# 1a3m_0.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 Jul 3 05:03:01 2023 File name: 1a3m_0.pdb no. of DNA/RNA chains: 2 [A=14, B=13] no. of nucleotides: 27 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 13 base pair(s) 1 1:A.G1 1:B.C27 [G-C] WC 19-XIX cWW cW-W -162.1(anti) C3'-endo lambda=49.2; -141.6(anti) O4'-endo lambda=49.6 d(C1'-C1')=11.41 d(N1-N9)=9.47 d(C6-C8)=10.18 tor(N1-C1'-C1'-N9)=10.9 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.11]; N1(imino)-N3[3.14]; N2(amino)-O2(carbonyl)[3.15]" bp_pars: [-0.19 0.19 0.25 12.44 15.36 -2.03] 2 1:A.G2 1:B.C26 [G-C] WC 19-XIX cWW cW-W -158.2(anti) C3'-endo lambda=49.4; -147.2(anti) C1'-exo lambda=50.5 d(C1'-C1')=11.30 d(N1-N9)=9.38 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-0.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.00]; N1(imino)-N3[3.15]; N2(amino)-O2(carbonyl)[3.09]" bp_pars: [-0.14 0.03 -0.78 7.71 -4.60 -2.81] 3 1:A.C3 1:B.G25 [C-G] WC 19-XIX cWW cW-W -155.0(anti) C3'-endo lambda=54.8; -166.0(anti) C3'-endo lambda=52.1 d(C1'-C1')=11.14 d(N1-N9)=9.36 d(C6-C8)=10.14 tor(N1-C1'-C1'-N9)=-5.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.02]; N3-N1(imino)[3.13]; N4(amino)-O6(carbonyl)[3.10]" bp_pars: [0.19 0.09 -0.90 10.89 -13.16 1.25] 4 1:A.G4 1:B.C24 [G-C] WC 19-XIX cWW cW-W -173.2(anti) C3'-endo lambda=52.5; -152.5(anti) C3'-endo lambda=54.7 d(C1'-C1')=11.17 d(N1-N9)=9.39 d(C6-C8)=10.15 tor(N1-C1'-C1'-N9)=-4.4 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.17]; N1(imino)-N3[3.09]; N2(amino)-O2(carbonyl)[3.11]" bp_pars: [-0.21 0.16 -0.15 -13.12 -21.93 -0.22] 5 1:A.U5 1:B.U23 [U-U] 00-n/a cWW cW-W -162.9(anti) C3'-endo lambda=54.8; -155.6(anti) C3'-endo lambda=42.7 d(C1'-C1')=10.07 d(N1-N9)=8.12 d(C6-C8)=9.05 tor(N1-C1'-C1'-N9)=-22.4 H-bonds[2]: "N3(imino)-O4(carbonyl)[3.33]; O4(carbonyl)*O4(carbonyl)[2.91]" bp_pars: [0.79 -1.12 0.20 -15.47 -25.23 -13.16] 6 1:A.C6 1:B.G22 [C-G] WC 19-XIX cWW cW-W -160.0(anti) C3'-endo lambda=52.5; -174.2(anti) C2'-exo lambda=47.1 d(C1'-C1')=11.29 d(N1-N9)=9.37 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-23.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.19]; N3-N1(imino)[3.08]; N4(amino)-O6(carbonyl)[3.17]" bp_pars: [0.04 0.14 0.47 -17.95 -25.10 -3.47] 7 1:A.A7 1:B.A21 [A-A] 00-n/a cWW cW-W -162.8(anti) C3'-endo lambda=54.1; -168.1(anti) C2'-exo lambda=38.1 d(C1'-C1')=13.33 d(N1-N9)=11.28 d(C6-C8)=11.42 tor(N1-C1'-C1'-N9)=-15.7 H-bonds[1]: "N1-N6(amino)[3.32]" bp_pars: [1.49 1.81 1.00 -22.78 -3.31 -16.58] 8 1:A.C8 1:B.G19 [C-G] WC 19-XIX cWW cW-W -155.3(anti) C3'-endo lambda=49.4; -147.1(anti) C4'-exo lambda=48.4 d(C1'-C1')=11.46 d(N1-N9)=9.49 d(C6-C8)=10.17 tor(N1-C1'-C1'-N9)=-20.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.19]; N3-N1(imino)[3.11]; N4(amino)-O6(carbonyl)[3.17]" bp_pars: [0.11 0.13 0.37 3.27 -25.94 -4.64] 9 1:A.C8 1:B.A20 [C-A] 00-n/a tW. cW-. -155.3(anti) C3'-endo lambda=73.7; -153.7(anti) C3'-endo lambda=16.3 d(C1'-C1')=12.43 d(N1-N9)=10.63 d(C6-C8)=10.94 tor(N1-C1'-C1'-N9)=-31.7 H-bonds[1]: "O2(carbonyl)-N6(amino)[3.87]" bp_pars: [6.17 -0.89 1.62 -10.44 10.57 -16.16] 10 1:A.A9 1:B.U18 [A-U] WC 20-XX cWW cW-W -163.2(anti) C3'-endo lambda=50.9; -160.6(anti) C3'-endo lambda=49.6 d(C1'-C1')=11.29 d(N1-N9)=9.38 d(C6-C8)=10.12 tor(N1-C1'-C1'-N9)=-24.2 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.16]; N1-N3(imino)[3.06]" bp_pars: [0.25 0.14 0.36 -9.84 -29.60 -7.33] 11 1:A.C10 1:B.G17 [C-G] WC 19-XIX cWW cW-W -159.7(anti) C3'-endo lambda=52.5; -157.2(anti) C3'-endo lambda=48.6 d(C1'-C1')=11.33 d(N1-N9)=9.44 d(C6-C8)=10.18 tor(N1-C1'-C1'-N9)=-23.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.14]; N3-N1(imino)[3.11]; N4(amino)-O6(carbonyl)[3.18]" bp_pars: [0.05 0.16 0.54 -10.44 -20.00 -2.74] 12 1:A.C11 1:B.G16 [C-G] WC 19-XIX cWW cW-W -160.6(anti) C3'-endo lambda=54.0; -162.9(anti) C3'-endo lambda=48.3 d(C1'-C1')=11.32 d(N1-N9)=9.45 d(C6-C8)=10.18 tor(N1-C1'-C1'-N9)=-12.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.10]; N3-N1(imino)[3.14]; N4(amino)-O6(carbonyl)[3.18]" bp_pars: [0.30 0.13 0.56 -4.72 -11.79 -2.62] 13 1:A.U12 1:B.G15 [U+G] 00-n/a tSW tm+W -154.9(anti) C3'-endo lambda=101.2; 32.8(...) C3'-endo lambda=27.9 d(C1'-C1')=9.59 d(N1-N9)=8.82 d(C6-C8)=10.40 tor(N1-C1'-C1'-N9)=-163.1 H-bonds[3]: "O2'(hydroxyl)-O6(carbonyl)[2.80]; O2(carbonyl)-N1(imino)[2.96]; O2(carbonyl)-N2(amino)[3.11]" bp_pars: [0.53 -5.89 0.94 -9.50 -14.21 -108.79] **************************************************************************** List of 1 helix helix=1[2] bps=12 1 1:A.G1 1:B.C27 [G-C] WC 19-XIX cWW cW-W 2 1:A.G2 1:B.C26 [G-C] WC 19-XIX cWW cW-W 3 1:A.C3 1:B.G25 [C-G] WC 19-XIX cWW cW-W 4 1:A.G4 1:B.C24 [G-C] WC 19-XIX cWW cW-W 5 1:A.U5 1:B.U23 [U-U] 00-n/a cWW cW-W 6 1:A.C6 1:B.G22 [C-G] WC 19-XIX cWW cW-W 7 1:A.A7 1:B.A21 [A-A] 00-n/a cWW cW-W 8 1:A.C8 1:B.G19 [C-G] WC 19-XIX cWW cW-W 9 1:A.A9 1:B.U18 [A-U] WC 20-XX cWW cW-W 10 1:A.C10 1:B.G17 [C-G] WC 19-XIX cWW cW-W 11 1:A.C11 1:B.G16 [C-G] WC 19-XIX cWW cW-W 12 1:A.U12 1:B.G15 [U+G] 00-n/a tSW tm+W **************************************************************************** List of 2 stems stem=1[#1] bps=4 1 1:A.G1 1:B.C27 [G-C] WC 19-XIX cWW cW-W 2 1:A.G2 1:B.C26 [G-C] WC 19-XIX cWW cW-W 3 1:A.C3 1:B.G25 [C-G] WC 19-XIX cWW cW-W 4 1:A.G4 1:B.C24 [G-C] WC 19-XIX cWW cW-W stem=2[#1] bps=4 1 1:A.C8 1:B.G19 [C-G] WC 19-XIX cWW cW-W 2 1:A.A9 1:B.U18 [A-U] WC 20-XX cWW cW-W 3 1:A.C10 1:B.G17 [C-G] WC 19-XIX cWW cW-W 4 1:A.C11 1:B.G16 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 lone WC/wobble pair(s) -1 1:A.C6 1:B.G22 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 2 stems: [#1, #2] **************************************************************************** List of 2 internal loop(s) 1 symmetric internal loop: 6 nts; [1x1]; linked by [#1, #-1] 1:A.G4+1:A.U5+1:A.C6+1:B.G22+1:B.U23+1:B.C24 [GUCGUC] 2 asymmetric internal loop: 7 nts; [1x2]; linked by [#-1, #2] 1:A.C6+1:A.A7+1:A.C8+1:B.G19+1:B.A20+1:B.A21+1:B.G22 [CACGAAG] **************************************************************************** >chain-A #1 RNA with 14 nts GGCGUCACACCUUC ((((.(.((((... >chain-B #2 RNA with 13 nts GGGUGAAGUCGCC .))))..).)))) DONE!