# 5k7c_clean_onechain_renumber_as_puzzle_srr.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 Jun 13 01:04:06 2023 File name: 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb no. of DNA/RNA chains: 1 [A=58] no. of nucleotides: 58 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 35 base pair(s) 1 A.C1 A.G16 [C-G] WC 19-XIX cWW cW-W -172.1(anti) C3'-endo lambda=52.0; -121.2(anti) C2'-endo lambda=60.5 d(C1'-C1')=10.36 d(N1-N9)=8.73 d(C6-C8)=9.71 tor(N1-C1'-C1'-N9)=-3.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.58]; N3-N1(imino)[2.77]; N4(amino)-O6(carbonyl)[2.85]" bp_pars: [0.02 -0.23 0.03 -12.63 -5.19 2.93] 2 A.G2 A.C15 [G-C] WC 19-XIX cWW cW-W -162.7(anti) C3'-endo lambda=54.3; -162.6(anti) C3'-endo lambda=57.8 d(C1'-C1')=10.55 d(N1-N9)=8.91 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-11.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.97]; N1(imino)-N3[2.90]; N2(amino)-O2(carbonyl)[2.80]" bp_pars: [-0.31 -0.12 -0.33 -7.81 -13.04 2.45] 3 A.G2 A.U18 [G+U] 00-n/a tS. cm+. -162.7(anti) C3'-endo lambda=101.0; -39.0(...) C2'-endo lambda=14.8 d(C1'-C1')=10.32 d(N1-N9)=9.25 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-29.6 H-bonds[1]: "N2(amino)-O4(carbonyl)[2.52]" bp_pars: [4.56 -0.81 2.36 -41.58 -12.00 -61.84] 4 A.U3 A.A14 [U-A] WC 20-XX cWW cW-W -164.4(anti) C3'-endo lambda=52.8; -158.7(anti) C3'-endo lambda=55.8 d(C1'-C1')=10.58 d(N1-N9)=8.86 d(C6-C8)=9.73 tor(N1-C1'-C1'-N9)=-11.0 H-bonds[2]: "N3(imino)-N1[2.78]; O4(carbonyl)-N6(amino)[2.73]" bp_pars: [-0.26 -0.20 -0.16 -1.89 -10.21 -2.45] 5 A.U3 A.A19 [U+A] 00-n/a cSH cm+M -164.4(anti) C3'-endo lambda=122.7; -44.8(...) C2'-endo lambda=27.0 d(C1'-C1')=7.91 d(N1-N9)=7.48 d(C6-C8)=7.60 tor(N1-C1'-C1'-N9)=-55.3 H-bonds[2]: "O2'(hydroxyl)-N7[2.97]; O2(carbonyl)-N6(amino)[2.45]" bp_pars: [5.58 -0.77 2.24 -42.59 -13.16 -22.66] 6 A.G4 A.C13 [G-C] WC 19-XIX cWW cW-W -162.5(anti) C3'-endo lambda=55.5; -175.6(anti) C3'-endo lambda=57.4 d(C1'-C1')=10.43 d(N1-N9)=8.81 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-7.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.77]; N1(imino)-N3[2.78]; N2(amino)-O2(carbonyl)[2.71]" bp_pars: [-0.21 -0.28 0.29 1.04 -7.52 -0.13] 7 A.G4 A.A21 [G+A] 00-n/a tSW cm+W -162.5(anti) C3'-endo lambda=119.7; -140.0(anti) C3'-endo lambda=25.8 d(C1'-C1')=9.94 d(N1-N9)=9.42 d(C6-C8)=10.44 tor(N1-C1'-C1'-N9)=75.2 H-bonds[1]: "N2(amino)-N1[3.30]" bp_pars: [4.26 -3.48 0.31 -37.34 31.19 -66.92] 8 A.G5 A.C12 [G-C] WC 19-XIX cWW cW-W -155.5(anti) C3'-endo lambda=52.2; -156.5(anti) C3'-endo lambda=50.9 d(C1'-C1')=10.76 d(N1-N9)=8.93 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-4.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.70]; N1(imino)-N3[2.81]; N2(amino)-O2(carbonyl)[2.82]" bp_pars: [-0.04 -0.23 -0.04 7.52 -2.18 -3.61] 9 A.G5 A.G24 [G+G] 04-IV tSS tm+m -155.5(anti) C3'-endo lambda=81.7; -145.0(anti) C3'-endo lambda=74.5 d(C1'-C1')=8.28 d(N1-N9)=8.20 d(C6-C8)=10.64 tor(N1-C1'-C1'-N9)=177.1 H-bonds[3]: "O2'(hydroxyl)-N2(amino)[3.07]; N2(amino)-N3[3.21]; N3-N2(amino)[2.95]" bp_pars: [-2.99 -8.20 -0.70 7.44 19.56 -169.96] 10 A.U6 A.A39 [U-A] WC 20-XX cWW cW-W -173.5(anti) C3'-endo lambda=49.6; -172.4(anti) C3'-endo lambda=56.7 d(C1'-C1')=10.74 d(N1-N9)=8.98 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=-14.4 H-bonds[2]: "N3(imino)-N1[2.93]; O4(carbonyl)-N6(amino)[3.14]" bp_pars: [-0.25 -0.05 0.65 9.67 -14.79 -1.41] 11 A.U7 A.A38 [U-A] WC 20-XX cWW cW-W -161.8(anti) C3'-endo lambda=54.0; -158.0(anti) C3'-endo lambda=57.5 d(C1'-C1')=10.63 d(N1-N9)=8.97 d(C6-C8)=9.97 tor(N1-C1'-C1'-N9)=-6.3 H-bonds[2]: "N3(imino)-N1[2.93]; O4(carbonyl)-N6(amino)[3.06]" bp_pars: [-0.13 -0.01 0.43 0.23 -3.93 0.80] 12 A.A8 A.U37 [A-U] WC 20-XX cWW cW-W -159.3(anti) C3'-endo lambda=55.0; -161.3(anti) C3'-endo lambda=56.3 d(C1'-C1')=10.46 d(N1-N9)=8.80 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-0.5 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.88]; N1-N3(imino)[2.70]" bp_pars: [0.18 -0.19 0.27 3.02 0.56 2.10] 13 A.G9 A.C36 [G-C] WC 19-XIX cWW cW-W -161.9(anti) C3'-endo lambda=54.0; -174.1(anti) C3'-endo lambda=57.1 d(C1'-C1')=10.50 d(N1-N9)=8.83 d(C6-C8)=9.80 tor(N1-C1'-C1'-N9)=-9.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.90]; N1(imino)-N3[2.82]; N2(amino)-O2(carbonyl)[2.66]" bp_pars: [-0.22 -0.23 0.37 3.62 -6.92 1.54] 14 A.G10 A.C35 [G-C] WC 19-XIX cWW cW-W -175.0(anti) C3'-endo lambda=51.8; -168.5(anti) C3'-endo lambda=51.7 d(C1'-C1')=10.68 d(N1-N9)=8.86 d(C6-C8)=9.72 tor(N1-C1'-C1'-N9)=-4.4 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.70]; N1(imino)-N3[2.78]; N2(amino)-O2(carbonyl)[2.69]" bp_pars: [-0.17 -0.30 -0.02 -4.65 -10.29 -2.75] 15 A.G11 A.C34 [G-C] WC 19-XIX cWW cW-W -164.4(anti) C3'-endo lambda=58.6; -149.6(anti) C3'-endo lambda=54.8 d(C1'-C1')=10.46 d(N1-N9)=8.85 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-11.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.96]; N1(imino)-N3[2.90]; N2(amino)-O2(carbonyl)[2.82]" bp_pars: [-0.30 -0.12 -0.54 -17.78 -18.29 2.50] 16 A.A14 A.A20 [A-A] 00-n/a cSW cm-W -158.7(anti) C3'-endo lambda=120.4; -162.9(anti) C3'-endo lambda=36.3 d(C1'-C1')=9.36 d(N1-N9)=8.95 d(C6-C8)=10.29 tor(N1-C1'-C1'-N9)=-25.8 H-bonds[2]: "O2'(hydroxyl)-N1[2.88]; N3-N6(amino)[2.97]" bp_pars: [5.83 -0.18 0.91 -36.62 -14.76 46.72] 17 A.C15 A.A19 [C-A] 00-n/a cSW cm-W -162.6(anti) C3'-endo lambda=127.4; -44.8(...) C2'-endo lambda=30.6 d(C1'-C1')=9.35 d(N1-N9)=9.01 d(C6-C8)=10.21 tor(N1-C1'-C1'-N9)=29.3 H-bonds[2]: "O2'(hydroxyl)-N1[2.87]; O2(carbonyl)-N6(amino)[3.16]" bp_pars: [6.83 -0.77 0.25 -28.47 16.16 54.38] 18 A.G16 A.U17 [G-U] Platform 00-n/a cSW cm-W -121.2(anti) C2'-endo lambda=140.7; 22.9(...) C2'-endo lambda=52.0 d(C1'-C1')=6.49 d(N1-N9)=6.73 d(C6-C8)=8.72 tor(N1-C1'-C1'-N9)=31.7 H-bonds[1]: "N2(amino)-O4(carbonyl)[2.42]" bp_pars: [4.44 0.28 -1.58 -26.52 17.04 84.06] 19 A.U25 A.A62 [U-A] WC 20-XX cWW cW-W 154.7(...) C3'-endo lambda=50.8; 177.3(anti) C3'-endo lambda=52.0 d(C1'-C1')=10.72 d(N1-N9)=8.88 d(C6-C8)=9.52 tor(N1-C1'-C1'-N9)=-13.1 H-bonds[2]: "N3(imino)-N1[3.01]; O4(carbonyl)-N6(amino)[2.64]" bp_pars: [-0.39 -0.29 1.85 -27.58 6.03 -9.45] 20 A.U26 A.A61 [U-A] 00-n/a cWW cW-W -135.1(anti) C3'-endo lambda=65.7; -168.8(anti) C3'-endo lambda=67.9 d(C1'-C1')=9.78 d(N1-N9)=8.61 d(C6-C8)=10.03 tor(N1-C1'-C1'-N9)=-16.8 H-bonds[1]: "N3(imino)-N1[3.08]" bp_pars: [0.30 0.39 0.58 17.21 -22.95 23.32] 21 A.G27 A.C60 [G-C] WC 19-XIX cWW cW-W -153.2(anti) C3'-endo lambda=55.9; -156.3(anti) C3'-endo lambda=63.0 d(C1'-C1')=10.35 d(N1-N9)=8.85 d(C6-C8)=10.02 tor(N1-C1'-C1'-N9)=3.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.55]; N1(imino)-N3[3.01]; N2(amino)-O2(carbonyl)[2.37]" bp_pars: [-0.76 0.06 -0.21 6.78 5.83 12.99] 22 A.C28 A.G59 [C-G] WC 19-XIX cWW cW-W -163.9(anti) C3'-endo lambda=61.7; -169.8(anti) C3'-endo lambda=56.9 d(C1'-C1')=10.15 d(N1-N9)=8.64 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=1.0 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.22]; N3-N1(imino)[2.80]; N4(amino)-O6(carbonyl)[3.24]" bp_pars: [0.66 -0.16 -0.38 12.06 -2.34 11.55] 23 A.U29 A.U58 [U-U] 16-XVI cWW cW-W -173.2(anti) C3'-endo lambda=75.2; -167.8(anti) C2'-exo lambda=49.5 d(C1'-C1')=8.46 d(N1-N9)=7.15 d(C6-C8)=8.55 tor(N1-C1'-C1'-N9)=-20.0 H-bonds[2]: "O2(carbonyl)-N3(imino)[2.92]; N3(imino)-O4(carbonyl)[3.23]" bp_pars: [2.11 -1.69 1.02 7.95 -17.69 16.17] 24 A.U30 A.A32 [U-A] 00-n/a ... t... -177.8(anti) C3'-endo lambda=73.7; -150.3(anti) C3'-endo lambda=37.1 d(C1'-C1')=7.20 d(N1-N9)=6.07 d(C6-C8)=6.02 tor(N1-C1'-C1'-N9)=-160.1 H-bonds[1]: "O2(carbonyl)*N7[2.84]" bp_pars: [5.62 -6.96 -1.36 28.41 7.38 -83.86] 25 A.G33 A.A39 [G-A] 00-n/a c.W c.-W -143.6(anti) C3'-endo lambda=21.0; -172.4(anti) C3'-endo lambda=27.8 d(C1'-C1')=15.13 d(N1-N9)=12.46 d(C6-C8)=11.82 tor(N1-C1'-C1'-N9)=19.5 H-bonds[1]: "O6(carbonyl)-N6(amino)[3.76]" bp_pars: [-0.97 3.29 -1.87 12.12 -9.98 -62.01] 26 A.G33 A.G40 [G-G] 00-n/a c.. c.-. -143.6(anti) C3'-endo lambda=25.5; -113.1(anti) C2'-endo lambda=89.3 d(C1'-C1')=13.08 d(N1-N9)=11.77 d(C6-C8)=12.54 tor(N1-C1'-C1'-N9)=-9.0 H-bonds[1]: "O6(carbonyl)-N2(amino)[3.50]" bp_pars: [-6.93 0.41 1.75 -2.91 12.70 7.54] 27 A.G33 A.C41 [G-C] WC 19-XIX cWW cW-W -143.6(anti) C3'-endo lambda=54.2; -164.3(anti) C3'-endo lambda=56.1 d(C1'-C1')=10.61 d(N1-N9)=8.92 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=-6.6 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.97]; N1(imino)-N3[2.90]; N2(amino)-O2(carbonyl)[2.72]" bp_pars: [-0.14 -0.12 0.13 -4.41 -7.38 1.84] 28 A.G40 A.C41 [G+C] Platform 00-n/a cSH cm+M -113.1(anti) C2'-endo lambda=137.4; -164.3(anti) C3'-endo lambda=40.0 d(C1'-C1')=6.78 d(N1-N9)=6.72 d(C6-C8)=6.64 tor(N1-C1'-C1'-N9)=22.7 H-bonds[2]: "N2(amino)*N4(amino)[2.90]; N3-N4(amino)[2.94]" bp_pars: [6.92 0.45 1.13 -0.80 20.30 5.05] 29 A.G40 A.G42 [G+G] 00-n/a cSH cm+M -113.1(anti) C2'-endo lambda=121.5; -160.6(anti) C3'-endo lambda=24.4 d(C1'-C1')=9.28 d(N1-N9)=8.74 d(C6-C8)=9.10 tor(N1-C1'-C1'-N9)=29.8 H-bonds[1]: "N2(amino)-O6(carbonyl)[2.71]" bp_pars: [5.78 -0.92 -1.74 4.59 11.51 -37.30] 30 A.G42 A.G57 [G-G] 00-n/a tHS cM-m -160.6(anti) C3'-endo lambda=20.0; -162.6(anti) O4'-endo lambda=89.8 d(C1'-C1')=11.38 d(N1-N9)=10.05 d(C6-C8)=10.66 tor(N1-C1'-C1'-N9)=28.4 H-bonds[1]: "O6(carbonyl)-N2(amino)[2.52]" bp_pars: [-6.51 -1.56 -1.46 7.27 1.62 -2.01] 31 A.U43 A.G56 [U-G] 00-n/a cWW cW-W -164.6(anti) C3'-endo lambda=41.5; -143.8(anti) C3'-endo lambda=83.6 d(C1'-C1')=11.72 d(N1-N9)=10.47 d(C6-C8)=11.56 tor(N1-C1'-C1'-N9)=4.0 H-bonds[1]: "O4(carbonyl)-N2(amino)[2.75]" bp_pars: [-5.12 0.32 -1.70 17.63 -11.60 16.31] 32 A.U43 A.G57 [U-G] 00-n/a cWS cW-m -164.6(anti) C3'-endo lambda=43.8; -162.6(anti) O4'-endo lambda=106.1 d(C1'-C1')=9.80 d(N1-N9)=9.14 d(C6-C8)=10.59 tor(N1-C1'-C1'-N9)=-5.1 H-bonds[1]: "O4(carbonyl)-N2(amino)[2.79]" bp_pars: [-5.22 -0.50 1.80 12.15 -0.01 34.37] 33 A.U44 A.A55 [U-A] WC 20-XX cWW cW-W -158.4(anti) C3'-endo lambda=63.5; -158.9(anti) C3'-endo lambda=57.4 d(C1'-C1')=10.46 d(N1-N9)=9.01 d(C6-C8)=10.07 tor(N1-C1'-C1'-N9)=-9.8 H-bonds[2]: "N3(imino)-N1[3.22]; O4(carbonyl)-N6(amino)[3.40]" bp_pars: [0.72 0.10 -0.72 8.99 -18.86 5.71] 34 A.G45 A.C54 [G-C] WC 19-XIX cWW cW-W -163.3(anti) C3'-endo lambda=56.1; -157.6(anti) C3'-endo lambda=58.9 d(C1'-C1')=10.77 d(N1-N9)=9.18 d(C6-C8)=10.25 tor(N1-C1'-C1'-N9)=-5.2 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.48]; N1(imino)-N3[3.17]; N2(amino)-O2(carbonyl)[2.83]" bp_pars: [-0.00 0.24 -0.36 -3.63 -10.19 7.86] 35 A.A46 A.U53 [A-U] WC 20-XX cWW cW-W -161.0(anti) C3'-endo lambda=53.9; -162.5(anti) C3'-endo lambda=61.4 d(C1'-C1')=10.44 d(N1-N9)=8.87 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-3.7 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.35]; N1-N3(imino)[3.09]" bp_pars: [-0.86 -0.04 -0.24 3.16 -3.64 5.25] **************************************************************************** List of 6 multiplet(s) 1 nts=3 A.C1+A.G16+A.U17 [CGU] 2 nts=3 A.G2+A.C15+A.A19 [GCA] 3 nts=3 A.U3+A.A14+A.A20 [UAA] 4 nts=3 A.G4+A.C13+A.A21 [GCA] 5 nts=3 A.G5+A.C12+A.G24 [GCG] 6 nts=3 A.G33+A.G40+A.C41 [GGC] **************************************************************************** List of 2 helices helix=1[3] bps=17 1 A.C1 A.G16 [C-G] WC 19-XIX cWW cW-W 2 A.G2 A.C15 [G-C] WC 19-XIX cWW cW-W 3 A.U3 A.A14 [U-A] WC 20-XX cWW cW-W 4 A.G4 A.C13 [G-C] WC 19-XIX cWW cW-W 5 A.G5 A.C12 [G-C] WC 19-XIX cWW cW-W 6 A.C34 A.G11 [C-G] WC 19-XIX cWW cW-W 7 A.C35 A.G10 [C-G] WC 19-XIX cWW cW-W 8 A.C36 A.G9 [C-G] WC 19-XIX cWW cW-W 9 A.U37 A.A8 [U-A] WC 20-XX cWW cW-W 10 A.A38 A.U7 [A-U] WC 20-XX cWW cW-W 11 A.A39 A.U6 [A-U] WC 20-XX cWW cW-W 12 A.C41 A.G33 [C-G] WC 19-XIX cWW cW-W 13 A.G42 A.G57 [G-G] 00-n/a tHS cM-m 14 A.U43 A.G56 [U-G] 00-n/a cWW cW-W 15 A.U44 A.A55 [U-A] WC 20-XX cWW cW-W 16 A.G45 A.C54 [G-C] WC 19-XIX cWW cW-W 17 A.A46 A.U53 [A-U] WC 20-XX cWW cW-W helix=2[1] bps=5 1 A.U25 A.A62 [U-A] WC 20-XX cWW cW-W 2 A.U26 A.A61 [U-A] 00-n/a cWW cW-W 3 A.G27 A.C60 [G-C] WC 19-XIX cWW cW-W 4 A.C28 A.G59 [C-G] WC 19-XIX cWW cW-W 5 A.U29 A.U58 [U-U] 16-XVI cWW cW-W **************************************************************************** List of 4 stems stem=1[#1] bps=5 1 A.C1 A.G16 [C-G] WC 19-XIX cWW cW-W 2 A.G2 A.C15 [G-C] WC 19-XIX cWW cW-W 3 A.U3 A.A14 [U-A] WC 20-XX cWW cW-W 4 A.G4 A.C13 [G-C] WC 19-XIX cWW cW-W 5 A.G5 A.C12 [G-C] WC 19-XIX cWW cW-W stem=2[#1] bps=6 1 A.U6 A.A39 [U-A] WC 20-XX cWW cW-W 2 A.U7 A.A38 [U-A] WC 20-XX cWW cW-W 3 A.A8 A.U37 [A-U] WC 20-XX cWW cW-W 4 A.G9 A.C36 [G-C] WC 19-XIX cWW cW-W 5 A.G10 A.C35 [G-C] WC 19-XIX cWW cW-W 6 A.G11 A.C34 [G-C] WC 19-XIX cWW cW-W stem=3[#2] bps=2 1 A.G27 A.C60 [G-C] WC 19-XIX cWW cW-W 2 A.C28 A.G59 [C-G] WC 19-XIX cWW cW-W stem=4[#1] bps=3 1 A.U44 A.A55 [U-A] WC 20-XX cWW cW-W 2 A.G45 A.C54 [G-C] WC 19-XIX cWW cW-W 3 A.A46 A.U53 [A-U] WC 20-XX cWW cW-W **************************************************************************** List of 2 lone WC/wobble pair(s) -1 A.U25 A.A62 [U-A] WC 20-XX cWW cW-W -2 A.G33 A.C41 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 3 stems: [#1, #2, #4] **************************************************************************** List of 3 hairpin loop(s) 1 nts=6 UUAGGG closed by pair {A.G5+A.C12 [GC], #1} A.G5+A.U6+A.U7+A.A8+A.G9+A.G10+A.G11+A.C12 [GUUAGGGC] 2 nts=22 CCACGUUAAAUAGUUGCUUAAG closed by pair {A.G11+A.C34 [GC], #2} A.G11+A.C12+A.C13+A.A14+A.C15+A.G16+A.U17+A.U18+A.A19+A.A20+A.A21+A.U22+A.A23+A.G24+A.U25+A.U26+A.G27+A.C28+A.U29+A.U30+A.A31+A.A32+A.G33+A.C34 [GCCACGUUAAAUAGUUGCUUAAGC] 3 nts=7 CCCUAAG closed by pair {A.G33+A.C41 [GC], #-2} A.G33+A.C34+A.C35+A.C36+A.U37+A.A38+A.A39+A.G40+A.C41 [GCCCUAAGC] **************************************************************************** List of 1 internal loop(s) 1 symmetric internal loop: 6 nts; [1x1]; linked by [#-1, #3] A.U25+A.U26+A.G27+A.C60+A.A61+A.A62 [UUGCAA] **************************************************************************** List of 2 junction(s) 1* 4-way junctions: 9 nts; [0x1x0x0]; linked by [#1, #2, #-2, #2] A.G5+A.U6+A.A39+A.G40+A.C41+A.G33+A.C34+A.G11+A.C12 [GUAGCGCGC] 2 3-way junctions: 15 nts; [4x2x3]; linked by [#3, #-2, #4] A.C28+A.U29+A.U30+A.A31+A.A32+A.G33+A.C41+A.G42+A.U43+A.U44+A.A55+A.G56+A.G57+A.U58+A.G59 [CUUAAGCGUUAGGUG] This structure contains pseudo-knot(s). **************************************************************************** List of 1 A-minor motif(s) 1 type=II A/G-C A.A23 vs A.G4+A.C13 [WC] +A.G4 H-bonds[0]: "" -A.C13 H-bonds[3]: "O2'(hydroxyl)-O3'[3.13]; O2'(hydroxyl)-O2'(hydroxyl)[2.99]; N3-O2'(hydroxyl)[2.81]" **************************************************************************** List of 1 ribose zipper(s) 1 nts=4 A.C12+A.C13+A.A23+A.G24 [CCAG] **************************************************************************** >chain-A #1 RNA[57]/1* with 58 nts CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUAUCAGGUGCAA ((((([[[[[[)))))........[.[[....[]]]]]].]..(((..)))...]].] DONE!