# 5U3G.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 Mar 3 16:38:50 2026 File name: 5U3G.pdb no. of DNA/RNA chains: 1 [B=85] no. of nucleotides: 85 no. of waters: 21 no. of metals: 25 [Mg=24, K=1] **************************************************************************** List of 43 base pair(s) 1 B.GTP1 B.C40 [g-C] WC 19-XIX cWW cW-W -179.4(anti) C3'-endo lambda=39.3; -166.8(anti) C3'-endo lambda=60.5 d(C1'-C1')=10.52 d(N1-N9)=8.77 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=3.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.84]; N1(imino)-N3[2.54]; N2(amino)-O2(carbonyl)[2.34]" bp_pars: [-0.24 -0.29 -0.16 0.05 0.34 4.53] 2 B.G2 B.C39 [G-C] WC 19-XIX cWW cW-W -169.4(anti) C3'-endo lambda=54.1; -175.6(anti) C3'-endo lambda=53.5 d(C1'-C1')=10.61 d(N1-N9)=8.86 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=2.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.79]; N1(imino)-N3[2.82]; N2(amino)-O2(carbonyl)[2.68]" bp_pars: [-0.16 -0.23 -0.20 -5.36 -3.13 0.32] 3 B.U3 B.A38 [U-A] WC 20-XX cWW cW-W -166.3(anti) C3'-endo lambda=55.2; -159.5(anti) C3'-endo lambda=54.6 d(C1'-C1')=10.61 d(N1-N9)=8.92 d(C6-C8)=9.89 tor(N1-C1'-C1'-N9)=3.3 H-bonds[2]: "N3(imino)-N1[2.89]; O4(carbonyl)-N6(amino)[2.95]" bp_pars: [-0.04 -0.06 -0.21 1.06 -0.44 0.15] 4 B.G4 B.U37 [G-U] Wobble 28-XXVIII cWW cW-W -165.2(anti) C3'-endo lambda=40.0; -161.4(anti) C3'-endo lambda=68.8 d(C1'-C1')=10.47 d(N1-N9)=8.82 d(C6-C8)=9.68 tor(N1-C1'-C1'-N9)=-4.7 H-bonds[2]: "O6(carbonyl)-N3(imino)[2.77]; N1(imino)-O2(carbonyl)[2.81]" bp_pars: [-2.39 -0.62 0.02 3.93 -8.00 -2.77] 5 B.A5 B.U36 [A-U] WC 20-XX cWW cW-W -162.6(anti) C3'-endo lambda=54.0; -161.4(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.54 d(N1-N9)=8.82 d(C6-C8)=9.78 tor(N1-C1'-C1'-N9)=-8.9 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.91]; N1-N3(imino)[2.77]" bp_pars: [0.09 -0.17 0.12 3.63 -12.56 0.59] 6 B.C6 B.G35 [C-G] WC 19-XIX cWW cW-W -170.2(anti) C3'-endo lambda=58.0; -169.8(anti) C3'-endo lambda=54.7 d(C1'-C1')=10.46 d(N1-N9)=8.84 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-8.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.70]; N3-N1(imino)[2.86]; N4(amino)-O6(carbonyl)[2.98]" bp_pars: [0.22 -0.17 0.26 0.80 -8.28 2.29] 7 B.U7 B.A32 [U-A] rHoogsteen 24-XXIV tWH tW-M -164.3(anti) C3'-endo lambda=37.0; -168.4(anti) C3'-exo lambda=16.4 d(C1'-C1')=9.65 d(N1-N9)=7.18 d(C6-C8)=6.35 tor(N1-C1'-C1'-N9)=152.1 H-bonds[2]: "O2(carbonyl)-N6(amino)[2.69]; N3(imino)-N7[2.88]" bp_pars: [4.23 -2.30 0.04 -8.27 -6.27 -91.62] 8 B.A8 B.G31 [A-G] Sheared 11-XI tHS cM-m -157.7(anti) C3'-endo lambda=5.6; -151.5(anti) C3'-endo lambda=94.1 d(C1'-C1')=9.44 d(N1-N9)=8.21 d(C6-C8)=8.59 tor(N1-C1'-C1'-N9)=-33.9 H-bonds[3]: "N7-N2(amino)[2.72]; N6(amino)-O2'(hydroxyl)[3.14]; N6(amino)-N3[3.16]" bp_pars: [-6.73 -4.53 0.16 0.79 -13.78 -8.03] 9 B.G9 B.C30 [G-C] WC 19-XIX cWW cW-W -171.7(anti) C3'-endo lambda=52.0; -167.4(anti) C3'-endo lambda=55.9 d(C1'-C1')=10.57 d(N1-N9)=8.85 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-4.4 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.84]; N1(imino)-N3[2.85]; N2(amino)-O2(carbonyl)[2.74]" bp_pars: [-0.40 -0.25 0.15 -3.80 -6.16 -0.79] 10 B.G9 B.A74 [G-A] 00-n/a cWS cW-m -171.7(anti) C3'-endo lambda=100.3; -152.2(anti) C3'-endo lambda=133.1 d(C1'-C1')=6.68 d(N1-N9)=8.01 d(C6-C8)=10.61 tor(N1-C1'-C1'-N9)=-43.3 H-bonds[1]: "N2(amino)-N3[2.92]" bp_pars: [-1.77 6.62 2.43 29.23 -35.30 133.50] 11 B.G10 B.C29 [G-C] WC 19-XIX cWW cW-W -172.3(anti) C3'-endo lambda=54.4; -166.2(anti) C3'-endo lambda=52.2 d(C1'-C1')=10.73 d(N1-N9)=8.98 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=-9.2 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.05]; N1(imino)-N3[2.99]; N2(amino)-O2(carbonyl)[2.85]" bp_pars: [-0.13 0.02 -0.12 -19.42 -16.64 0.60] 12 B.G10 B.A72 [G-A] 00-n/a cSW cm-W -172.3(anti) C3'-endo lambda=103.7; -151.6(anti) C3'-endo lambda=74.0 d(C1'-C1')=9.31 d(N1-N9)=9.41 d(C6-C8)=11.64 tor(N1-C1'-C1'-N9)=-75.3 H-bonds[1]: "N2(amino)-N1[3.02]" bp_pars: [2.44 5.13 0.99 -8.52 -62.25 108.18] 13 B.G11 B.U13 [G+U] 00-n/a cWH cW+M -167.7(anti) C3'-endo lambda=91.5; 178.1(anti) C3'-endo lambda=48.9 d(C1'-C1')=10.96 d(N1-N9)=10.05 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=-28.1 H-bonds[1]: "N2(amino)-O4(carbonyl)[3.29]" bp_pars: [6.37 3.96 0.17 -27.93 -23.28 -28.49] 14 B.G11 B.U28 [G-U] 00-n/a cW. cW-. -167.7(anti) C3'-endo lambda=50.4; -173.4(anti) C3'-endo lambda=16.8 d(C1'-C1')=13.00 d(N1-N9)=10.68 d(C6-C8)=10.56 tor(N1-C1'-C1'-N9)=15.1 H-bonds[2]: "N1(imino)-O4(carbonyl)[2.87]; N2(amino)-O4(carbonyl)[3.14]" bp_pars: [4.23 0.56 -0.47 -18.62 -11.46 -46.36] 15 B.G11 B.A71 [G-A] 00-n/a cSW cm-W -167.7(anti) C3'-endo lambda=112.1; -172.5(anti) C3'-endo lambda=58.5 d(C1'-C1')=9.54 d(N1-N9)=9.40 d(C6-C8)=11.44 tor(N1-C1'-C1'-N9)=-56.1 H-bonds[1]: "N2(amino)-N1[2.97]" bp_pars: [3.89 3.40 1.55 -22.45 -46.59 84.01] 16 B.U12 B.C14 [U+C] 00-n/a cWH cW+M -128.8(anti) C2'-endo lambda=101.2; -166.3(anti) C3'-endo lambda=25.4 d(C1'-C1')=9.68 d(N1-N9)=8.67 d(C6-C8)=9.02 tor(N1-C1'-C1'-N9)=1.9 H-bonds[1]: "O2(carbonyl)-N4(amino)[2.91]" bp_pars: [4.29 0.58 0.85 -15.06 5.06 -55.52] 17 B.U13 B.U28 [U-U] 00-n/a cWW cW-W 178.1(anti) C3'-endo lambda=27.6; -173.4(anti) C3'-endo lambda=65.9 d(C1'-C1')=10.00 d(N1-N9)=8.12 d(C6-C8)=8.76 tor(N1-C1'-C1'-N9)=13.5 H-bonds[1]: "O4(carbonyl)-N3(imino)[2.62]" bp_pars: [-3.13 -1.74 -0.30 13.97 3.90 -17.78] 18 B.C14 B.G27 [C-G] WC 19-XIX cWW cW-W -166.3(anti) C3'-endo lambda=56.5; -173.5(anti) C3'-endo lambda=56.4 d(C1'-C1')=10.47 d(N1-N9)=8.85 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=0.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.67]; N3-N1(imino)[2.84]; N4(amino)-O6(carbonyl)[2.95]" bp_pars: [0.21 -0.16 -0.14 4.36 -5.10 2.86] 19 B.C15 B.G26 [C-G] WC 19-XIX cWW cW-W -163.6(anti) C3'-endo lambda=57.6; -171.1(anti) C3'-endo lambda=56.5 d(C1'-C1')=10.54 d(N1-N9)=8.94 d(C6-C8)=9.96 tor(N1-C1'-C1'-N9)=1.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.78]; N3-N1(imino)[2.96]; N4(amino)-O6(carbonyl)[3.08]" bp_pars: [0.25 -0.06 -0.20 2.90 -2.25 3.24] 20 B.G16 B.C25 [G-C] WC 19-XIX cWW cW-W -159.8(anti) C3'-endo lambda=54.5; -160.5(anti) C3'-endo lambda=57.4 d(C1'-C1')=10.56 d(N1-N9)=8.92 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-3.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.02]; N1(imino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.77]" bp_pars: [-0.29 -0.12 -0.21 -0.44 -10.61 2.50] 21 B.G17 B.C24 [G-C] WC 19-XIX cWW cW-W -170.3(anti) C3'-endo lambda=55.4; -168.1(anti) C3'-endo lambda=56.1 d(C1'-C1')=10.53 d(N1-N9)=8.87 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=-13.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.94]; N1(imino)-N3[2.85]; N2(amino)-O2(carbonyl)[2.64]" bp_pars: [-0.19 -0.19 0.42 -1.74 -12.94 1.61] 22 B.C18 B.G23 [C-G] WC 19-XIX cWW cW-W -162.7(anti) C3'-endo lambda=57.1; -174.8(anti) C3'-endo lambda=52.1 d(C1'-C1')=10.55 d(N1-N9)=8.86 d(C6-C8)=9.80 tor(N1-C1'-C1'-N9)=-8.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.78]; N3-N1(imino)[2.86]; N4(amino)-O6(carbonyl)[2.87]" bp_pars: [0.31 -0.22 0.48 -7.99 -4.97 -0.83] 23 B.G19 B.A22 [G-A] 00-n/a t.H t.-M -162.8(anti) C3'-endo lambda=79.0; -167.3(anti) C3'-endo lambda=24.0 d(C1'-C1')=10.63 d(N1-N9)=9.25 d(C6-C8)=9.04 tor(N1-C1'-C1'-N9)=-158.0 H-bonds[3]: "N1(imino)-OP2[2.82]; N2(amino)-OP2[2.58]; N2(amino)-N7[3.19]" bp_pars: [8.23 -4.97 -0.21 16.97 3.05 -55.97] 24 B.C29 B.A71 [C+A] 00-n/a tSW cm+W -166.2(anti) C3'-endo lambda=122.4; -172.5(anti) C3'-endo lambda=9.9 d(C1'-C1')=9.48 d(N1-N9)=8.89 d(C6-C8)=9.60 tor(N1-C1'-C1'-N9)=86.4 H-bonds[2]: "O2'(hydroxyl)-N6(amino)[3.18]; O2(carbonyl)-N6(amino)[3.03]" bp_pars: [4.16 -3.96 0.99 -10.95 36.09 -59.11] 25 B.G33 B.A61 [G+A] Linker 00-n/a tSS tm+m -169.8(anti) C3'-endo lambda=81.4; -151.0(anti) C3'-endo lambda=61.6 d(C1'-C1')=8.09 d(N1-N9)=7.66 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=156.1 H-bonds[2]: "O2'(hydroxyl)-N1[2.70]; N2(amino)-N3[2.84]" bp_pars: [-2.73 -7.30 1.06 -37.44 -17.72 -155.57] 26 B.G41 B.U58 [G-U] Wobble 28-XXVIII cWW cW-W -172.3(anti) C3'-endo lambda=41.3; -137.5(anti) C3'-endo lambda=66.8 d(C1'-C1')=11.20 d(N1-N9)=9.52 d(C6-C8)=10.37 tor(N1-C1'-C1'-N9)=4.1 H-bonds[2]: "O6(carbonyl)-N3(imino)[3.44]; N1(imino)-O2(carbonyl)[3.53]" bp_pars: [-2.30 0.10 -0.24 -0.57 -2.27 -5.30] 27 B.A42 B.U57 [A-U] WC 20-XX cWW cW-W -165.0(anti) C3'-endo lambda=51.9; -160.3(anti) C3'-endo lambda=55.4 d(C1'-C1')=10.67 d(N1-N9)=8.93 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-8.3 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.97]; N1-N3(imino)[2.89]" bp_pars: [0.02 -0.06 0.12 11.99 -9.47 -1.00] 28 B.C43 B.G56 [C-G] WC 19-XIX cWW cW-W -177.8(anti) C3'-endo lambda=57.8; -174.6(anti) C3'-endo lambda=54.0 d(C1'-C1')=10.57 d(N1-N9)=8.92 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-10.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.73]; N3-N1(imino)[2.90]; N4(amino)-O6(carbonyl)[3.01]" bp_pars: [0.24 -0.14 0.49 2.10 -11.80 1.58] 29 B.C44 B.G55 [C-G] WC 19-XIX cWW cW-W -164.8(anti) C3'-endo lambda=57.5; -172.0(anti) C3'-endo lambda=55.8 d(C1'-C1')=10.50 d(N1-N9)=8.88 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=-5.0 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.72]; N3-N1(imino)[2.86]; N4(amino)-O6(carbonyl)[2.89]" bp_pars: [0.21 -0.17 0.18 -0.84 -6.56 1.21] 30 B.G45 B.C54 [G-C] WC 19-XIX cWW cW-W -169.2(anti) C3'-endo lambda=55.0; -168.6(anti) C3'-endo lambda=56.1 d(C1'-C1')=10.57 d(N1-N9)=8.90 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-4.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.94]; N1(imino)-N3[2.87]; N2(amino)-O2(carbonyl)[2.74]" bp_pars: [-0.21 -0.15 0.09 -3.08 -6.70 0.87] 31 B.C46 B.G53 [C-G] WC 19-XIX cWW cW-W -173.3(anti) C3'-endo lambda=57.0; -168.6(anti) C3'-endo lambda=55.4 d(C1'-C1')=10.61 d(N1-N9)=8.97 d(C6-C8)=9.95 tor(N1-C1'-C1'-N9)=-2.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.77]; N3-N1(imino)[2.93]; N4(amino)-O6(carbonyl)[3.03]" bp_pars: [0.26 -0.08 0.23 0.58 -3.21 1.87] 32 B.C47 B.G52 [C-G] WC 19-XIX cWW cW-W -166.2(anti) C3'-endo lambda=58.6; -171.0(anti) C3'-endo lambda=58.3 d(C1'-C1')=10.49 d(N1-N9)=8.94 d(C6-C8)=9.98 tor(N1-C1'-C1'-N9)=1.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.73]; N3-N1(imino)[2.93]; N4(amino)-O6(carbonyl)[3.04]" bp_pars: [0.22 -0.06 -0.16 1.03 -0.92 3.49] 33 B.G48 B.A51 [G-A] 00-n/a tSH tm-M -165.9(anti) C3'-endo lambda=92.4; -140.7(anti) C3'-endo lambda=10.7 d(C1'-C1')=9.46 d(N1-N9)=8.24 d(C6-C8)=8.37 tor(N1-C1'-C1'-N9)=-132.3 H-bonds[2]: "N2(amino)-OP2[2.55]; N2(amino)-N7[2.93]" bp_pars: [7.16 -5.39 0.81 5.08 -2.50 -23.80] 34 B.C60 B.G80 [C-G] WC 19-XIX cWW cW-W -168.8(anti) C3'-endo lambda=53.0; -109.6(anti) C2'-endo lambda=53.0 d(C1'-C1')=10.65 d(N1-N9)=8.88 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-17.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.78]; N3-N1(imino)[2.87]; N4(amino)-O6(carbonyl)[2.89]" bp_pars: [0.25 -0.21 0.33 12.03 -16.11 -2.19] 35 B.C62 B.G83 [C-G] WC 19-XIX cWW cW-W -177.7(anti) C3'-endo lambda=54.1; -164.3(anti) C3'-endo lambda=54.9 d(C1'-C1')=10.64 d(N1-N9)=8.92 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=1.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.74]; N3-N1(imino)[2.88]; N4(amino)-O6(carbonyl)[2.97]" bp_pars: [0.18 -0.14 -0.08 -2.39 0.62 1.47] 36 B.G63 B.A82 [G-A] Sheared 11-XI tSH cm-M -163.6(anti) C3'-endo lambda=97.4; -166.5(anti) C3'-endo lambda=7.1 d(C1'-C1')=9.43 d(N1-N9)=8.26 d(C6-C8)=8.71 tor(N1-C1'-C1'-N9)=-12.4 H-bonds[3]: "O2'(hydroxyl)-N6(amino)[2.97]; N2(amino)-N7[2.89]; N3-N6(amino)[3.00]" bp_pars: [6.73 -4.36 0.12 3.05 -0.28 -2.23] 37 B.G64 B.G81 [G-G] 07-VII tHW tM-W 170.8(anti) C2'-exo lambda=37.8; 179.6(anti) C3'-endo lambda=24.1 d(C1'-C1')=11.15 d(N1-N9)=8.77 d(C6-C8)=7.41 tor(N1-C1'-C1'-N9)=177.0 H-bonds[2]: "N7-N1(imino)[2.87]; O6(carbonyl)-N2(amino)[3.07]" bp_pars: [-5.46 -0.01 -0.70 1.11 -11.05 -118.64] 38 B.C65 B.G79 [C+G] 00-n/a cH. cM+. -172.4(anti) C3'-endo lambda=18.7; -127.8(anti) C2'-endo lambda=22.9 d(C1'-C1')=13.62 d(N1-N9)=10.87 d(C6-C8)=9.72 tor(N1-C1'-C1'-N9)=-20.4 H-bonds[1]: "N4(amino)-O6(carbonyl)[2.88]" bp_pars: [1.91 -6.19 -1.01 9.48 -4.19 138.80] 39 B.G66 B.C78 [G-C] WC 19-XIX cWW cW-W -171.3(anti) C3'-endo lambda=54.1; -150.1(anti) C3'-endo lambda=59.2 d(C1'-C1')=10.55 d(N1-N9)=8.93 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-0.4 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.00]; N1(imino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.77]" bp_pars: [-0.20 -0.11 -0.29 -3.95 -3.06 2.03] 40 B.G67 B.C77 [G-C] WC 19-XIX cWW cW-W -177.4(anti) C3'-endo lambda=54.8; -165.7(anti) C3'-endo lambda=55.1 d(C1'-C1')=10.60 d(N1-N9)=8.92 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=-5.9 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.82]; N1(imino)-N3[2.88]; N2(amino)-O2(carbonyl)[2.84]" bp_pars: [-0.20 -0.20 0.10 -2.07 -7.93 -2.14] 41 B.G68 B.C76 [G-C] WC 19-XIX cWW cW-W -160.2(anti) C3'-endo lambda=54.2; 174.7(anti) C3'-endo lambda=51.3 d(C1'-C1')=10.62 d(N1-N9)=8.84 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-13.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.85]; N1(imino)-N3[2.84]; N2(amino)-O2(carbonyl)[2.75]" bp_pars: [-0.29 -0.22 0.11 -8.85 -13.99 -0.43] 42 B.A69 B.A74 [A+A] 02-II tHH tM+M 67.4(syn) C1'-exo lambda=15.5; -152.2(anti) C3'-endo lambda=13.1 d(C1'-C1')=11.15 d(N1-N9)=8.32 d(C6-C8)=6.32 tor(N1-C1'-C1'-N9)=-146.3 H-bonds[3]: "N7-N6(amino)[3.12]; N6(amino)-OP2[3.14]; N6(amino)-N7[3.14]" bp_pars: [6.23 -5.28 0.15 8.37 1.50 179.62] 43 B.G84 B.A85 [G+A] Platform 00-n/a cSH cm+M -176.9(anti) C3'-exo lambda=120.6; 174.9(anti) C1'-exo lambda=78.5 d(C1'-C1')=5.95 d(N1-N9)=6.40 d(C6-C8)=6.66 tor(N1-C1'-C1'-N9)=6.8 H-bonds[2]: "O2'(hydroxyl)-O4'[2.77]; N2(amino)-N7[2.49]" bp_pars: [6.58 4.03 -1.15 -7.67 16.67 19.47] **************************************************************************** List of 5 multiplet(s) 1 nts=3 B.G10+B.C29+B.A72 [GCA] 2 nts=3 B.G11+B.U13+B.U28 [GUU] 3 nts=3* B.G11+B.C29+B.A71 [GCA] 4 nts=3 B.U12+B.C14+B.G27 [UCG] 5 nts=4 B.G9+B.C30+B.A69+B.A74 [GCAA] **************************************************************************** List of 2 helices helix=1[4] bps=25 1 B.A22 B.G19 [A-G] 00-n/a tH. tM-. 2 B.G23 B.C18 [G-C] WC 19-XIX cWW cW-W 3 B.C24 B.G17 [C-G] WC 19-XIX cWW cW-W 4 B.C25 B.G16 [C-G] WC 19-XIX cWW cW-W 5 B.G26 B.C15 [G-C] WC 19-XIX cWW cW-W 6 B.G27 B.C14 [G-C] WC 19-XIX cWW cW-W 7 B.U28 B.G11 [U-G] 00-n/a c.W c.-W 8 B.C29 B.G10 [C-G] WC 19-XIX cWW cW-W 9 B.C30 B.G9 [C-G] WC 19-XIX cWW cW-W 10 B.G31 B.A8 [G-A] Sheared 11-XI tSH cm-M 11 B.A32 B.U7 [A-U] rHoogsteen 24-XXIV tHW tM-W 12 B.G35 B.C6 [G-C] WC 19-XIX cWW cW-W 13 B.U36 B.A5 [U-A] WC 20-XX cWW cW-W 14 B.U37 B.G4 [U-G] Wobble 28-XXVIII cWW cW-W 15 B.A38 B.U3 [A-U] WC 20-XX cWW cW-W 16 B.C39 B.G2 [C-G] WC 19-XIX cWW cW-W 17 B.C40 B.GTP1 [C-g] WC 19-XIX cWW cW-W 18 B.G41 B.U58 [G-U] Wobble 28-XXVIII cWW cW-W 19 B.A42 B.U57 [A-U] WC 20-XX cWW cW-W 20 B.C43 B.G56 [C-G] WC 19-XIX cWW cW-W 21 B.C44 B.G55 [C-G] WC 19-XIX cWW cW-W 22 B.G45 B.C54 [G-C] WC 19-XIX cWW cW-W 23 B.C46 B.G53 [C-G] WC 19-XIX cWW cW-W 24 B.C47 B.G52 [C-G] WC 19-XIX cWW cW-W 25 B.G48 B.A51 [G-A] 00-n/a tSH tm-M helix=2[1] bps=9 1 B.A74 B.A69 [A+A] 02-II tHH tM+M 2 B.C76 B.G68 [C-G] WC 19-XIX cWW cW-W 3 B.C77 B.G67 [C-G] WC 19-XIX cWW cW-W 4 B.C78 B.G66 [C-G] WC 19-XIX cWW cW-W 5 B.G79 B.C65 [G+C] 00-n/a c.H c.+M 6 B.G81 B.G64 [G-G] 07-VII tWH tW-M 7 B.A82 B.G63 [A-G] Sheared 11-XI tHS cM-m 8 B.G83 B.C62 [G-C] WC 19-XIX cWW cW-W 9 B.G84 B.A85 [G+A] Platform 00-n/a cSH cm+M **************************************************************************** List of 5 stems stem=1[#1] bps=6 1 B.GTP1 B.C40 [g-C] WC 19-XIX cWW cW-W 2 B.G2 B.C39 [G-C] WC 19-XIX cWW cW-W 3 B.U3 B.A38 [U-A] WC 20-XX cWW cW-W 4 B.G4 B.U37 [G-U] Wobble 28-XXVIII cWW cW-W 5 B.A5 B.U36 [A-U] WC 20-XX cWW cW-W 6 B.C6 B.G35 [C-G] WC 19-XIX cWW cW-W stem=2[#1] bps=2 1 B.G9 B.C30 [G-C] WC 19-XIX cWW cW-W 2 B.G10 B.C29 [G-C] WC 19-XIX cWW cW-W stem=3[#1] bps=5 1 B.C14 B.G27 [C-G] WC 19-XIX cWW cW-W 2 B.C15 B.G26 [C-G] WC 19-XIX cWW cW-W 3 B.G16 B.C25 [G-C] WC 19-XIX cWW cW-W 4 B.G17 B.C24 [G-C] WC 19-XIX cWW cW-W 5 B.C18 B.G23 [C-G] WC 19-XIX cWW cW-W stem=4[#1] bps=7 1 B.G41 B.U58 [G-U] Wobble 28-XXVIII cWW cW-W 2 B.A42 B.U57 [A-U] WC 20-XX cWW cW-W 3 B.C43 B.G56 [C-G] WC 19-XIX cWW cW-W 4 B.C44 B.G55 [C-G] WC 19-XIX cWW cW-W 5 B.G45 B.C54 [G-C] WC 19-XIX cWW cW-W 6 B.C46 B.G53 [C-G] WC 19-XIX cWW cW-W 7 B.C47 B.G52 [C-G] WC 19-XIX cWW cW-W stem=5[#2] bps=3 1 B.G66 B.C78 [G-C] WC 19-XIX cWW cW-W 2 B.G67 B.C77 [G-C] WC 19-XIX cWW cW-W 3 B.G68 B.C76 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 2 lone WC/wobble pair(s) -1 B.C60 B.G80 [C-G] WC 19-XIX cWW cW-W -2 B.C62 B.G83 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 4 stems: [#1, #2, #3, #4] **************************************************************************** List of 3 hairpin loop(s) 1 nts=4 GAAA closed by pair {B.C18+B.G23 [CG], #3} B.C18+B.G19+B.A20+B.A21+B.A22+B.G23 [CGAAAG] 2 nts=4 GAAA closed by pair {B.C47+B.G52 [CG], #4} B.C47+B.G48+B.A49+B.A50+B.A51+B.G52 [CGAAAG] 3 nts=7 AAAAAAG closed by pair {B.G68+B.C76 [GC], #5} B.G68+B.A69+B.A70+B.A71+B.A72+B.A73+B.A74+B.G75+B.C76 [GAAAAAAGC] **************************************************************************** List of 2 internal loop(s) 1 asymmetric internal loop: 10 nts; [2x4]; linked by [#1, #2] B.C6+B.U7+B.A8+B.G9+B.C30+B.G31+B.A32+B.G33+B.A34+B.G35 [CUAGCGAGAG] 2 asymmetric internal loop: 8 nts; [3x1]; linked by [#2, #3] B.G10+B.G11+B.U12+B.U13+B.C14+B.G27+B.U28+B.C29 [GGUUCGUC] This structure contains pseudo-knot(s). **************************************************************************** List of 1 ribose zipper(s) 1 nts=4 B.G10+B.G11+B.A72+B.A73 [GGAA] **************************************************************************** >chain-B #1 RNA with 85 nts gGUGACUAGGGUUCCGGCGAAAGCCGGUCCGAGAGUUACCGACCGCCGAAAGGCGGUUACACGGCGGGAAAAAAGCCCGGGAGGA ((((((..((...(((((....))))).))....))))))(((((((....))))))).(.[...(((.......))).)..].. DONE!