# PAIR1-52a89310_sim_minE_TOTAL-000001_AA.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 Apr 23 01:56:28 2024 File name: PAIR1-52a89310_sim_minE_TOTAL-000001_AA.pdb no. of DNA/RNA chains: 1 [A=21] no. of nucleotides: 21 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 9 base pair(s) 1 A.G2 A.C21 [G-C] 00-n/a cWW cW-W -160.7(anti) C3'-exo lambda=59.4; -161.0(anti) C3'-endo lambda=47.0 d(C1'-C1')=11.95 d(N1-N9)=10.21 d(C6-C8)=10.87 tor(N1-C1'-C1'-N9)=27.5 H-bonds[1]: "O6(carbonyl)-N4(amino)[3.73]" bp_pars: [0.58 0.97 -1.50 -23.29 -8.99 -9.98] 2 A.G3 A.U20 [G-U] 00-n/a ... c... -176.5(anti) C4'-exo lambda=33.1; -162.6(anti) C3'-endo lambda=36.8 d(C1'-C1')=12.82 d(N1-N9)=10.35 d(C6-C8)=10.48 tor(N1-C1'-C1'-N9)=-7.5 H-bonds[1]: "O6(carbonyl)*O4(carbonyl)[3.09]" bp_pars: [-0.29 0.80 -1.74 -5.43 -17.05 -32.90] 3 A.G3 A.C21 [G-C] WC 19-XIX cWW cW-W -176.5(anti) C4'-exo lambda=56.5; -161.0(anti) C3'-endo lambda=56.5 d(C1'-C1')=10.05 d(N1-N9)=8.35 d(C6-C8)=9.43 tor(N1-C1'-C1'-N9)=-24.4 H-bonds[2]: "O6(carbonyl)-N4(amino)[2.94]; N1(imino)-N3[2.51]" bp_pars: [-0.03 -0.62 1.02 -6.97 -14.63 5.35] 4 A.G4 A.U20 [G-U] Wobble 28-XXVIII cWW cW-W -170.1(anti) C3'-endo lambda=47.1; -162.6(anti) C3'-endo lambda=58.7 d(C1'-C1')=10.20 d(N1-N9)=8.49 d(C6-C8)=9.39 tor(N1-C1'-C1'-N9)=-9.3 H-bonds[3]: "O6(carbonyl)-N3(imino)[2.72]; N1(imino)-O2(carbonyl)[2.66]; N2(amino)-O2(carbonyl)[2.73]" bp_pars: [-1.24 -0.70 0.20 -1.73 -11.68 -2.04] 5 A.G5 A.U19 [G-U] Wobble 28-XXVIII cWW cW-W -158.4(anti) C3'-endo lambda=52.0; -163.5(anti) C3'-endo lambda=65.2 d(C1'-C1')=10.30 d(N1-N9)=8.76 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=9.2 H-bonds[3]: "O6(carbonyl)-N3(imino)[3.17]; N1(imino)-O2(carbonyl)[2.99]; N2(amino)-O2(carbonyl)[2.85]" bp_pars: [-1.20 -0.31 -0.42 2.85 -7.43 3.47] 6 A.G6 A.C18 [G-C] WC 19-XIX cWW cW-W -168.0(anti) C3'-endo lambda=57.9; -163.2(anti) C3'-endo lambda=54.4 d(C1'-C1')=10.97 d(N1-N9)=9.34 d(C6-C8)=10.39 tor(N1-C1'-C1'-N9)=-5.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.56]; N1(imino)-N3[3.33]; N2(amino)-O2(carbonyl)[2.97]" bp_pars: [-0.01 0.40 0.07 -7.39 -1.81 5.75] 7 A.U7 A.A17 [U-A] WC 20-XX cWW cW-W -165.5(anti) C3'-endo lambda=50.5; -156.1(anti) C3'-endo lambda=57.8 d(C1'-C1')=10.65 d(N1-N9)=9.01 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-25.7 H-bonds[2]: "N3(imino)-N1[2.94]; O4(carbonyl)-N6(amino)[3.04]" bp_pars: [-0.08 -0.02 0.23 -5.71 -19.10 -1.61] 8 A.C8 A.G16 [C-G] WC 19-XIX cWW cW-W -168.6(anti) C3'-endo lambda=48.8; -166.0(anti) C3'-endo lambda=54.2 d(C1'-C1')=11.20 d(N1-N9)=9.30 d(C6-C8)=10.21 tor(N1-C1'-C1'-N9)=-19.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.11]; N3-N1(imino)[3.19]; N4(amino)-O6(carbonyl)[3.16]" bp_pars: [-0.01 0.18 0.18 0.93 2.26 -0.89] 9 A.A9 A.G15 [A-G] 08-VIII cWW cW-W -147.8(anti) C3'-endo lambda=61.0; -172.0(anti) C4'-exo lambda=41.4 d(C1'-C1')=11.33 d(N1-N9)=9.74 d(C6-C8)=10.34 tor(N1-C1'-C1'-N9)=51.0 H-bonds[2]: "N6(amino)-O6(carbonyl)[3.21]; N1-N1(imino)[2.93]" bp_pars: [2.43 0.30 -0.45 16.13 7.31 -8.32] **************************************************************************** List of 1 helix helix=1[1] bps=7 1 A.G3 A.C21 [G-C] WC 19-XIX cWW cW-W 2 A.G4 A.U20 [G-U] Wobble 28-XXVIII cWW cW-W 3 A.G5 A.U19 [G-U] Wobble 28-XXVIII cWW cW-W 4 A.G6 A.C18 [G-C] WC 19-XIX cWW cW-W 5 A.U7 A.A17 [U-A] WC 20-XX cWW cW-W 6 A.C8 A.G16 [C-G] WC 19-XIX cWW cW-W 7 A.A9 A.G15 [A-G] 08-VIII cWW cW-W **************************************************************************** List of 1 stem stem=1[#1] bps=6 1 A.G3 A.C21 [G-C] WC 19-XIX cWW cW-W 2 A.G4 A.U20 [G-U] Wobble 28-XXVIII cWW cW-W 3 A.G5 A.U19 [G-U] Wobble 28-XXVIII cWW cW-W 4 A.G6 A.C18 [G-C] WC 19-XIX cWW cW-W 5 A.U7 A.A17 [U-A] WC 20-XX cWW cW-W 6 A.C8 A.G16 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 hairpin loop(s) 1 nts=7 AGGUGGG closed by pair {A.C8+A.G16 [CG], #1} A.C8+A.A9+A.G10+A.G11+A.U12+A.G13+A.G14+A.G15+A.G16 [CAGGUGGGG] **************************************************************************** >chain-A #1 RNA with 21 nts UGGGGGUCAGGUGGGGACUUC ..((((((.......)))))) DONE!