# dsRNA18_4IG8.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: Wed Nov 15 07:08:18 2023 File name: dsRNA18_4IG8.pdb no. of DNA/RNA chains: 2 [A=18, B=18] no. of nucleotides: 36 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 18 base pair(s) 1 B.G1 A.C18 [G-C] WC 19-XIX cWW cW-W -173.8(anti) C3'-endo lambda=54.3; -161.0(anti) C3'-endo lambda=56.8 d(C1'-C1')=10.58 d(N1-N9)=8.91 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-9.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.02]; N1(imino)-N3[2.90]; N2(amino)-O2(carbonyl)[2.68]" bp_pars: [-0.33 -0.13 0.19 -3.65 -11.43 2.37] 2 B.G2 A.C17 [G-C] WC 19-XIX cWW cW-W -169.5(anti) C3'-endo lambda=52.0; -160.3(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.63 d(N1-N9)=8.87 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-13.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.94]; N1(imino)-N3[2.86]; N2(amino)-O2(carbonyl)[2.77]" bp_pars: [-0.38 -0.21 0.22 -9.36 -16.63 -0.60] 3 B.C3 A.G16 [C-G] WC 19-XIX cWW cW-W -162.3(anti) C3'-endo lambda=56.5; -160.2(anti) C3'-endo lambda=51.2 d(C1'-C1')=10.72 d(N1-N9)=8.98 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=-15.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.83]; N3-N1(imino)[2.96]; N4(amino)-O6(carbonyl)[3.15]" bp_pars: [0.28 -0.07 0.43 -8.15 -18.50 1.59] 4 B.U4 A.A15 [U-A] WC 20-XX cWW cW-W -165.0(anti) C3'-endo lambda=57.1; -157.5(anti) C3'-endo lambda=54.1 d(C1'-C1')=10.54 d(N1-N9)=8.87 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=-13.4 H-bonds[2]: "N3(imino)-N1[2.87]; O4(carbonyl)-N6(amino)[3.04]" bp_pars: [0.11 -0.09 0.38 -9.61 -15.85 0.50] 5 B.U5 A.A14 [U-A] WC 20-XX cWW cW-W -163.7(anti) C3'-endo lambda=54.6; -160.6(anti) C3'-endo lambda=57.7 d(C1'-C1')=10.72 d(N1-N9)=9.08 d(C6-C8)=10.09 tor(N1-C1'-C1'-N9)=-13.4 H-bonds[2]: "N3(imino)-N1[3.05]; O4(carbonyl)-N6(amino)[3.31]" bp_pars: [-0.33 0.14 0.28 -3.43 -16.43 3.05] 6 B.U6 A.A13 [U-A] WC 20-XX cWW cW-W -167.4(anti) C3'-endo lambda=52.3; -154.6(anti) C3'-endo lambda=54.2 d(C1'-C1')=10.45 d(N1-N9)=8.68 d(C6-C8)=9.61 tor(N1-C1'-C1'-N9)=-13.3 H-bonds[2]: "N3(imino)-N1[2.62]; O4(carbonyl)-N6(amino)[2.75]" bp_pars: [-0.22 -0.32 0.15 -5.01 -17.82 -0.34] 7 B.U7 A.A12 [U-A] WC 20-XX cWW cW-W -159.8(anti) C3'-endo lambda=56.4; -166.7(anti) C3'-endo lambda=59.2 d(C1'-C1')=10.49 d(N1-N9)=8.92 d(C6-C8)=9.96 tor(N1-C1'-C1'-N9)=-10.0 H-bonds[2]: "N3(imino)-N1[2.91]; O4(carbonyl)-N6(amino)[3.19]" bp_pars: [-0.15 0.01 0.44 -3.52 -9.29 3.81] 8 B.G8 A.C11 [G-C] WC 19-XIX cWW cW-W -179.8(anti) C3'-endo lambda=50.1; -162.1(anti) C3'-endo lambda=57.1 d(C1'-C1')=10.56 d(N1-N9)=8.81 d(C6-C8)=9.72 tor(N1-C1'-C1'-N9)=-5.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.78]; N1(imino)-N3[2.80]; N2(amino)-O2(carbonyl)[2.72]" bp_pars: [-0.53 -0.33 0.16 1.04 -8.74 -1.05] 9 B.A9 A.U10 [A-U] WC 20-XX cWW cW-W -162.8(anti) C3'-endo lambda=57.3; -161.5(anti) C3'-endo lambda=59.6 d(C1'-C1')=10.15 d(N1-N9)=8.61 d(C6-C8)=9.65 tor(N1-C1'-C1'-N9)=-6.8 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.87]; N1-N3(imino)[2.68]" bp_pars: [-0.35 -0.29 0.10 4.02 -9.83 3.87] 10 B.C10 A.G9 [C-G] WC 19-XIX cWW cW-W -162.5(anti) C3'-endo lambda=56.7; -167.1(anti) C3'-endo lambda=58.9 d(C1'-C1')=10.46 d(N1-N9)=8.89 d(C6-C8)=9.97 tor(N1-C1'-C1'-N9)=-8.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.53]; N3-N1(imino)[2.88]; N4(amino)-O6(carbonyl)[3.18]" bp_pars: [-0.10 -0.03 0.00 4.37 -13.44 6.99] 11 B.C11 A.G8 [C-G] WC 19-XIX cWW cW-W -158.5(anti) C3'-endo lambda=60.9; -165.9(anti) C3'-endo lambda=54.2 d(C1'-C1')=10.36 d(N1-N9)=8.78 d(C6-C8)=9.81 tor(N1-C1'-C1'-N9)=-4.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.66]; N3-N1(imino)[2.88]; N4(amino)-O6(carbonyl)[3.02]" bp_pars: [0.73 -0.25 -0.19 1.61 -10.22 4.32] 12 B.U12 A.A7 [U-A] WC 20-XX cWW cW-W -156.6(anti) C3'-endo lambda=57.5; -165.6(anti) C3'-endo lambda=59.1 d(C1'-C1')=10.34 d(N1-N9)=8.78 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-1.9 H-bonds[2]: "N3(imino)-N1[2.80]; O4(carbonyl)-N6(amino)[3.11]" bp_pars: [-0.28 -0.08 -0.20 3.55 -6.14 6.12] 13 B.U13 A.A6 [U-A] WC 20-XX cWW cW-W -177.4(anti) C3'-endo lambda=46.4; -165.3(anti) C3'-endo lambda=54.2 d(C1'-C1')=10.50 d(N1-N9)=8.62 d(C6-C8)=9.42 tor(N1-C1'-C1'-N9)=-10.1 H-bonds[2]: "N3(imino)-N1[2.47]; O4(carbonyl)-N6(amino)[2.34]" bp_pars: [-0.50 -0.52 -0.04 -3.51 -15.02 -6.08] 14 B.U14 A.A5 [U-A] WC 20-XX cWW cW-W -164.1(anti) C3'-endo lambda=56.6; -167.0(anti) C3'-endo lambda=53.7 d(C1'-C1')=10.51 d(N1-N9)=8.83 d(C6-C8)=9.76 tor(N1-C1'-C1'-N9)=-4.8 H-bonds[2]: "N3(imino)-N1[2.85]; O4(carbonyl)-N6(amino)[2.90]" bp_pars: [0.25 -0.17 0.48 -9.20 -3.74 -1.30] 15 B.A15 A.U4 [A-U] WC 20-XX cWW cW-W -157.5(anti) C3'-endo lambda=56.3; -161.9(anti) C3'-endo lambda=57.3 d(C1'-C1')=10.40 d(N1-N9)=8.79 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=-3.0 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.15]; N1-N3(imino)[2.84]" bp_pars: [-0.20 -0.08 0.02 -0.99 -4.88 5.75] 16 B.U16 A.A3 [U-A] WC 20-XX cWW cW-W -157.7(anti) C3'-endo lambda=62.5; -161.2(anti) C3'-endo lambda=59.2 d(C1'-C1')=10.15 d(N1-N9)=8.72 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-12.1 H-bonds[2]: "N3(imino)-N1[2.87]; O4(carbonyl)-N6(amino)[3.36]" bp_pars: [0.41 -0.03 0.13 -1.43 -17.10 10.26] 17 B.G17 A.C2 [G-C] WC 19-XIX cWW cW-W -157.0(anti) C3'-endo lambda=55.3; -161.2(anti) C3'-endo lambda=55.6 d(C1'-C1')=10.57 d(N1-N9)=8.89 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=-7.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.94]; N1(imino)-N3[2.83]; N2(amino)-O2(carbonyl)[2.65]" bp_pars: [-0.07 -0.16 -0.01 -1.26 -11.70 2.30] 18 B.C18 A.G1 [C-G] WC 19-XIX cWW cW-W -157.6(anti) C3'-endo lambda=55.0; -171.4(anti) C3'-endo lambda=55.1 d(C1'-C1')=10.80 d(N1-N9)=9.11 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=-6.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.83]; N3-N1(imino)[3.06]; N4(amino)-O6(carbonyl)[3.17]" bp_pars: [0.02 0.09 0.03 7.08 -8.71 2.45] **************************************************************************** List of 1 helix helix=1[1] bps=18 1 A.G1 B.C18 [G-C] WC 19-XIX cWW cW-W 2 A.C2 B.G17 [C-G] WC 19-XIX cWW cW-W 3 A.A3 B.U16 [A-U] WC 20-XX cWW cW-W 4 A.U4 B.A15 [U-A] WC 20-XX cWW cW-W 5 A.A5 B.U14 [A-U] WC 20-XX cWW cW-W 6 A.A6 B.U13 [A-U] WC 20-XX cWW cW-W 7 A.A7 B.U12 [A-U] WC 20-XX cWW cW-W 8 A.G8 B.C11 [G-C] WC 19-XIX cWW cW-W 9 A.G9 B.C10 [G-C] WC 19-XIX cWW cW-W 10 A.U10 B.A9 [U-A] WC 20-XX cWW cW-W 11 A.C11 B.G8 [C-G] WC 19-XIX cWW cW-W 12 A.A12 B.U7 [A-U] WC 20-XX cWW cW-W 13 A.A13 B.U6 [A-U] WC 20-XX cWW cW-W 14 A.A14 B.U5 [A-U] WC 20-XX cWW cW-W 15 A.A15 B.U4 [A-U] WC 20-XX cWW cW-W 16 A.G16 B.C3 [G-C] WC 19-XIX cWW cW-W 17 A.C17 B.G2 [C-G] WC 19-XIX cWW cW-W 18 A.C18 B.G1 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 stem stem=1[#1] bps=18 1 A.G1 B.C18 [G-C] WC 19-XIX cWW cW-W 2 A.C2 B.G17 [C-G] WC 19-XIX cWW cW-W 3 A.A3 B.U16 [A-U] WC 20-XX cWW cW-W 4 A.U4 B.A15 [U-A] WC 20-XX cWW cW-W 5 A.A5 B.U14 [A-U] WC 20-XX cWW cW-W 6 A.A6 B.U13 [A-U] WC 20-XX cWW cW-W 7 A.A7 B.U12 [A-U] WC 20-XX cWW cW-W 8 A.G8 B.C11 [G-C] WC 19-XIX cWW cW-W 9 A.G9 B.C10 [G-C] WC 19-XIX cWW cW-W 10 A.U10 B.A9 [U-A] WC 20-XX cWW cW-W 11 A.C11 B.G8 [C-G] WC 19-XIX cWW cW-W 12 A.A12 B.U7 [A-U] WC 20-XX cWW cW-W 13 A.A13 B.U6 [A-U] WC 20-XX cWW cW-W 14 A.A14 B.U5 [A-U] WC 20-XX cWW cW-W 15 A.A15 B.U4 [A-U] WC 20-XX cWW cW-W 16 A.G16 B.C3 [G-C] WC 19-XIX cWW cW-W 17 A.C17 B.G2 [C-G] WC 19-XIX cWW cW-W 18 A.C18 B.G1 [C-G] WC 19-XIX cWW cW-W **************************************************************************** >chain-A #1 RNA with 18 nts GCAUAAAGGUCAAAAGCC )))))))))))))))))) >chain-B #2 RNA with 18 nts GGCUUUUGACCUUUAUGC (((((((((((((((((( DONE!