# renumb_3a3a.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: Thu Aug 24 08:31:40 2023 File name: renumb_3a3a.pdb no. of DNA/RNA chains: 1 [A=86] no. of nucleotides: 86 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 38 base pair(s) 1 A.G1 A.C86 [G-C] WC 19-XIX cWW cW-W -162.9(anti) C3'-endo lambda=49.4; -166.8(anti) C3'-endo lambda=51.8 d(C1'-C1')=11.03 d(N1-N9)=9.18 d(C6-C8)=9.98 tor(N1-C1'-C1'-N9)=-8.2 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.84]; N1(imino)-N3[3.03]; N2(amino)-O2(carbonyl)[3.10]" bp_pars: [-0.01 -0.02 0.20 6.85 -4.28 -5.72] 2 A.C2 A.G85 [C-G] WC 19-XIX cWW cW-W -154.3(anti) C3'-endo lambda=56.1; -166.8(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.57 d(N1-N9)=8.92 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-4.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.76]; N3-N1(imino)[2.92]; N4(amino)-O6(carbonyl)[2.98]" bp_pars: [0.20 -0.09 0.09 13.62 -2.03 1.17] 3 A.C3 A.G84 [C-G] WC 19-XIX cWW cW-W -166.4(anti) C3'-endo lambda=54.4; -174.9(anti) C3'-endo lambda=55.2 d(C1'-C1')=10.72 d(N1-N9)=9.03 d(C6-C8)=9.99 tor(N1-C1'-C1'-N9)=-1.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.79]; N3-N1(imino)[2.95]; N4(amino)-O6(carbonyl)[2.97]" bp_pars: [0.03 -0.04 0.03 5.26 -3.41 0.76] 4 A.C4 A.G83 [C-G] WC 19-XIX cWW cW-W -162.8(anti) C3'-endo lambda=56.8; -176.0(anti) C3'-endo lambda=55.5 d(C1'-C1')=10.61 d(N1-N9)=8.97 d(C6-C8)=9.96 tor(N1-C1'-C1'-N9)=0.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.75]; N3-N1(imino)[2.94]; N4(amino)-O6(carbonyl)[3.00]" bp_pars: [0.22 -0.07 -0.01 3.75 -4.54 2.09] 5 A.G5 A.C82 [G-C] WC 19-XIX cWW cW-W -171.4(anti) C3'-endo lambda=55.0; -164.2(anti) C3'-endo lambda=54.9 d(C1'-C1')=10.65 d(N1-N9)=8.97 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=3.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.91]; N1(imino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.79]" bp_pars: [-0.13 -0.12 0.12 -1.46 -1.41 0.09] 6 A.G6 A.U81 [G-U] Wobble 28-XXVIII cWW cW-W -177.8(anti) C3'-endo lambda=45.2; -162.7(anti) C3'-endo lambda=71.4 d(C1'-C1')=10.39 d(N1-N9)=8.90 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=4.8 H-bonds[2]: "O6(carbonyl)-N3(imino)[3.04]; N1(imino)-O2(carbonyl)[2.80]" bp_pars: [-2.50 -0.40 -0.02 1.92 1.54 4.33] 7 A.A7 A.U80 [A-U] WC 20-XX cWW cW-W -168.9(anti) C3'-endo lambda=62.7; -160.1(anti) C3'-endo lambda=62.9 d(C1'-C1')=9.73 d(N1-N9)=8.39 d(C6-C8)=9.67 tor(N1-C1'-C1'-N9)=-0.1 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.24]; N1-N3(imino)[2.62]" bp_pars: [-0.06 -0.19 0.10 -1.41 -0.82 14.78] 8 A.U8 A.U79 [U-U] 16-XVI cWW cW-W -151.9(anti) C3'-endo lambda=75.0; -160.0(anti) C3'-endo lambda=48.0 d(C1'-C1')=8.57 d(N1-N9)=7.22 d(C6-C8)=8.56 tor(N1-C1'-C1'-N9)=-9.6 H-bonds[2]: "O2(carbonyl)-N3(imino)[2.93]; N3(imino)-O4(carbonyl)[2.97]" bp_pars: [2.06 -1.72 0.29 -0.21 -10.85 13.42] 9 A.G9 A.C78 [G-C] WC 19-XIX cWW cW-W -103.8(anti) C2'-endo lambda=52.8; -163.5(anti) C3'-endo lambda=54.4 d(C1'-C1')=10.79 d(N1-N9)=9.05 d(C6-C8)=9.98 tor(N1-C1'-C1'-N9)=-4.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.98]; N1(imino)-N3[2.98]; N2(amino)-O2(carbonyl)[2.88]" bp_pars: [-0.18 -0.05 0.07 -1.85 -7.20 -0.36] 10 A.C12 A.G27 [C-G] WC 19-XIX cWW cW-W 177.9(anti) C3'-endo lambda=51.3; -169.1(anti) C3'-endo lambda=53.0 d(C1'-C1')=10.88 d(N1-N9)=9.08 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=3.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.93]; N3-N1(imino)[2.97]; N4(amino)-O6(carbonyl)[2.87]" bp_pars: [-0.00 -0.07 -0.18 -5.18 2.24 -2.97] 11 A.C13 A.G26 [C-G] WC 19-XIX cWW cW-W -164.6(anti) C3'-endo lambda=54.2; -162.7(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.71 d(N1-N9)=9.01 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=4.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.82]; N3-N1(imino)[2.95]; N4(amino)-O6(carbonyl)[2.94]" bp_pars: [0.09 -0.07 -0.12 -5.92 2.20 -0.05] 12 A.U14 A.G25 [U-G] Wobble 28-XXVIII cWW cW-W -157.0(anti) C3'-endo lambda=69.7; -175.8(anti) C3'-endo lambda=41.9 d(C1'-C1')=10.58 d(N1-N9)=8.99 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=1.9 H-bonds[2]: "O2(carbonyl)-N1(imino)[2.88]; N3(imino)-O6(carbonyl)[3.03]" bp_pars: [2.52 -0.39 -0.06 1.95 0.99 1.69] 13 A.C15 A.G24 [C-G] WC 19-XIX cWW cW-W -160.2(anti) C3'-endo lambda=54.5; -172.9(anti) C3'-endo lambda=55.1 d(C1'-C1')=10.71 d(N1-N9)=9.03 d(C6-C8)=9.98 tor(N1-C1'-C1'-N9)=3.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.81]; N3-N1(imino)[2.95]; N4(amino)-O6(carbonyl)[2.95]" bp_pars: [0.08 -0.05 -0.01 3.46 3.06 0.47] 14 A.A16 A.U23 [A-U] WC 20-XX cWW cW-W -170.9(anti) C3'-endo lambda=58.3; -163.2(anti) C3'-endo lambda=56.6 d(C1'-C1')=10.39 d(N1-N9)=8.81 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=-0.4 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.02]; N1-N3(imino)[2.80]" bp_pars: [0.03 -0.10 -0.02 0.46 -1.44 3.98] 15 A.G17 A.C22 [G-C] WC 19-XIX cWW cW-W -163.0(anti) C3'-endo lambda=54.1; 179.2(anti) C3'-endo lambda=54.3 d(C1'-C1')=10.77 d(N1-N9)=9.05 d(C6-C8)=9.99 tor(N1-C1'-C1'-N9)=3.9 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.98]; N1(imino)-N3[2.99]; N2(amino)-O2(carbonyl)[2.85]" bp_pars: [-0.11 -0.04 -0.17 -1.66 3.12 -0.02] 16 A.U18 A.U72 [U+U] 13-XIII tWW tW+W -163.9(anti) C3'-endo lambda=43.7; -164.7(anti) C3'-endo lambda=46.5 d(C1'-C1')=8.65 d(N1-N9)=6.89 d(C6-C8)=8.63 tor(N1-C1'-C1'-N9)=-157.3 H-bonds[2]: "O2(carbonyl)-N3(imino)[3.00]; N3(imino)-O2(carbonyl)[2.87]" bp_pars: [2.16 3.42 0.09 -16.83 2.69 177.20] 17 A.G19 A.U68 [G+U] 00-n/a tWS tW+m -143.2(anti) C2'-endo lambda=25.7; -155.0(anti) C3'-endo lambda=106.4 d(C1'-C1')=9.05 d(N1-N9)=8.40 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-154.5 H-bonds[3]: "O6(carbonyl)-O2'(hydroxyl)[3.39]; N1(imino)-O2(carbonyl)[2.68]; N2(amino)-O2(carbonyl)[2.93]" bp_pars: [-0.60 5.61 -0.02 -11.67 -2.31 99.59] 18 A.G20 A.U21 [G+U] Platform 00-n/a cSH cm+M -65.6(anti) C3'-exo lambda=128.0; -137.5(anti) C2'-endo lambda=65.2 d(C1'-C1')=6.27 d(N1-N9)=6.57 d(C6-C8)=6.59 tor(N1-C1'-C1'-N9)=23.2 H-bonds[2]: "O2'(hydroxyl)-OP2[2.36]; N2(amino)-O4(carbonyl)[2.43]" bp_pars: [7.27 2.99 -0.81 7.58 22.15 16.38] 19 A.G20 A.C69 [G-C] WC 19-XIX cWW cW-W -65.6(anti) C3'-exo lambda=51.2; -176.6(anti) C3'-endo lambda=46.1 d(C1'-C1')=10.90 d(N1-N9)=8.97 d(C6-C8)=9.69 tor(N1-C1'-C1'-N9)=-9.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.43]; N1(imino)-N3[2.74]; N2(amino)-O2(carbonyl)[2.97]" bp_pars: [0.33 -0.31 -0.18 -6.13 -8.67 -8.71] 20 A.U28 A.A46 [U-A] WC 20-XX cWW cW-W -167.0(anti) C3'-endo lambda=55.1; -131.4(anti) C2'-endo lambda=52.8 d(C1'-C1')=10.69 d(N1-N9)=8.97 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=0.8 H-bonds[2]: "N3(imino)-N1[2.92]; O4(carbonyl)-N6(amino)[2.93]" bp_pars: [0.05 -0.06 0.08 4.80 2.86 -1.55] 21 A.G29 A.U45 [G-U] Wobble 28-XXVIII cWW cW-W -173.8(anti) C3'-endo lambda=41.7; -162.8(anti) C3'-endo lambda=73.2 d(C1'-C1')=10.28 d(N1-N9)=8.78 d(C6-C8)=9.76 tor(N1-C1'-C1'-N9)=-0.1 H-bonds[2]: "O6(carbonyl)-N3(imino)[2.88]; N1(imino)-O2(carbonyl)[2.68]" bp_pars: [-2.81 -0.65 -0.18 -2.48 -3.33 3.71] 22 A.C30 A.G44 [C-G] WC 19-XIX cWW cW-W -172.1(anti) C3'-endo lambda=55.3; -168.3(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.63 d(N1-N9)=8.95 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=-2.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.78]; N3-N1(imino)[2.90]; N4(amino)-O6(carbonyl)[2.92]" bp_pars: [0.15 -0.12 -0.07 -0.47 -7.25 0.93] 23 A.A31 A.U43 [A-U] WC 20-XX cWW cW-W -163.9(anti) C3'-endo lambda=58.8; -159.1(anti) C3'-endo lambda=56.5 d(C1'-C1')=10.46 d(N1-N9)=8.89 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-2.6 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.11]; N1-N3(imino)[2.89]" bp_pars: [0.02 -0.02 -0.13 -2.38 -2.77 3.93] 24 A.G32 A.C42 [G-C] WC 19-XIX cWW cW-W -171.0(anti) C3'-endo lambda=56.8; -166.1(anti) C3'-endo lambda=52.6 d(C1'-C1')=10.74 d(N1-N9)=9.05 d(C6-C8)=9.99 tor(N1-C1'-C1'-N9)=3.5 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.91]; N1(imino)-N3[2.94]; N2(amino)-O2(carbonyl)[2.85]" bp_pars: [0.20 -0.05 -0.14 0.53 0.68 -0.33] 25 A.G33 A.C41 [G-C] WC 19-XIX cWW cW-W -157.8(anti) C3'-endo lambda=53.1; -165.2(anti) C3'-endo lambda=54.0 d(C1'-C1')=10.74 d(N1-N9)=9.00 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-12.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.96]; N1(imino)-N3[2.94]; N2(amino)-O2(carbonyl)[2.84]" bp_pars: [-0.13 -0.09 0.16 -4.44 -11.51 -0.53] 26 A.C34 A.C37 [C-C] 00-n/a tWH tW-M -164.1(anti) C3'-endo lambda=17.3; -108.2(anti) C3'-endo lambda=21.2 d(C1'-C1')=10.82 d(N1-N9)=8.09 d(C6-C8)=6.98 tor(N1-C1'-C1'-N9)=-151.8 H-bonds[1]: "N3-N4(amino)[2.95]" bp_pars: [3.47 0.06 2.50 10.84 62.13 -112.82] 27 A.G47 A.A62 [G-A] Imino 08-VIII cWW cW-W -173.1(anti) C3'-endo lambda=48.5; -125.5(anti) C2'-endo lambda=54.9 d(C1'-C1')=12.44 d(N1-N9)=10.63 d(C6-C8)=11.26 tor(N1-C1'-C1'-N9)=6.1 H-bonds[2]: "O6(carbonyl)-N6(amino)[3.12]; N1(imino)-N1[2.77]" bp_pars: [-0.26 1.47 0.12 -11.03 5.36 -8.09] 28 A.C48 A.G61 [C-G] WC 19-XIX cWW cW-W -163.7(anti) C3'-endo lambda=54.1; -160.5(anti) C3'-endo lambda=55.1 d(C1'-C1')=10.70 d(N1-N9)=9.00 d(C6-C8)=9.95 tor(N1-C1'-C1'-N9)=-11.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.87]; N3-N1(imino)[2.95]; N4(amino)-O6(carbonyl)[2.98]" bp_pars: [0.07 -0.07 0.15 -3.24 -12.35 0.11] 29 A.U49 A.A60 [U-A] WC 20-XX cWW cW-W -160.4(anti) C3'-endo lambda=54.4; -167.4(anti) C3'-endo lambda=54.7 d(C1'-C1')=10.66 d(N1-N9)=8.96 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-4.3 H-bonds[2]: "N3(imino)-N1[2.91]; O4(carbonyl)-N6(amino)[2.93]" bp_pars: [-0.01 -0.06 0.27 -3.73 -4.28 -1.58] 30 A.G50 A.C59 [G-C] WC 19-XIX cWW cW-W -167.4(anti) C3'-endo lambda=55.6; -172.9(anti) C3'-endo lambda=52.6 d(C1'-C1')=10.92 d(N1-N9)=9.20 d(C6-C8)=10.12 tor(N1-C1'-C1'-N9)=0.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.01]; N1(imino)-N3[3.08]; N2(amino)-O2(carbonyl)[2.99]" bp_pars: [0.13 0.08 0.04 0.09 1.57 -1.31] 31 A.U51 A.A58 [U-A] WC 20-XX cWW cW-W -163.6(anti) C3'-endo lambda=53.0; -160.6(anti) C3'-endo lambda=53.0 d(C1'-C1')=10.78 d(N1-N9)=9.02 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-4.6 H-bonds[2]: "N3(imino)-N1[2.92]; O4(carbonyl)-N6(amino)[2.90]" bp_pars: [0.01 -0.05 0.09 -0.80 -3.33 -2.80] 32 A.C52 A.G57 [C-G] WC 19-XIX cWW cW-W -174.2(anti) C3'-endo lambda=57.6; -163.8(anti) C3'-endo lambda=53.7 d(C1'-C1')=10.81 d(N1-N9)=9.15 d(C6-C8)=10.14 tor(N1-C1'-C1'-N9)=2.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.87]; N3-N1(imino)[3.10]; N4(amino)-O6(carbonyl)[3.17]" bp_pars: [0.23 0.11 -0.04 1.87 2.82 2.32] 33 A.U53 A.C56 [U-C] 00-n/a tSH tm-M -155.0(anti) C3'-endo lambda=93.8; -158.2(anti) C3'-endo lambda=20.2 d(C1'-C1')=8.86 d(N1-N9)=7.80 d(C6-C8)=7.91 tor(N1-C1'-C1'-N9)=-128.8 H-bonds[1]: "O2(carbonyl)-N4(amino)[3.86]" bp_pars: [7.09 -6.46 0.74 26.81 20.87 -30.06] 34 A.G63 A.C77 [G-C] WC 19-XIX cWW cW-W 168.1(anti) C3'-endo lambda=54.0; -159.1(anti) C3'-endo lambda=55.6 d(C1'-C1')=10.55 d(N1-N9)=8.87 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-5.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.90]; N1(imino)-N3[2.87]; N2(amino)-O2(carbonyl)[2.84]" bp_pars: [-0.20 -0.15 0.03 -15.71 -10.83 -0.76] 35 A.U64 A.A76 [U-A] WC 20-XX cWW cW-W -163.5(anti) C3'-endo lambda=58.2; -152.1(anti) C3'-endo lambda=60.4 d(C1'-C1')=10.09 d(N1-N9)=8.60 d(C6-C8)=9.70 tor(N1-C1'-C1'-N9)=-14.6 H-bonds[2]: "N3(imino)-N1[2.70]; O4(carbonyl)-N6(amino)[3.08]" bp_pars: [-0.24 -0.15 0.24 -14.33 -13.68 6.99] 36 A.G65 A.C75 [G-C] WC 19-XIX cWW cW-W -169.3(anti) C3'-endo lambda=54.3; -172.7(anti) C3'-endo lambda=55.1 d(C1'-C1')=10.52 d(N1-N9)=8.85 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-6.9 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.82]; N1(imino)-N3[2.79]; N2(amino)-O2(carbonyl)[2.69]" bp_pars: [-0.15 -0.24 0.14 -1.70 0.35 0.00] 37 A.G66 A.C74 [G-C] WC 19-XIX cWW cW-W -161.2(anti) C3'-endo lambda=54.4; -165.5(anti) C3'-endo lambda=53.6 d(C1'-C1')=10.38 d(N1-N9)=8.67 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=-15.6 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.66]; N1(imino)-N3[2.60]; N2(amino)-O2(carbonyl)[2.61]" bp_pars: [-0.12 -0.40 -0.08 -2.08 -13.68 0.41] 38 A.U67 A.A71 [U-A] rHoogsteen 24-XXIV tWH tW-M -149.8(anti) C3'-endo lambda=27.2; -83.8(anti) C2'-endo lambda=19.2 d(C1'-C1')=9.37 d(N1-N9)=6.78 d(C6-C8)=5.69 tor(N1-C1'-C1'-N9)=162.3 H-bonds[2]: "O2(carbonyl)-N6(amino)[2.70]; N3(imino)-N7[2.35]" bp_pars: [3.73 -1.92 -0.13 -9.32 -2.48 -103.78] **************************************************************************** List of 1 multiplet(s) 1 nts=3 A.G20+A.U21+A.C69 [GUC] **************************************************************************** List of 3 helices helix=1[2] bps=16 1 A.G1 A.C86 [G-C] WC 19-XIX cWW cW-W 2 A.C2 A.G85 [C-G] WC 19-XIX cWW cW-W 3 A.C3 A.G84 [C-G] WC 19-XIX cWW cW-W 4 A.C4 A.G83 [C-G] WC 19-XIX cWW cW-W 5 A.G5 A.C82 [G-C] WC 19-XIX cWW cW-W 6 A.G6 A.U81 [G-U] Wobble 28-XXVIII cWW cW-W 7 A.A7 A.U80 [A-U] WC 20-XX cWW cW-W 8 A.U8 A.U79 [U-U] 16-XVI cWW cW-W 9 A.G9 A.C78 [G-C] WC 19-XIX cWW cW-W 10 A.G63 A.C77 [G-C] WC 19-XIX cWW cW-W 11 A.U64 A.A76 [U-A] WC 20-XX cWW cW-W 12 A.G65 A.C75 [G-C] WC 19-XIX cWW cW-W 13 A.G66 A.C74 [G-C] WC 19-XIX cWW cW-W 14 A.U67 A.A71 [U-A] rHoogsteen 24-XXIV tWH tW-M 15 A.U68 A.G19 [U+G] 00-n/a tSW tm+W 16 A.C69 A.G20 [C-G] WC 19-XIX cWW cW-W helix=2[2] bps=14 1 A.C37 A.C34 [C-C] 00-n/a tHW tM-W 2 A.C41 A.G33 [C-G] WC 19-XIX cWW cW-W 3 A.C42 A.G32 [C-G] WC 19-XIX cWW cW-W 4 A.U43 A.A31 [U-A] WC 20-XX cWW cW-W 5 A.G44 A.C30 [G-C] WC 19-XIX cWW cW-W 6 A.U45 A.G29 [U-G] Wobble 28-XXVIII cWW cW-W 7 A.A46 A.U28 [A-U] WC 20-XX cWW cW-W 8 A.C12 A.G27 [C-G] WC 19-XIX cWW cW-W 9 A.C13 A.G26 [C-G] WC 19-XIX cWW cW-W 10 A.U14 A.G25 [U-G] Wobble 28-XXVIII cWW cW-W 11 A.C15 A.G24 [C-G] WC 19-XIX cWW cW-W 12 A.A16 A.U23 [A-U] WC 20-XX cWW cW-W 13 A.G17 A.C22 [G-C] WC 19-XIX cWW cW-W 14 A.U18 A.U72 [U+U] 13-XIII tWW tW+W helix=3[1] bps=7 1 A.G47 A.A62 [G-A] Imino 08-VIII cWW cW-W 2 A.C48 A.G61 [C-G] WC 19-XIX cWW cW-W 3 A.U49 A.A60 [U-A] WC 20-XX cWW cW-W 4 A.G50 A.C59 [G-C] WC 19-XIX cWW cW-W 5 A.U51 A.A58 [U-A] WC 20-XX cWW cW-W 6 A.C52 A.G57 [C-G] WC 19-XIX cWW cW-W 7 A.U53 A.C56 [U-C] 00-n/a tSH tm-M **************************************************************************** List of 5 stems stem=1[#1] bps=7 1 A.G1 A.C86 [G-C] WC 19-XIX cWW cW-W 2 A.C2 A.G85 [C-G] WC 19-XIX cWW cW-W 3 A.C3 A.G84 [C-G] WC 19-XIX cWW cW-W 4 A.C4 A.G83 [C-G] WC 19-XIX cWW cW-W 5 A.G5 A.C82 [G-C] WC 19-XIX cWW cW-W 6 A.G6 A.U81 [G-U] Wobble 28-XXVIII cWW cW-W 7 A.A7 A.U80 [A-U] WC 20-XX cWW cW-W stem=2[#2] bps=6 1 A.C12 A.G27 [C-G] WC 19-XIX cWW cW-W 2 A.C13 A.G26 [C-G] WC 19-XIX cWW cW-W 3 A.U14 A.G25 [U-G] Wobble 28-XXVIII cWW cW-W 4 A.C15 A.G24 [C-G] WC 19-XIX cWW cW-W 5 A.A16 A.U23 [A-U] WC 20-XX cWW cW-W 6 A.G17 A.C22 [G-C] WC 19-XIX cWW cW-W stem=3[#2] bps=6 1 A.U28 A.A46 [U-A] WC 20-XX cWW cW-W 2 A.G29 A.U45 [G-U] Wobble 28-XXVIII cWW cW-W 3 A.C30 A.G44 [C-G] WC 19-XIX cWW cW-W 4 A.A31 A.U43 [A-U] WC 20-XX cWW cW-W 5 A.G32 A.C42 [G-C] WC 19-XIX cWW cW-W 6 A.G33 A.C41 [G-C] WC 19-XIX cWW cW-W stem=4[#3] bps=5 1 A.C48 A.G61 [C-G] WC 19-XIX cWW cW-W 2 A.U49 A.A60 [U-A] WC 20-XX cWW cW-W 3 A.G50 A.C59 [G-C] WC 19-XIX cWW cW-W 4 A.U51 A.A58 [U-A] WC 20-XX cWW cW-W 5 A.C52 A.G57 [C-G] WC 19-XIX cWW cW-W stem=5[#1] bps=4 1 A.G63 A.C77 [G-C] WC 19-XIX cWW cW-W 2 A.U64 A.A76 [U-A] WC 20-XX cWW cW-W 3 A.G65 A.C75 [G-C] WC 19-XIX cWW cW-W 4 A.G66 A.C74 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 2 lone WC/wobble pair(s) -1 A.G9 A.C78 [G-C] WC 19-XIX cWW cW-W -2 A.G20 A.C69 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 2 coaxial stack(s) 1 Helix#1 contains 2 stems: [#1, #5] 2 Helix#2 contains 2 stems: [#2, #3] **************************************************************************** List of 4 hairpin loop(s) 1 nts=4 UGGU closed by pair {A.G17+A.C22 [GC], #2} A.G17+A.U18+A.G19+A.G20+A.U21+A.C22 [GUGGUC] 2 nts=7 CUUCAAA closed by pair {A.G33+A.C41 [GC], #3} A.G33+A.C34+A.U35+A.U36+A.C37+A.A38+A.A39+A.A40+A.C41 [GCUUCAAAC] 3 nts=4 UAGC closed by pair {A.C52+A.G57 [CG], #4} A.C52+A.U53+A.A54+A.G55+A.C56+A.G57 [CUAGCG] 4 nts=7 UUCAAUU closed by pair {A.G66+A.C74 [GC], #5} A.G66+A.U67+A.U68+A.C69+A.A70+A.A71+A.U72+A.U73+A.C74 [GUUCAAUUC] **************************************************************************** List of 1 internal loop(s) 1 symmetric internal loop: 6 nts; [1x1]; linked by [#1, #-1] A.A7+A.U8+A.G9+A.C78+A.U79+A.U80 [AUGCUU] **************************************************************************** List of 1 junction(s) 1 5-way junctions: 14 nts; [2x0x1x1x0]; linked by [#-1, #2, #3, #4, #5] A.G9+A.A10+A.U11+A.C12+A.G27+A.U28+A.A46+A.G47+A.C48+A.G61+A.A62+A.G63+A.C77+A.C78 [GAUCGUAGCGAGCC] This structure contains pseudo-knot(s). **************************************************************************** >chain-A #1 RNA with 86 nts GCCCGGAUGAUCCUCAGUGGUCUGGGGUGCAGGCUUCAAACCUGUAGCUGUCUAGCGACAGAGUGGUUCAAUUCCACCUUUCGGGC (((((((.(..((((((..[.))))))((((((.......)))))).(((((....))))).((((..]....))))).))))))) DONE!