# 3DHS_05.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 Aug 13 15:32:40 2023 File name: 3DHS_05.pdb no. of DNA/RNA chains: 1 [0=137] no. of nucleotides: 137 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 32 base pair(s) 1 0.RG5/1 0.C265 [g-C] WC 19-XIX cWW cW-W -179.2(anti) C2'-exo lambda=55.9; -140.0(anti) C1'-endo lambda=52.3 d(C1'-C1')=10.60 d(N1-N9)=8.82 d(C6-C8)=9.18 tor(N1-C1'-C1'-N9)=-6.1 H-bonds[2]: "N1(imino)-N3[2.96]; O6(carbonyl)-N4(amino)[3.17]" bp_pars: [-0.05 -0.27 -0.19 4.80 -30.83 -6.61] 2 0.U3 0.A263 [U-A] WC 20-XX cWW cW-W -141.0(anti) C1'-endo lambda=49.1; -158.6(anti) C2'-exo lambda=50.0 d(C1'-C1')=10.58 d(N1-N9)=8.68 d(C6-C8)=8.56 tor(N1-C1'-C1'-N9)=-9.4 H-bonds[2]: "N3(imino)-N1[3.19]; O4(carbonyl)-N6(amino)[3.13]" bp_pars: [0.42 -0.47 -0.28 -11.37 -30.32 -27.60] 3 0.A5 0.U261 [A-U] WC 20-XX cWW cW-W 172.0(anti) C2'-exo lambda=44.2; -139.7(anti) C1'-endo lambda=46.4 d(C1'-C1')=11.27 d(N1-N9)=9.23 d(C6-C8)=9.32 tor(N1-C1'-C1'-N9)=-14.4 H-bonds[2]: "N1-N3(imino)[3.67]; N6(amino)-O4(carbonyl)[3.63]" bp_pars: [-0.56 0.15 0.20 2.87 -28.53 -26.57] 4 0.G10 0.C256 [G-C] WC 19-XIX cWW cW-W -168.7(anti) C2'-exo lambda=54.7; -145.7(anti) C1'-endo lambda=50.8 d(C1'-C1')=10.63 d(N1-N9)=8.85 d(C6-C8)=9.08 tor(N1-C1'-C1'-N9)=-8.1 H-bonds[2]: "N1(imino)-N3[3.17]; O6(carbonyl)-N4(amino)[3.13]" bp_pars: [0.02 -0.24 -0.11 1.38 -31.74 -11.98] 5 0.U12 0.A254 [U-A] 00-n/a cWW cW-W -142.3(anti) C1'-endo lambda=58.4; -165.7(anti) C2'-exo lambda=48.6 d(C1'-C1')=9.55 d(N1-N9)=7.81 d(C6-C8)=7.98 tor(N1-C1'-C1'-N9)=-9.0 H-bonds[1]: "N3(imino)-N1[2.69]" bp_pars: [1.08 -1.28 0.43 -8.96 -26.24 -18.41] 6 0.C13 0.G253 [C-G] 00-n/a cWW cW-W -143.4(anti) C1'-endo lambda=58.1; -170.5(anti) C2'-exo lambda=56.7 d(C1'-C1')=9.00 d(N1-N9)=7.42 d(C6-C8)=7.99 tor(N1-C1'-C1'-N9)=-10.6 H-bonds[1]: "O2(carbonyl)-N2(amino)[2.48]" bp_pars: [0.04 -1.50 1.20 -7.07 -15.51 -10.86] 7 0.G16 0.G119 [G+G] 00-n/a ... c... -161.5(anti) C1'-endo lambda=103.3; -172.8(anti) C1'-endo lambda=90.6 d(C1'-C1')=7.87 d(N1-N9)=8.22 d(C6-C8)=8.74 tor(N1-C1'-C1'-N9)=-2.0 H-bonds[4]: "O2'(hydroxyl)-O5'[2.95]; N1(imino)-OP1[2.67]; N2(amino)-O5'[3.04]; N2(amino)-OP2[2.24]" bp_pars: [4.95 7.07 1.22 23.50 -17.56 15.37] 8 0.U17 0.G239 [U+G] 00-n/a cHW cM+W -138.5(anti) C1'-endo lambda=62.7; -162.7(anti) C1'-endo lambda=91.8 d(C1'-C1')=6.25 d(N1-N9)=5.61 d(C6-C8)=6.45 tor(N1-C1'-C1'-N9)=6.4 H-bonds[3]: "N3(imino)*N2(amino)[2.43]; O4(carbonyl)-N2(amino)[2.81]; O5'-O2'(hydroxyl)[2.86]" bp_pars: [-1.24 -3.34 -0.03 40.32 -21.55 35.95] 9 0.A49 0.U248 [A-U] 00-n/a cWW cW-W -152.6(anti) C4'-endo lambda=47.8; -149.0(anti) C1'-endo lambda=37.3 d(C1'-C1')=10.67 d(N1-N9)=8.59 d(C6-C8)=7.82 tor(N1-C1'-C1'-N9)=-22.9 H-bonds[1]: "N1-N3(imino)[2.90]" bp_pars: [0.09 -0.68 -1.09 0.52 -54.77 -46.05] 10 0.A49 0.U249 [A-U] 00-n/a cWW cW-W -152.6(anti) C4'-endo lambda=72.8; -141.9(anti) C1'-endo lambda=54.1 d(C1'-C1')=9.11 d(N1-N9)=7.87 d(C6-C8)=8.23 tor(N1-C1'-C1'-N9)=-30.6 H-bonds[1]: "N1-N3(imino)[2.37]" bp_pars: [0.81 -1.44 2.00 9.41 -39.44 -7.18] 11 0.G51 0.G246 [G-G] 00-n/a ... c... -161.7(anti) C2'-exo lambda=42.6; -174.7(anti) C2'-exo lambda=45.5 d(C1'-C1')=10.90 d(N1-N9)=8.72 d(C6-C8)=8.33 tor(N1-C1'-C1'-N9)=-7.8 H-bonds[1]: "N1(imino)*N1(imino)[2.22]" bp_pars: [-0.42 0.04 -0.34 -12.95 -23.36 -49.30] 12 0.U56 0.C242 [U-C] 00-n/a cWW cW-W -144.3(anti) C1'-endo lambda=36.0; -145.2(anti) C1'-endo lambda=41.7 d(C1'-C1')=10.91 d(N1-N9)=8.65 d(C6-C8)=8.84 tor(N1-C1'-C1'-N9)=-7.2 H-bonds[1]: "O4(carbonyl)-N4(amino)[3.00]" bp_pars: [-1.17 -0.93 -1.88 10.21 -59.15 -16.13] 13 0.C62 0.G83 [C-G] 00-n/a cWW cW-W -148.2(anti) C2'-exo lambda=53.3; -171.8(anti) C2'-exo lambda=44.7 d(C1'-C1')=10.58 d(N1-N9)=8.64 d(C6-C8)=8.53 tor(N1-C1'-C1'-N9)=-7.5 H-bonds[2]: "N3-N1(imino)[3.42]; N4(amino)-O6(carbonyl)[2.63]" bp_pars: [1.03 -0.84 -1.83 10.30 -51.45 -16.44] 14 0.C62 0.U84 [C-U] 00-n/a cWW cW-W -148.2(anti) C2'-exo lambda=66.2; -156.7(anti) C1'-endo lambda=66.0 d(C1'-C1')=7.94 d(N1-N9)=6.79 d(C6-C8)=7.91 tor(N1-C1'-C1'-N9)=-31.4 H-bonds[2]: "O2(carbonyl)*O2(carbonyl)[2.97]; N3-N3(imino)[3.60]" bp_pars: [0.91 -1.62 2.01 20.72 -46.59 18.87] 15 0.U70 0.A74 [U-A] 00-n/a tWH tW-M -137.2(anti) C1'-endo lambda=48.9; -176.9(anti) C2'-exo lambda=19.6 d(C1'-C1')=9.69 d(N1-N9)=7.56 d(C6-C8)=6.36 tor(N1-C1'-C1'-N9)=150.1 H-bonds[1]: "N3(imino)-N7[3.93]" bp_pars: [5.27 -2.92 -2.17 1.52 -17.17 -91.02] 16 0.G71 0.G73 [G-G] 00-n/a tSH tm-M -161.0(anti) C2'-exo lambda=88.4; -164.5(anti) C2'-exo lambda=35.8 d(C1'-C1')=7.11 d(N1-N9)=6.33 d(C6-C8)=6.40 tor(N1-C1'-C1'-N9)=-155.1 H-bonds[4]: "O2'(hydroxyl)-N7[2.72]; N2(amino)-O3'[2.60]; N2(amino)-N7[3.16]; N2(amino)-OP1[3.08]" bp_pars: [6.09 -7.05 -1.43 32.19 0.22 -83.35] 17 0.U81 0.A82 [U+A] Platform 00-n/a cSH cm+M -143.3(anti) C2'-exo lambda=126.8; 176.7(anti) C2'-exo lambda=48.3 d(C1'-C1')=4.22 d(N1-N9)=4.22 d(C6-C8)=3.83 tor(N1-C1'-C1'-N9)=-10.5 H-bonds[2]: "O2'(hydroxyl)-OP2[3.09]; O2(carbonyl)-N6(amino)[2.34]" bp_pars: [3.82 0.93 -1.43 -17.64 -0.64 9.77] 18 0.G89 0.C98 [G-C] WC 19-XIX cWW cW-W -172.4(anti) C2'-exo lambda=52.6; -143.0(anti) C1'-endo lambda=52.7 d(C1'-C1')=10.52 d(N1-N9)=8.74 d(C6-C8)=9.01 tor(N1-C1'-C1'-N9)=-14.8 H-bonds[2]: "N1(imino)-N3[3.26]; O6(carbonyl)-N4(amino)[3.19]" bp_pars: [-0.44 -0.31 0.61 0.28 -28.26 -11.42] 19 0.U90 0.A97 [U-A] 00-n/a cWW cW-W -143.7(anti) C1'-endo lambda=53.0; 177.4(anti) C2'-exo lambda=46.5 d(C1'-C1')=10.31 d(N1-N9)=8.47 d(C6-C8)=8.69 tor(N1-C1'-C1'-N9)=-13.3 H-bonds[1]: "N3(imino)-N1[3.22]" bp_pars: [1.01 -0.66 0.88 -3.34 -27.11 -21.49] 20 0.G123 0.G189 [G-G] 00-n/a cHW cM-W -172.3(anti) C1'-endo lambda=33.6; -155.2(anti) C2'-exo lambda=29.5 d(C1'-C1')=10.18 d(N1-N9)=7.77 d(C6-C8)=6.43 tor(N1-C1'-C1'-N9)=42.0 H-bonds[2]: "N7*O6(carbonyl)[2.42]; O6(carbonyl)-N1(imino)[2.73]" bp_pars: [-0.49 -0.19 -0.76 31.29 11.30 -82.17] 21 0.G126 0.U188 [G-U] 00-n/a ... c... 179.8(anti) C1'-endo lambda=32.1; -143.5(anti) C2'-exo lambda=145.7 d(C1'-C1')=3.48 d(N1-N9)=3.54 d(C6-C8)=4.55 tor(N1-C1'-C1'-N9)=-27.0 H-bonds[5]: "N1(imino)-O3'[3.29]; N1(imino)-OP2[2.50]; N2(amino)-O2'(hydroxyl)[2.47]; N2(amino)-OP2[3.21]; N7*O4'[3.25]" bp_pars: [-2.98 -4.96 1.59 27.57 -11.91 52.60] 22 0.U131 0.A156 [U-A] WC 20-XX cWW cW-W -149.0(anti) C1'-endo lambda=50.5; -178.2(anti) C3'-endo lambda=48.8 d(C1'-C1')=10.48 d(N1-N9)=8.58 d(C6-C8)=8.52 tor(N1-C1'-C1'-N9)=-2.1 H-bonds[2]: "N3(imino)-N1[3.21]; O4(carbonyl)-N6(amino)[3.14]" bp_pars: [0.55 -0.54 -0.24 -7.99 -27.32 -26.99] 23 0.U132 0.A155 [U-A] WC 20-XX cWW cW-W -143.8(anti) C1'-endo lambda=47.0; -176.5(anti) C3'-endo lambda=52.8 d(C1'-C1')=10.37 d(N1-N9)=8.47 d(C6-C8)=8.57 tor(N1-C1'-C1'-N9)=-3.9 H-bonds[2]: "N3(imino)-N1[2.78]; O4(carbonyl)-N6(amino)[2.84]" bp_pars: [-0.21 -0.63 -0.25 -6.82 -28.85 -25.93] 24 0.A161 0.U178 [A-U] WC 20-XX cWW cW-W -175.5(anti) C2'-exo lambda=49.5; -139.7(anti) C1'-endo lambda=51.1 d(C1'-C1')=10.75 d(N1-N9)=8.91 d(C6-C8)=8.98 tor(N1-C1'-C1'-N9)=-2.6 H-bonds[2]: "N1-N3(imino)[3.38]; N6(amino)-O4(carbonyl)[3.40]" bp_pars: [-0.46 -0.19 0.03 1.57 -26.26 -22.52] 25 0.C167 0.G172 [C-G] 00-n/a cWW cW-W -145.8(anti) C1'-endo lambda=58.6; -173.0(anti) C2'-exo lambda=42.1 d(C1'-C1')=9.88 d(N1-N9)=8.00 d(C6-C8)=8.11 tor(N1-C1'-C1'-N9)=-0.4 H-bonds[2]: "O2(carbonyl)-N1(imino)[2.97]; N3-N1(imino)[2.96]" bp_pars: [1.33 -1.25 0.76 -2.58 -9.90 -21.11] 26 0.U184 0.U188 [U-U] 00-n/a ... t... -144.9(anti) C1'-endo lambda=155.5; -143.5(anti) C2'-exo lambda=21.4 d(C1'-C1')=6.32 d(N1-N9)=6.28 d(C6-C8)=6.70 tor(N1-C1'-C1'-N9)=-96.8 H-bonds[3]: "O4'-N3(imino)[2.34]; O5'*O2(carbonyl)[2.92]; O5'-N3(imino)[3.18]" bp_pars: [6.31 -3.04 -0.33 30.98 -12.46 104.26] 27 0.C197 0.G234 [C-G] 00-n/a cWW cW-W -151.3(anti) C1'-endo lambda=43.9; -163.3(anti) C2'-exo lambda=52.1 d(C1'-C1')=11.16 d(N1-N9)=9.17 d(C6-C8)=9.21 tor(N1-C1'-C1'-N9)=-7.6 H-bonds[1]: "N4(amino)-O6(carbonyl)[3.25]" bp_pars: [-0.42 0.06 0.41 -7.36 -33.05 -25.05] 28 0.U203 0.A228 [U-A] WC 20-XX cWW cW-W -143.0(anti) C1'-endo lambda=50.8; 172.6(anti) C2'-exo lambda=46.4 d(C1'-C1')=10.61 d(N1-N9)=8.65 d(C6-C8)=8.80 tor(N1-C1'-C1'-N9)=-8.5 H-bonds[2]: "N3(imino)-N1[3.30]; O4(carbonyl)-N6(amino)[3.33]" bp_pars: [0.47 -0.34 0.16 -7.11 -25.45 -26.56] 29 0.A204 0.G226 [A-G] 00-n/a c.W c.-W -164.5(anti) C2'-exo lambda=32.4; -172.1(anti) C2'-exo lambda=37.2 d(C1'-C1')=12.79 d(N1-N9)=10.38 d(C6-C8)=9.08 tor(N1-C1'-C1'-N9)=3.4 H-bonds[1]: "N6(amino)-O6(carbonyl)[3.22]" bp_pars: [-1.10 1.32 -2.04 1.90 -40.00 -59.51] 30 0.A204 0.U227 [A-U] WC 20-XX cWW cW-W -164.5(anti) C2'-exo lambda=50.6; -148.3(anti) C1'-endo lambda=52.1 d(C1'-C1')=10.67 d(N1-N9)=8.82 d(C6-C8)=8.85 tor(N1-C1'-C1'-N9)=-16.7 H-bonds[2]: "N1-N3(imino)[3.25]; N6(amino)-O4(carbonyl)[3.49]" bp_pars: [-0.32 -0.37 1.25 9.13 -28.79 -23.99] 31 0.C205 0.G226 [C-G] WC 19-XIX cWW cW-W -137.1(anti) C1'-endo lambda=53.7; -172.1(anti) C2'-exo lambda=54.5 d(C1'-C1')=10.30 d(N1-N9)=8.60 d(C6-C8)=8.92 tor(N1-C1'-C1'-N9)=-17.9 H-bonds[2]: "N3-N1(imino)[3.18]; N4(amino)-O6(carbonyl)[3.38]" bp_pars: [0.60 -0.46 1.29 -5.15 -31.21 -7.59] 32 0.C210 0.G216 [C-G] WC 19-XIX cWW cW-W -145.6(anti) C1'-endo lambda=49.3; -165.8(anti) C2'-exo lambda=49.7 d(C1'-C1')=10.65 d(N1-N9)=8.72 d(C6-C8)=8.96 tor(N1-C1'-C1'-N9)=-2.7 H-bonds[2]: "N3-N1(imino)[3.04]; N4(amino)-O6(carbonyl)[2.84]" bp_pars: [0.32 -0.39 0.24 -5.71 -19.90 -16.71] **************************************************************************** List of 5 helices helix=1[0] bps=2 1 0.U12 0.A254 [U-A] 00-n/a cWW cW-W 2 0.C13 0.G253 [C-G] 00-n/a cWW cW-W helix=2[0] bps=2 1 0.U70 0.A74 [U-A] 00-n/a tWH tW-M 2 0.G71 0.G73 [G-G] 00-n/a tSH tm-M helix=3[0] bps=2 1 0.G89 0.C98 [G-C] WC 19-XIX cWW cW-W 2 0.U90 0.A97 [U-A] 00-n/a cWW cW-W helix=4[1] bps=2 1 0.U131 0.A156 [U-A] WC 20-XX cWW cW-W 2 0.U132 0.A155 [U-A] WC 20-XX cWW cW-W helix=5[1] bps=3 1 0.U203 0.A228 [U-A] WC 20-XX cWW cW-W 2 0.A204 0.U227 [A-U] WC 20-XX cWW cW-W 3 0.C205 0.G226 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems stem=1[#4] bps=2 1 0.U131 0.A156 [U-A] WC 20-XX cWW cW-W 2 0.U132 0.A155 [U-A] WC 20-XX cWW cW-W stem=2[#5] bps=3 1 0.U203 0.A228 [U-A] WC 20-XX cWW cW-W 2 0.A204 0.U227 [A-U] WC 20-XX cWW cW-W 3 0.C205 0.G226 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 7 lone WC/wobble pair(s) -1 0.RG5/1 0.C265 [g-C] WC 19-XIX cWW cW-W -2 0.U3 0.A263 [U-A] WC 20-XX cWW cW-W -3 0.A5 0.U261 [A-U] WC 20-XX cWW cW-W -4 0.G10 0.C256 [G-C] WC 19-XIX cWW cW-W -5 0.G89 0.C98 [G-C] WC 19-XIX cWW cW-W -6 0.A161 0.U178 [A-U] WC 20-XX cWW cW-W -7 0.C210 0.G216 [C-G] WC 19-XIX cWW cW-W **************************************************************************** >chain-0 #1 RNA* with 137 nts gUAGCUCGGUAAUUGCUGGAGUGCGUGAGAGCGUAGUGUUGUGACGGGAAAUAUGGGGGACUUCCGAAAUGAGGAAGCACCGGCACUUGUAGUGAACAGUACGAGGCGCUUGCGUAAAGGAGACUGGUUGACUAUAC ((((....................................(...)................((...........))..(.......)............(((....().....)))...............)..))) DONE!