# 1F27.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: Fri Jul 31 13:37:18 2026 File name: 1F27.pdb no. of DNA/RNA chains: 2 [A=19, B=11] no. of nucleotides: 30 no. of waters: 184 no. of metals: 6 [Mg=6] **************************************************************************** List of 13 base pair(s) 1 A.A3 A.U20 [A-U] WC 20-XX cWW cW-W -158.0(anti) C3'-endo lambda=54.4; -155.4(anti) C3'-endo lambda=53.8 d(C1'-C1')=10.59 d(N1-N9)=8.87 d(C6-C8)=9.78 tor(N1-C1'-C1'-N9)=-10.1 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.80]; N1-N3(imino)[2.83]" bp_pars: [0.10 -0.15 0.06 6.29 -11.25 -2.21] 2 A.C4 A.G19 [C-G] WC 19-XIX cWW cW-W -159.1(anti) C3'-endo lambda=57.2; -166.5(anti) C3'-endo lambda=56.5 d(C1'-C1')=10.43 d(N1-N9)=8.84 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-16.0 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.70]; N3-N1(imino)[2.83]; N4(amino)-O6(carbonyl)[3.00]" bp_pars: [0.30 -0.16 -0.03 10.90 -18.80 3.05] 3 A.C5 A.G18 [C-G] WC 19-XIX cWW cW-W -157.8(anti) C3'-endo lambda=54.3; -167.6(anti) C3'-endo lambda=55.2 d(C1'-C1')=10.62 d(N1-N9)=8.94 d(C6-C8)=9.89 tor(N1-C1'-C1'-N9)=-10.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.80]; N3-N1(imino)[2.91]; N4(amino)-O6(carbonyl)[2.89]" bp_pars: [0.14 -0.13 -0.15 5.29 -12.61 -0.35] 4 A.G6 A.C17 [G-C] WC 19-XIX cWW cW-W -159.6(anti) C3'-endo lambda=55.3; -160.9(anti) C3'-endo lambda=53.9 d(C1'-C1')=10.62 d(N1-N9)=8.93 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-3.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.82]; N1(imino)-N3[2.87]; N2(amino)-O2(carbonyl)[2.80]" bp_pars: [0.04 -0.16 0.07 3.09 -5.58 -1.12] 5 A.U7 A.A16 [U-A] WC 20-XX cWW cW-W -118.2(anti) C1'-exo lambda=63.7; -154.5(anti) C3'-endo lambda=58.6 d(C1'-C1')=9.98 d(N1-N9)=8.58 d(C6-C8)=9.73 tor(N1-C1'-C1'-N9)=12.1 H-bonds[2]: "N3(imino)-N1[2.77]; O4(carbonyl)-N6(amino)[3.19]" bp_pars: [0.20 -0.06 -0.37 18.69 1.32 9.52] 6 A.G10 B.C32 [G-C] WC 19-XIX cWW cW-W -169.3(anti) C3'-endo lambda=55.5; -156.6(anti) C3'-endo lambda=58.1 d(C1'-C1')=10.45 d(N1-N9)=8.84 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=-6.4 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.94]; N1(imino)-N3[2.83]; N2(amino)-O2(carbonyl)[2.64]" bp_pars: [-0.27 -0.18 0.07 -4.82 -9.78 2.77] 7 A.A11 B.U31 [A-U] WC 20-XX cWW cW-W -163.5(anti) C3'-endo lambda=51.6; -161.8(anti) C3'-endo lambda=56.8 d(C1'-C1')=10.36 d(N1-N9)=8.66 d(C6-C8)=9.59 tor(N1-C1'-C1'-N9)=-14.7 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.75]; N1-N3(imino)[2.66]" bp_pars: [-0.17 -0.35 0.21 -0.73 -10.90 -0.64] 8 A.G12 B.C30 [G-C] WC 19-XIX cWW cW-W -162.3(anti) C3'-endo lambda=56.5; -165.3(anti) C3'-endo lambda=54.9 d(C1'-C1')=10.52 d(N1-N9)=8.88 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-12.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.90]; N1(imino)-N3[2.84]; N2(amino)-O2(carbonyl)[2.78]" bp_pars: [-0.10 -0.17 0.02 -2.29 -12.85 0.94] 9 A.G13 B.C29 [G-C] WC 19-XIX cWW cW-W -175.8(anti) C3'-endo lambda=54.3; -162.4(anti) C3'-endo lambda=55.4 d(C1'-C1')=10.64 d(N1-N9)=8.96 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-12.2 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.93]; N1(imino)-N3[2.90]; N2(amino)-O2(carbonyl)[2.76]" bp_pars: [-0.21 -0.11 -0.01 -9.76 -16.80 0.56] 10 A.A14 B.U28 [A-U] WC 20-XX cWW cW-W -158.5(anti) C3'-endo lambda=54.5; -162.3(anti) C3'-endo lambda=55.4 d(C1'-C1')=10.54 d(N1-N9)=8.86 d(C6-C8)=9.80 tor(N1-C1'-C1'-N9)=-12.8 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.90]; N1-N3(imino)[2.82]" bp_pars: [-0.00 -0.11 0.00 -10.55 -10.69 -0.31] 11 A.C15 B.G27 [C-G] WC 19-XIX cWW cW-W -161.3(anti) C3'-endo lambda=57.7; -81.9(anti) C1'-exo lambda=56.5 d(C1'-C1')=10.46 d(N1-N9)=8.87 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-2.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.68]; N3-N1(imino)[2.87]; N4(amino)-O6(carbonyl)[2.92]" bp_pars: [0.26 -0.12 0.16 -12.70 -4.60 2.00] 12 A.C17 B.A26 [C-A] 00-n/a cSW cm-W -160.9(anti) C3'-endo lambda=130.8; -164.6(anti) C3'-endo lambda=39.8 d(C1'-C1')=8.86 d(N1-N9)=8.71 d(C6-C8)=10.17 tor(N1-C1'-C1'-N9)=35.5 H-bonds[2]: "O2'(hydroxyl)-N1[2.69]; O2(carbonyl)-N6(amino)[3.07]" bp_pars: [6.59 -0.72 -1.82 -9.54 19.16 60.72] 13 A.G19 B.A23 [G-A] 00-n/a c.S c.-m -166.5(anti) C3'-endo lambda=109.0; -150.6(anti) C3'-endo lambda=147.0 d(C1'-C1')=5.63 d(N1-N9)=7.37 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-35.4 H-bonds[3]: "O2'(hydroxyl)-O2'(hydroxyl)[2.67]; N2(amino)-N3[2.99]; N3-O2'(hydroxyl)[2.74]" bp_pars: [-2.07 7.03 -1.71 -28.29 3.68 149.69] **************************************************************************** List of 2 multiplet(s) 1 nts=3 A.C4+A.G19+B.A23 [CGA] 2 nts=3 A.G6+A.C17+B.A26 [GCA] **************************************************************************** List of 1 helix helix=1[2] bps=11 1 A.A3 A.U20 [A-U] WC 20-XX cWW cW-W 2 A.C4 A.G19 [C-G] WC 19-XIX cWW cW-W 3 A.C5 A.G18 [C-G] WC 19-XIX cWW cW-W 4 A.G6 A.C17 [G-C] WC 19-XIX cWW cW-W 5 A.U7 A.A16 [U-A] WC 20-XX cWW cW-W 6 B.G27 A.C15 [G-C] WC 19-XIX cWW cW-W 7 B.U28 A.A14 [U-A] WC 20-XX cWW cW-W 8 B.C29 A.G13 [C-G] WC 19-XIX cWW cW-W 9 B.C30 A.G12 [C-G] WC 19-XIX cWW cW-W 10 B.U31 A.A11 [U-A] WC 20-XX cWW cW-W 11 B.C32 A.G10 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems stem=1[#1] bps=5 1 A.A3 A.U20 [A-U] WC 20-XX cWW cW-W 2 A.C4 A.G19 [C-G] WC 19-XIX cWW cW-W 3 A.C5 A.G18 [C-G] WC 19-XIX cWW cW-W 4 A.G6 A.C17 [G-C] WC 19-XIX cWW cW-W 5 A.U7 A.A16 [U-A] WC 20-XX cWW cW-W stem=2[#1] bps=6 1 A.G10 B.C32 [G-C] WC 19-XIX cWW cW-W 2 A.A11 B.U31 [A-U] WC 20-XX cWW cW-W 3 A.G12 B.C30 [G-C] WC 19-XIX cWW cW-W 4 A.G13 B.C29 [G-C] WC 19-XIX cWW cW-W 5 A.A14 B.U28 [A-U] WC 20-XX cWW cW-W 6 A.C15 B.G27 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 2 stems: [#1, #2] **************************************************************************** List of 1 hairpin loop(s) 1 nts=8 CAGAGGAC closed by pair {A.U7+A.A16 [UA], #1} A.U7+A.C8+A.A9+A.G10+A.A11+A.G12+A.G13+A.A14+A.C15+A.A16 [UCAGAGGACA] **************************************************************************** List of 1 A-minor motif(s) 1 type=I A/C-G B.A23 vs A.C4+A.G19 [WC] +A.C4 H-bonds[1]: "N1-O2'(hydroxyl)[2.71]" -A.G19 H-bonds[3]: "O2'(hydroxyl)-O2'(hydroxyl)[2.67]; O2'(hydroxyl)-N3[2.74]; N3-N2(amino)[2.99]" **************************************************************************** >chain-A #1 RNA with 19 nts ACCGUCAGAGGACACGGUU (((((..(((((())))). >chain-B #2 RNA with 11 nts AAAAAGUCCUC .....)))))) DONE!