# H_UMH5.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 May 17 12:31:49 2023 File name: H_UMH5.pdb no. of DNA/RNA chains: 1 [A=35] no. of nucleotides: 35 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 8 base pair(s) 1 A.U12 A.A28 [U-A] 00-n/a tWH tW-M 47.2(syn) C3'-endo lambda=18.9; 61.0(syn) C3'-endo lambda=55.6 d(C1'-C1')=8.57 d(N1-N9)=6.56 d(C6-C8)=6.06 tor(N1-C1'-C1'-N9)=-159.2 H-bonds[2]: "N3(imino)-N7[3.66]; O4(carbonyl)-O2'(hydroxyl)[3.82]" bp_pars: [4.84 -1.17 -0.87 23.77 -50.23 -142.87] 2 A.G13 A.A28 [G-A] 00-n/a tWH tW-M -3.2(...) C2'-exo lambda=37.5; 61.0(syn) C3'-endo lambda=65.3 d(C1'-C1')=10.08 d(N1-N9)=8.53 d(C6-C8)=7.72 tor(N1-C1'-C1'-N9)=-118.9 H-bonds[1]: "N2(amino)-N7[3.49]" bp_pars: [7.34 -0.71 -1.10 40.74 -6.18 -142.67] 3 A.A14 A.G27 [A-G] Imino 08-VIII cWW cW-W -171.8(anti) C3'-endo lambda=48.7; -176.0(anti) C3'-endo lambda=53.2 d(C1'-C1')=12.84 d(N1-N9)=11.00 d(C6-C8)=11.62 tor(N1-C1'-C1'-N9)=2.6 H-bonds[3]: "N1-N1(imino)[3.09]; N1-N2(amino)[3.22]; N6(amino)-O6(carbonyl)[3.45]" bp_pars: [-0.57 1.78 0.01 1.87 4.73 -7.94] 4 A.G15 A.C26 [G-C] WC 19-XIX cWW cW-W -164.2(anti) C3'-endo lambda=53.4; -154.3(anti) C3'-endo lambda=56.3 d(C1'-C1')=10.52 d(N1-N9)=8.83 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-2.2 H-bonds[3]: "N1(imino)-N3[2.83]; N2(amino)-O2(carbonyl)[2.67]; O6(carbonyl)-N4(amino)[2.89]" bp_pars: [-0.38 -0.20 -0.23 -10.42 -6.05 1.56] 5 A.G16 A.C25 [G-C] WC 19-XIX cWW cW-W -163.2(anti) C3'-endo lambda=50.2; -162.1(anti) C3'-endo lambda=58.0 d(C1'-C1')=10.52 d(N1-N9)=8.80 d(C6-C8)=9.74 tor(N1-C1'-C1'-N9)=-1.7 H-bonds[3]: "N1(imino)-N3[2.89]; N2(amino)-O2(carbonyl)[2.76]; O6(carbonyl)-N4(amino)[2.89]" bp_pars: [-0.80 -0.32 -0.08 -0.35 -2.90 0.30] 6 A.C17 A.G24 [C-G] WC 19-XIX cWW cW-W -159.8(anti) C3'-endo lambda=58.9; -164.6(anti) C3'-endo lambda=49.9 d(C1'-C1')=10.45 d(N1-N9)=8.75 d(C6-C8)=9.69 tor(N1-C1'-C1'-N9)=0.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.73]; N3-N1(imino)[2.87]; N4(amino)-O6(carbonyl)[2.89]" bp_pars: [0.90 -0.37 -0.24 5.30 -1.84 0.74] 7 A.C18 A.G23 [C-G] WC 19-XIX cWW cW-W -150.1(anti) C3'-endo lambda=56.6; -178.7(anti) C2'-exo lambda=50.5 d(C1'-C1')=10.52 d(N1-N9)=8.79 d(C6-C8)=9.68 tor(N1-C1'-C1'-N9)=5.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.74]; N3-N1(imino)[2.83]; N4(amino)-O6(carbonyl)[2.81]" bp_pars: [0.58 -0.32 -0.47 11.56 2.67 -1.20] 8 A.G19 A.A22 [G-A] Sheared 11-XI tSH cm-M -154.5(anti) C3'-endo lambda=101.2; -137.8(anti) C2'-exo lambda=12.2 d(C1'-C1')=8.84 d(N1-N9)=7.80 d(C6-C8)=8.21 tor(N1-C1'-C1'-N9)=-56.5 H-bonds[3]: "N2(amino)-N7[2.86]; N2(amino)-OP2[2.74]; N3-N6(amino)[3.35]" bp_pars: [6.55 -4.91 0.96 17.89 4.00 -2.09] **************************************************************************** List of 1 helix helix=1[1] bps=7 1 A.U12 A.A28 [U-A] 00-n/a tWH tW-M 2 A.A14 A.G27 [A-G] Imino 08-VIII cWW cW-W 3 A.G15 A.C26 [G-C] WC 19-XIX cWW cW-W 4 A.G16 A.C25 [G-C] WC 19-XIX cWW cW-W 5 A.C17 A.G24 [C-G] WC 19-XIX cWW cW-W 6 A.C18 A.G23 [C-G] WC 19-XIX cWW cW-W 7 A.G19 A.A22 [G-A] Sheared 11-XI tSH cm-M **************************************************************************** List of 1 stem stem=1[#1] bps=4 1 A.G15 A.C26 [G-C] WC 19-XIX cWW cW-W 2 A.G16 A.C25 [G-C] WC 19-XIX cWW cW-W 3 A.C17 A.G24 [C-G] WC 19-XIX cWW cW-W 4 A.C18 A.G23 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 hairpin loop(s) 1 nts=4 GAAA closed by pair {A.C18+A.G23 [CG], #1} A.C18+A.G19+A.A20+A.A21+A.A22+A.G23 [CGAAAG] **************************************************************************** >chain-A #1 RNA* with 35 nts CAGCAGACGAUGAGGCCGAAAGGCCGAAACACACA .............((((....)))).......... DONE!