 -47.62 18.47 36.27] 17 A.G20 A.C88 [G-C] WC 19-XIX cWW cW-W -169.3(anti) C4'-exo lambda=50.4; -177.0(anti) C4'-exo lambda=53.8 d(C1'-C1')=10.86 d(N1-N9)=9.05 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=-3.7 H-bonds[3]: "N1(imino)-N3[3.00]; N2(amino)-O2(carbonyl)[3.08]; O6(carbonyl)-N4(amino)[2.80]" bp_pars: [-0.46 -0.17 0.00 -1.06 -5.26 -5.74] 18 A.C21 A.G87 [C-G] WC 19-XIX cWW cW-W -166.8(anti) C3'-endo lambda=59.2; -166.8(anti) C4'-exo lambda=53.4 d(C1'-C1')=10.41 d(N1-N9)=8.78 d(C6-C8)=9.72 tor(N1-C1'-C1'-N9)=-5.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.80]; N3-N1(imino)[2.93]; N4(amino)-O6(carbonyl)[2.99]" bp_pars: [0.78 -0.20 -0.51 18.79 -15.51 2.45] 19 A.G23 A.C44 [G-C] WC 19-XIX cWW cW-W -167.8(anti) C3'-endo lambda=59.3; -165.6(anti) C3'-endo lambda=66.6 d(C1'-C1')=9.29 d(N1-N9)=7.96 d(C6-C8)=9.16 tor(N1-C1'-C1'-N9)=13.4 H-bonds[2]: "N1(imino)-N3[2.58]; O6(carbonyl)-N4(amino)[3.10]" bp_pars: [-0.34 -0.27 0.00 -36.33 20.60 17.06] 20 A.U24 A.A43 [U-A] WC 20-XX cWW cW-W -164.9(anti) C4'-exo lambda=49.5; -147.7(anti) C3'-endo lambda=54.0 d(C1'-C1')=11.05 d(N1-N9)=9.23 d(C6-C8)=10.01 tor(N1-C1'-C1'-N9)=-7.6 H-bonds[2]: "N3(imino)-N1[3.12]; O4(carbonyl)-N6(amino)[2.95]" bp_pars: [-0.53 0.18 0.25 -18.11 -8.90 -7.00] 21 A.U25 A.A42 [U-A] WC 20-XX cWW cW-W -137.9(anti) C4'-exo lambda=52.6; -151.3(anti) C3'-endo lambda=49.2 d(C1'-C1')=10.76 d(N1-N9)=8.91 d(C6-C8)=9.72 tor(N1-C1'-C1'-N9)=-13.5 H-bonds[2]: "N3(imino)-N1[2.89]; O4(carbonyl)-N6(amino)[2.75]" bp_pars: [0.15 -0.22 -0.39 -6.40 -24.01 -4.42] 22 A.C26 A.G41 [C-G] WC 19-XIX cWW cW-W -145.6(anti) C1'-exo lambda=55.7; -155.9(anti) C3'-endo lambda=51.0 d(C1'-C1')=10.78 d(N1-N9)=9.04 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-19.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.18]; N3-N1(imino)[3.05]; N4(amino)-O6(carbonyl)[3.15]" bp_pars: [0.60 -0.07 -0.40 9.14 -31.25 2.49] 23 A.C27 A.A42 [C-A] 00-n/a tHS cM-m -125.6(anti) C1'-endo lambda=16.7; -151.3(anti) C3'-endo lambda=103.3 d(C1'-C1')=8.85 d(N1-N9)=7.90 d(C6-C8)=8.33 tor(N1-C1'-C1'-N9)=88.2 H-bonds[1]: "N4(amino)-N3[3.09]" bp_pars: [-7.08 -4.98 0.37 22.36 39.95 3.73] 24 A.C28 A.G38 [C-G] WC 19-XIX cWW cW-W -175.6(anti) O4'-exo lambda=48.4; -150.6(anti) C3'-endo lambda=55.1 d(C1'-C1')=10.93 d(N1-N9)=9.13 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=28.7 H-bonds[4]: "O2(carbonyl)-N2(amino)[3.18]; N3-N1(imino)[3.15]; N3-N2(amino)[3.15]; N4(amino)-O6(carbonyl)[2.98]" bp_pars: [-1.05 -0.06 -1.37 24.56 5.91 -8.08] 25 A.C29 A.G37 [C-G] WC 19-XIX cWW cW-W -140.2(anti) C3'-endo lambda=50.9; -171.2(anti) C3'-endo lambda=55.9 d(C1'-C1')=10.58 d(N1-N9)=8.83 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=2.4 H-bonds[4]: "O2(carbonyl)-N2(amino)[2.92]; N3-N1(imino)[3.00]; N3-N2(amino)[3.22]; N4(amino)-O6(carbonyl)[2.94]" bp_pars: [-0.45 -0.01 -1.39 36.64 -12.69 -0.08] 26 A.U30 A.A36 [U-A] WC 20-XX cWW cW-W -155.3(anti) C4'-exo lambda=53.5; -146.0(anti) C2'-exo lambda=58.1 d(C1'-C1')=10.49 d(N1-N9)=8.85 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=3.9 H-bonds[2]: "N3(imino)-N1[2.84]; O4(carbonyl)-N6(amino)[2.97]" bp_pars: [-0.42 -0.09 -0.42 10.02 -4.57 1.78] 27 A.G31 A.A35 [G-A] 00-n/a cSH cm-M -135.5(anti) C4'-exo lambda=109.5; -120.4(anti) O4'-endo lambda=28.9 d(C1'-C1')=8.45 d(N1-N9)=7.69 d(C6-C8)=8.70 tor(N1-C1'-C1'-N9)=4.2 H-bonds[2]: "O2'(hydroxyl)-N1[2.33]; N2(amino)-N7[3.28]" bp_pars: [5.11 -2.70 -1.96 2.55 -7.33 31.11] 28 A.A51 A.U83 [A-U] 00-n/a tSW tm-W -119.0(anti) C2'-exo lambda=102.1; -138.0(anti) C4'-exo lambda=49.0 d(C1'-C1')=5.65 d(N1-N9)=5.34 d(C6-C8)=7.24 tor(N1-C1'-C1'-N9)=95.4 H-bonds[2]: "O4'-N3(imino)[3.32]; N3-N3(imino)[3.01]" bp_pars: [3.20 1.59 -1.43 2.55 58.78 131.89] 29 A.C52 A.G79 [C-G] WC 19-XIX cWW cW-W -146.4(anti) C2'-endo lambda=55.8; -147.1(anti) C3'-endo lambda=56.3 d(C1'-C1')=9.87 d(N1-N9)=8.23 d(C6-C8)=8.89 tor(N1-C1'-C1'-N9)=10.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.86]; N3-N1(imino)[2.82]; N4(amino)-O6(carbonyl)[2.68]" bp_pars: [0.59 0.00 1.15 -56.51 24.53 -2.90] 30 A.A53 A.U78 [A-U] WC 20-XX cWW cW-W -147.0(anti) C4'-exo lambda=58.1; -163.3(anti) C3'-endo lambda=52.3 d(C1'-C1')=10.60 d(N1-N9)=8.92 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-9.0 H-bonds[2]: "N1-N3(imino)[2.87]; N6(amino)-O4(carbonyl)[2.91]" bp_pars: [0.36 -0.04 -0.27 -16.23 -12.69 -1.44] 31 A.A53 A.G79 [A-G] 00-n/a cSW cm-W -147.0(anti) C4'-exo lambda=87.4; -147.1(anti) C3'-endo lambda=57.1 d(C1'-C1')=8.55 d(N1-N9)=7.69 d(C6-C8)=8.98 tor(N1-C1'-C1'-N9)=2.1 H-bonds[1]: "N1-N1(imino)[3.27]" bp_pars: [2.06 -0.96 2.24 -15.07 16.12 35.29] 32 A.A54 A.U77 [A-U] WC 20-XX cWW cW-W -163.8(anti) C4'-exo lambda=55.9; -139.3(anti) C4'-exo lambda=49.5 d(C1'-C1')=11.08 d(N1-N9)=9.29 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-5.6 H-bonds[2]: "N1-N3(imino)[3.17]; N6(amino)-O4(carbonyl)[3.01]" bp_pars: [0.52 0.24 -0.32 -18.82 -11.39 -6.52] 33 A.A55 A.U76 [A-U] WC 20-XX cWW cW-W -162.3(anti) C4'-exo lambda=57.6; -143.2(anti) C4'-exo lambda=51.5 d(C1'-C1')=10.67 d(N1-N9)=8.96 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-14.2 H-bonds[2]: "N1-N3(imino)[2.89]; N6(amino)-O4(carbonyl)[3.02]" bp_pars: [0.30 -0.01 -0.22 -15.09 -24.99 -0.52] 34 A.G56 A.C75 [G-C] WC 19-XIX cWW cW-W -154.9(anti) O4'-endo lambda=54.1; -145.8(anti) C4'-exo lambda=57.1 d(C1'-C1')=10.71 d(N1-N9)=9.05 d(C6-C8)=10.00 tor(N1-C1'-C1'-N9)=-13.4 H-bonds[3]: "N1(imino)-N3[3.09]; N2(amino)-O2(carbonyl)[2.94]; O6(carbonyl)-N4(amino)[3.20]" bp_pars: [-0.56 0.03 -0.33 -13.65 -18.20 2.57] 35 A.A57 A.U74 [A-U] WC 20-XX cWW cW-W -156.9(anti) C3'-endo lambda=51.2; -170.1(anti) C4'-exo lambda=48.7 d(C1'-C1')=11.25 d(N1-N9)=9.36 d(C6-C8)=10.04 tor(N1-C1'-C1'-N9)=3.9 H-bonds[2]: "N1-N3(imino)[3.14]; N6(amino)-O4(carbonyl)[2.78]" bp_pars: [0.37 0.13 -0.15 -5.48 -2.57 -12.00] 36 A.G58 A.C73 [G-C] WC 19-XIX cWW cW-W -149.1(anti) O4'-endo lambda=49.6; -150.7(anti) C3'-endo lambda=53.6 d(C1'-C1')=10.95 d(N1-N9)=9.11 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-4.4 H-bonds[3]: "N1(imino)-N3[3.05]; N2(amino)-O2(carbonyl)[3.16]; O6(carbonyl)-N4(amino)[2.80]" bp_pars: [-0.46 -0.13 -0.07 3.87 -5.01 -6.73] 37 A.A59 A.A71 [A-A] 00-n/a cWW cW-W 176.8(anti) C2'-exo lambda=25.7; -161.1(anti) C4'-exo lambda=35.4 d(C1'-C1')=13.44 d(N1-N9)=10.91 d(C6-C8)=10.45 tor(N1-C1'-C1'-N9)=-0.0 H-bonds[2]: "N6(amino)-N1[3.39]; N6(amino)*N6(amino)[2.53]" bp_pars: [-0.93 1.46 -2.42 -11.07 -30.82 -48.00] 38 A.A59 A.U72 [A-U] WC 20-XX cWW cW-W 176.8(anti) C2'-exo lambda=47.6; -143.6(anti) C4'-exo lambda=49.8 d(C1'-C1')=10.80 d(N1-N9)=8.87 d(C6-C8)=9.56 tor(N1-C1'-C1'-N9)=-25.5 H-bonds[2]: "N1-N3(imino)[2.88]; N6(amino)-O4(carbonyl)[2.86]" bp_pars: [-0.41 -0.33 0.52 -11.44 -26.64 -12.57] 39 A.U60 A.A71 [U-A] WC 20-XX cWW cW-W -163.1(anti) C4'-exo lambda=52.3; -161.1(anti) C4'-exo lambda=54.8 d(C1'-C1')=10.90 d(N1-N9)=9.15 d(C6-C8)=10.03 tor(N1-C1'-C1'-N9)=-14.3 H-bonds[2]: "N3(imino)-N1[3.04]; O4(carbonyl)-N6(amino)[3.08]" bp_pars: [-0.30 0.08 0.09 -5.88 -22.83 -3.25] 40 A.U61 A.A70 [U-A] WC 20-XX cWW cW-W -164.5(anti) C3'-endo lambda=51.9; -143.4(anti) C3'-endo lambda=55.4 d(C1'-C1')=10.66 d(N1-N9)=8.93 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=-24.9 H-bonds[2]: "N3(imino)-N1[2.86]; O4(carbonyl)-N6(amino)[2.99]" bp_pars: [-0.38 -0.10 -0.20 -1.24 -27.89 0.85] 41 A.U62 A.G69 [U-G] Wobble 28-XXVIII cWW cW-W -133.7(anti) C4'-exo lambda=73.8; -175.6(anti) C4'-exo lambda=42.0 d(C1'-C1')=10.39 d(N1-N9)=8.89 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-2.7 H-bonds[2]: "O2(carbonyl)-N1(imino)[2.75]; N3(imino)-O6(carbonyl)[3.02]" bp_pars: [2.88 -0.54 -0.07 -0.14 -7.55 5.05] 42 A.C63 A.G68 [C-G] WC 19-XIX cWW cW-W -123.3(anti) O4'-endo lambda=54.1; -159.5(anti) C3'-endo lambda=52.8 d(C1'-C1')=10.71 d(N1-N9)=8.97 d(C6-C8)=9.64 tor(N1-C1'-C1'-N9)=17.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.19]; N3-N1(imino)[3.11]; N4(amino)-O6(carbonyl)[2.87]" bp_pars: [-0.28 0.06 -1.48 37.60 -1.03 -8.57] 43 A.C63 A.G69 [C-G] 00-n/a cWW cW-W -123.3(anti) O4'-endo lambda=63.3; -175.6(anti) C4'-exo lambda=55.8 d(C1'-C1')=9.05 d(N1-N9)=7.56 d(C6-C8)=8.58 tor(N1-C1'-C1'-N9)=-7.7 H-bonds[2]: "N3-N1(imino)[3.01]; N4(amino)-O6(carbonyl)[2.98]" bp_pars: [0.91 -1.35 1.90 30.04 3.02 8.18] 44 A.U64 A.G67 [U+G] 00-n/a tWW tW+W -147.4(anti) C4'-exo lambda=85.1; 94.6(syn) O4'-endo lambda=28.7 d(C1'-C1')=9.76 d(N1-N9)=8.61 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-163.3 H-bonds[2]: "O2'(hydroxyl)-O6(carbonyl)[3.26]; O2(carbonyl)-N1(imino)[2.63]" bp_pars: [0.48 -4.54 -0.39 -4.64 -27.62 -124.12] **************************************************************************** List of 4 multiplet(s) 1 nts=3 A.C8+A.U101+A.G103 [CUG] 2 nts=3 A.A19+A.U89+A.A91 [AUA] 3 nts=3 A.U25+A.C27+A.A42 [UCA] 4 nts=3* A.C52+A.U78+A.G79 [CUG] **************************************************************************** List of 5 helices helix=1[1] bps=4 1 A.G1 A.C111 [G-C] WC 19-XIX cWW cW-W 2 A.G2 A.U110 [G-U] Wobble 28-XXVIII cWW cW-W 3 A.C3 A.G109 [C-G] WC 19-XIX cWW cW-W 4 A.A4 A.U108 [A-U] WC 20-XX cWW cW-W helix=2[1] bps=3 1 A.U6 A.A105 [U-A] WC 20-XX cWW cW-W 2 A.A7 A.U104 [A-U] WC 20-XX cWW cW-W 3 A.C8 A.G103 [C-G] WC 19-XIX cWW cW-W helix=3[2] bps=9 1 A.A13 A.A97 [A-A] 00-n/a tWH tW-M 2 A.U14 A.A96 [U-A] WC 20-XX cWW cW-W 3 A.G15 A.C95 [G-C] WC 19-XIX cWW cW-W 4 A.A16 A.U94 [A-U] WC 20-XX cWW cW-W 5 A.U17 A.A93 [U-A] WC 20-XX cWW cW-W 6 A.C18 A.G92 [C-G] WC 19-XIX cWW cW-W 7 A.A19 A.U89 [A-U] WC 20-XX cWW cW-W 8 A.G20 A.C88 [G-C] WC 19-XIX cWW cW-W 9 A.C21 A.G87 [C-G] WC 19-XIX cWW cW-W helix=4[2] bps=8 1 A.G23 A.C44 [G-C] WC 19-XIX cWW cW-W 2 A.U24 A.A43 [U-A] WC 20-XX cWW cW-W 3 A.U25 A.A42 [U-A] WC 20-XX cWW cW-W 4 A.C26 A.G41 [C-G] WC 19-XIX cWW cW-W 5 A.C28 A.G38 [C-G] WC 19-XIX cWW cW-W 6 A.C29 A.G37 [C-G] WC 19-XIX cWW cW-W 7 A.U30 A.A36 [U-A] WC 20-XX cWW cW-W 8 A.G31 A.A35 [G-A] 00-n/a cSH cm-M helix=5[1] bps=13 1 A.C52 A.G79 [C-G] WC 19-XIX cWW cW-W 2 A.A53 A.U78 [A-U] WC 20-XX cWW cW-W 3 A.A54 A.U77 [A-U] WC 20-XX cWW cW-W 4 A.A55 A.U76 [A-U] WC 20-XX cWW cW-W 5 A.G56 A.C75 [G-C] WC 19-XIX cWW cW-W 6 A.A57 A.U74 [A-U] WC 20-XX cWW cW-W 7 A.G58 A.C73 [G-C] WC 19-XIX cWW cW-W 8 A.A59 A.U72 [A-U] WC 20-XX cWW cW-W 9 A.U60 A.A71 [U-A] WC 20-XX cWW cW-W 10 A.U61 A.A70 [U-A] WC 20-XX cWW cW-W 11 A.U62 A.G69 [U-G] Wobble 28-XXVIII cWW cW-W 12 A.C63 A.G68 [C-G] WC 19-XIX cWW cW-W 13 A.U64 A.G67 [U+G] 00-n/a tWW tW+W **************************************************************************** List of 7 stems stem=1[#1] bps=4 1 A.G1 A.C111 [G-C] WC 19-XIX cWW cW-W 2 A.G2 A.U110 [G-U] Wobble 28-XXVIII cWW cW-W 3 A.C3 A.G109 [C-G] WC 19-XIX cWW cW-W 4 A.A4 A.U108 [A-U] WC 20-XX cWW cW-W stem=2[#2] bps=3 1 A.U6 A.A105 [U-A] WC 20-XX cWW cW-W 2 A.A7 A.U104 [A-U] WC 20-XX cWW cW-W 3 A.C8 A.G103 [C-G] WC 19-XIX cWW cW-W stem=3[#3] bps=5 1 A.U14 A.A96 [U-A] WC 20-XX cWW cW-W 2 A.G15 A.C95 [G-C] WC 19-XIX cWW cW-W 3 A.A16 A.U94 [A-U] WC 20-XX cWW cW-W 4 A.U17 A.A93 [U-A] WC 20-XX cWW cW-W 5 A.C18 A.G92 [C-G] WC 19-XIX cWW cW-W stem=4[#3] bps=3 1 A.A19 A.U89 [A-U] WC 20-XX cWW cW-W 2 A.G20 A.C88 [G-C] WC 19-XIX cWW cW-W 3 A.C21 A.G87 [C-G] WC 19-XIX cWW cW-W stem=5[#4] bps=4 1 A.G23 A.C44 [G-C] WC 19-XIX cWW cW-W 2 A.U24 A.A43 [U-A] WC 20-XX cWW cW-W 3 A.U25 A.A42 [U-A] WC 20-XX cWW cW-W 4 A.C26 A.G41 [C-G] WC 19-XIX cWW cW-W stem=6[#4] bps=3 1 A.C28 A.G38 [C-G] WC 19-XIX cWW cW-W 2 A.C29 A.G37 [C-G] WC 19-XIX cWW cW-W 3 A.U30 A.A36 [U-A] WC 20-XX cWW cW-W stem=7[#5] bps=12 1 A.C52 A.G79 [C-G] WC 19-XIX cWW cW-W 2 A.A53 A.U78 [A-U] WC 20-XX cWW cW-W 3 A.A54 A.U77 [A-U] WC 20-XX cWW cW-W 4 A.A55 A.U76 [A-U] WC 20-XX cWW cW-W 5 A.G56 A.C75 [G-C] WC 19-XIX cWW cW-W 6 A.A57 A.U74 [A-U] WC 20-XX cWW cW-W 7 A.G58 A.C73 [G-C] WC 19-XIX cWW cW-W 8 A.A59 A.U72 [A-U] WC 20-XX cWW cW-W 9 A.U60 A.A71 [U-A] WC 20-XX cWW cW-W 10 A.U61 A.A70 [U-A] WC 20-XX cWW cW-W 11 A.U62 A.G69 [U-G] Wobble 28-XXVIII cWW cW-W 12 A.C63 A.G68 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 2 coaxial stack(s) 1 Helix#3 contains 2 stems: [#3, #4] 2 Helix#4 contains 2 stems: [#5, #6] **************************************************************************** List of 2 hairpin loop(s) 1 nts=5 GCAUA closed by pair {A.U30+A.A36 [UA], #6} A.U30+A.G31+A.C32+A.A33+A.U34+A.A35+A.A36 [UGCAUAA] 2 nts=4 UUCG closed by pair {A.C63+A.G68 [CG], #7} A.C63+A.U64+A.U65+A.C66+A.G67+A.G68 [CUUCGG] **************************************************************************** List of 3 internal loop(s) 1 asymmetric internal loop: 7 nts; [1x2]; linked by [#1, #2] A.A4+A.A5+A.U6+A.A105+A.U106+A.C107+A.U108 [AAUAUCU] 2 asymmetric internal loop: 15 nts; [5x6]; linked by [#2, #3] A.C8+A.A9+A.G10+A.A11+A.G12+A.A13+A.U14+A.A96+A.A97+A.G98+A.U99+A.G100+A.U101+A.A102+A.G103 [CAGAGAUAAGUGUAG] 3 asymmetric internal loop: 7 nts; [1x2]; linked by [#5, #6] A.C26+A.C27+A.C28+A.G38+A.A39+A.U40+A.G41 [CCCGAUG] **************************************************************************** List of 1 junction(s) 1 3-way junctions: 21 nts; [1x7x7]; linked by [#4, #5, #7] A.C21+A.A22+A.G23+A.C44+A.C45+A.G46+A.U47+A.U48+A.U49+A.U50+A.A51+A.C52+A.G79+A.C80+A.C81+A.U82+A.U83+A.U84+A.U85+A.G86+A.G87 [CAGCCGUUUUACGCCUUUUGG] **************************************************************************** >chain-A #1 RNA with 111 nts GGCAAUACAGAGAUGAUCAGCAGUUCCCCUGCAUAAGGAUGAACCGUUUUACAAAGAGAUUUCUUCGGGAAUCUCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUC ((((.(((.....((((((((.((((.(((.....)))..)))).......((((((((((((....)))))))))))).......)))..)))))......)))..)))) DONE!