# 1ehz.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 Jul 20 21:48:15 2023 File name: 1ehz.pdb no. of DNA/RNA chains: 1 [A=76] no. of nucleotides: 76 no. of waters: 160 no. of metals: 9 [Mg=6, Mn=3] **************************************************************************** List of 34 base pair(s) 1 A.G1 A.C72 [G-C] WC 19-XIX cWW cW-W -167.8(anti) C3'-endo lambda=51.3; -161.6(anti) C3'-endo lambda=56.2 d(C1'-C1')=10.58 d(N1-N9)=8.85 d(C6-C8)=9.75 tor(N1-C1'-C1'-N9)=-0.6 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.83]; N1(imino)-N3[2.88]; N2(amino)-O2(carbonyl)[2.84]" bp_pars: [-0.55 -0.28 -0.43 -6.30 -9.83 -0.70] 2 A.C2 A.G71 [C-G] WC 19-XIX cWW cW-W -163.8(anti) C3'-endo lambda=53.0; -162.8(anti) C3'-endo lambda=52.7 d(C1'-C1')=10.83 d(N1-N9)=9.06 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-6.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.01]; N3-N1(imino)[2.97]; N4(amino)-O6(carbonyl)[2.86]" bp_pars: [0.13 -0.08 0.03 -7.96 -10.30 -2.67] 3 A.G3 A.C70 [G-C] WC 19-XIX cWW cW-W -161.9(anti) C3'-endo lambda=54.6; -152.0(anti) C3'-endo lambda=53.3 d(C1'-C1')=10.72 d(N1-N9)=8.99 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-2.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.94]; N1(imino)-N3[2.87]; N2(amino)-O2(carbonyl)[2.76]" bp_pars: [-0.09 -0.11 0.08 -4.80 -11.89 0.28] 4 A.G4 A.U69 [G-U] Wobble 28-XXVIII cWW cW-W -168.7(anti) C3'-endo lambda=41.5; -161.4(anti) C3'-endo lambda=70.2 d(C1'-C1')=10.50 d(N1-N9)=8.91 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=-4.8 H-bonds[2]: "O6(carbonyl)-N3(imino)[2.91]; N1(imino)-O2(carbonyl)[2.82]" bp_pars: [-2.56 -0.51 0.46 11.05 -9.69 -1.55] 5 A.A5 A.U68 [A-U] WC 20-XX cWW cW-W -162.9(anti) C3'-endo lambda=60.2; -160.1(anti) C3'-endo lambda=58.9 d(C1'-C1')=10.32 d(N1-N9)=8.84 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-16.3 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.15]; N1-N3(imino)[2.88]" bp_pars: [0.10 -0.02 0.07 3.41 -17.40 5.57] 6 A.U6 A.A67 [U-A] WC 20-XX cWW cW-W -160.0(anti) C3'-endo lambda=59.5; -162.8(anti) C3'-endo lambda=60.1 d(C1'-C1')=10.25 d(N1-N9)=8.77 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=-13.2 H-bonds[2]: "N3(imino)-N1[2.78]; O4(carbonyl)-N6(amino)[3.04]" bp_pars: [0.06 -0.13 -0.08 -0.63 -23.71 5.50] 7 A.U7 A.A66 [U-A] WC 20-XX cWW cW-W -133.1(anti) C2'-endo lambda=55.5; -164.9(anti) C3'-endo lambda=53.5 d(C1'-C1')=10.52 d(N1-N9)=8.81 d(C6-C8)=9.76 tor(N1-C1'-C1'-N9)=1.8 H-bonds[2]: "N3(imino)-N1[2.73]; O4(carbonyl)-N6(amino)[2.80]" bp_pars: [-0.01 -0.20 0.02 -3.19 -2.38 0.30] 8 A.U8 A.A14 [U-A] rHoogsteen 24-XXIV tWH tW-M -161.5(anti) C3'-endo lambda=28.3; -170.7(anti) C2'-exo lambda=21.5 d(C1'-C1')=9.63 d(N1-N9)=7.06 d(C6-C8)=6.00 tor(N1-C1'-C1'-N9)=172.3 H-bonds[2]: "O2(carbonyl)-N6(amino)[3.00]; N3(imino)-N7[2.74]" bp_pars: [4.14 -1.91 0.77 -4.62 12.12 -103.09] 9 A.U8 A.A21 [U+A] 00-n/a ... t... -161.5(anti) C3'-endo lambda=111.1; -160.2(anti) C3'-endo lambda=50.1 d(C1'-C1')=8.76 d(N1-N9)=8.70 d(C6-C8)=10.78 tor(N1-C1'-C1'-N9)=158.2 H-bonds[1]: "O2'(hydroxyl)-N1[2.68]" bp_pars: [-1.22 -8.06 -0.19 -9.35 19.04 -117.98] 10 A.A9 A.A23 [A+A] 02-II tHH tM+M -70.5(anti) C2'-endo lambda=14.1; -158.0(anti) C3'-endo lambda=11.5 d(C1'-C1')=10.98 d(N1-N9)=8.14 d(C6-C8)=6.20 tor(N1-C1'-C1'-N9)=153.2 H-bonds[3]: "N7-N6(amino)[2.86]; N6(amino)-OP2[3.12]; N6(amino)-N7[2.92]" bp_pars: [6.12 -5.06 -0.26 -10.73 1.60 177.88] 11 A.2MG10 A.C25 [g-C] WC 19-XIX cWW cW-W 169.6(anti) C3'-endo lambda=52.3; -160.3(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.72 d(N1-N9)=8.99 d(C6-C8)=9.89 tor(N1-C1'-C1'-N9)=-2.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.84]; N1(imino)-N3[2.92]; N2(amino)-O2(carbonyl)[2.92]" bp_pars: [-0.17 -0.11 -0.28 -9.56 -12.57 -0.80] 12 A.2MG10 A.G45 [g+G] 00-n/a cHS cM+m 169.6(anti) C3'-endo lambda=39.8; -149.3(anti) C3'-endo lambda=126.0 d(C1'-C1')=8.65 d(N1-N9)=8.38 d(C6-C8)=8.50 tor(N1-C1'-C1'-N9)=-4.4 H-bonds[1]: "O6(carbonyl)-N2(amino)[3.06]" bp_pars: [-7.21 -0.97 -0.92 25.58 -11.83 13.07] 13 A.C11 A.G24 [C-G] WC 19-XIX cWW cW-W -160.9(anti) C3'-endo lambda=55.8; -160.7(anti) C3'-endo lambda=54.2 d(C1'-C1')=10.54 d(N1-N9)=8.85 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-8.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.70]; N3-N1(imino)[2.82]; N4(amino)-O6(carbonyl)[3.00]" bp_pars: [0.23 -0.18 0.23 -6.25 -17.05 2.13] 14 A.U12 A.A23 [U-A] WC 20-XX cWW cW-W -158.3(anti) C3'-endo lambda=51.6; -158.0(anti) C3'-endo lambda=50.2 d(C1'-C1')=10.93 d(N1-N9)=9.07 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-9.3 H-bonds[2]: "N3(imino)-N1[2.95]; O4(carbonyl)-N6(amino)[2.81]" bp_pars: [-0.14 -0.01 0.19 -10.59 -4.26 -5.88] 15 A.C13 A.G22 [C-G] WC 19-XIX cWW cW-W -168.3(anti) C3'-endo lambda=54.6; -175.5(anti) C2'-exo lambda=54.0 d(C1'-C1')=10.67 d(N1-N9)=8.93 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=-2.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.73]; N3-N1(imino)[2.90]; N4(amino)-O6(carbonyl)[2.88]" bp_pars: [0.25 -0.15 0.00 5.91 1.20 0.48] 16 A.G15 A.C48 [G+C] rWC 22-XXII tWW tW+W -164.5(anti) C3'-endo lambda=35.8; -140.1(anti) C2'-endo lambda=59.9 d(C1'-C1')=10.55 d(N1-N9)=8.88 d(C6-C8)=10.38 tor(N1-C1'-C1'-N9)=-173.4 H-bonds[2]: "N1(imino)-O2(carbonyl)[2.78]; N2(amino)-N3[2.83]" bp_pars: [0.12 3.74 0.17 4.74 -0.97 155.68] 17 A.H2U16 A.U59 [u+U] 00-n/a tSW tm+W -85.8(anti) C3'-endo lambda=57.7; -165.6(anti) C3'-endo lambda=27.5 d(C1'-C1')=7.27 d(N1-N9)=5.51 d(C6-C8)=7.03 tor(N1-C1'-C1'-N9)=-179.6 H-bonds[2]: "O2'(hydroxyl)-O4(carbonyl)[2.89]; N3(imino)-O2(carbonyl)[2.80]" bp_pars: [-2.45 -3.67 0.11 -29.36 -48.29 -141.43] 18 A.G18 A.PSU55 [G+P] 00-n/a tWS tW+m -99.5(anti) C2'-endo lambda=29.1; -147.0(anti) C3'-endo lambda=110.9 d(C1'-C1')=8.69 d(N1-N9)=8.20 d(C6-C8)=9.60 tor(N1-C1'-C1'-N9)=-128.9 H-bonds[2]: "N1(imino)-O4[2.78]; N2(amino)-O4[2.94]" bp_pars: [-0.68 5.63 -0.20 -20.12 -2.80 90.54] 19 A.G19 A.C56 [G-C] WC 19-XIX cWW cW-W -80.3(anti) C2'-endo lambda=58.4; -161.5(anti) C3'-endo lambda=54.5 d(C1'-C1')=10.39 d(N1-N9)=8.79 d(C6-C8)=9.73 tor(N1-C1'-C1'-N9)=-27.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.03]; N1(imino)-N3[2.93]; N2(amino)-O2(carbonyl)[2.82]" bp_pars: [-0.46 -0.05 -0.07 -26.00 -24.90 0.73] 20 A.G22 A.7MG46 [G-g] 07-VII tHW tM-W -175.5(anti) C2'-exo lambda=32.1; -65.8(anti) C2'-endo lambda=29.1 d(C1'-C1')=11.23 d(N1-N9)=8.82 d(C6-C8)=7.59 tor(N1-C1'-C1'-N9)=179.6 H-bonds[2]: "N7-N1(imino)[2.87]; O6(carbonyl)-N2(amino)[2.99]" bp_pars: [-5.64 -0.35 -0.08 0.34 9.58 -114.56] 21 A.M2G26 A.A44 [g-A] Imino 08-VIII cWW cW-W -163.4(anti) C3'-endo lambda=44.8; -159.4(anti) C3'-endo lambda=49.7 d(C1'-C1')=12.58 d(N1-N9)=10.61 d(C6-C8)=11.01 tor(N1-C1'-C1'-N9)=-21.8 H-bonds[2]: "O6(carbonyl)-N6(amino)[2.84]; N1(imino)-N1[2.87]" bp_pars: [-0.31 1.43 -0.30 22.18 -34.08 -17.60] 22 A.C27 A.G43 [C-G] WC 19-XIX cWW cW-W -168.2(anti) C3'-endo lambda=51.5; -160.2(anti) C3'-endo lambda=52.4 d(C1'-C1')=10.83 d(N1-N9)=9.03 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=-18.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.02]; N3-N1(imino)[2.98]; N4(amino)-O6(carbonyl)[2.92]" bp_pars: [0.16 -0.12 0.37 6.67 -17.68 -4.27] 23 A.C28 A.G42 [C-G] WC 19-XIX cWW cW-W -160.6(anti) C3'-endo lambda=55.1; -169.0(anti) C3'-endo lambda=56.9 d(C1'-C1')=10.67 d(N1-N9)=9.02 d(C6-C8)=10.02 tor(N1-C1'-C1'-N9)=-10.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.77]; N3-N1(imino)[2.98]; N4(amino)-O6(carbonyl)[3.15]" bp_pars: [0.15 -0.02 0.37 2.46 -10.66 2.46] 24 A.A29 A.U41 [A-U] WC 20-XX cWW cW-W -165.9(anti) C3'-endo lambda=59.3; -169.0(anti) C3'-endo lambda=53.9 d(C1'-C1')=10.48 d(N1-N9)=8.87 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-5.5 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.06]; N1-N3(imino)[2.87]" bp_pars: [0.36 -0.06 -0.01 2.36 -9.48 2.56] 25 A.G30 A.5MC40 [G-c] WC 19-XIX cWW cW-W -171.7(anti) C3'-endo lambda=57.1; -162.6(anti) C3'-endo lambda=59.0 d(C1'-C1')=10.53 d(N1-N9)=8.98 d(C6-C8)=10.06 tor(N1-C1'-C1'-N9)=-9.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.36]; N1(imino)-N3[3.05]; N2(amino)-O2(carbonyl)[2.69]" bp_pars: [-0.43 0.11 -0.04 -15.02 -18.34 7.48] 26 A.A31 A.PSU39 [A-P] 00-n/a ... c... -156.7(anti) C3'-endo lambda=84.4; -165.6(anti) C3'-endo lambda=38.0 d(C1'-C1')=10.71 d(N1-N9)=9.39 d(C6-C8)=10.53 tor(N1-C1'-C1'-N9)=-2.4 H-bonds[1]: "N1*O2[3.18]" bp_pars: [4.28 -0.21 -0.11 -17.90 -8.14 13.00] 27 A.OMC32 A.A38 [c-A] 00-n/a c.. c.-. -149.9(anti) C3'-endo lambda=99.5; -169.4(anti) C3'-endo lambda=22.2 d(C1'-C1')=10.81 d(N1-N9)=9.74 d(C6-C8)=10.61 tor(N1-C1'-C1'-N9)=2.9 H-bonds[1]: "O2(carbonyl)-N6(amino)[3.01]" bp_pars: [6.79 -1.66 0.71 -5.43 9.64 16.62] 28 A.U33 A.A36 [U-A] 00-n/a ... t... -148.2(anti) C3'-endo lambda=94.1; -158.4(anti) C4'-exo lambda=39.2 d(C1'-C1')=6.74 d(N1-N9)=6.18 d(C6-C8)=6.17 tor(N1-C1'-C1'-N9)=-159.7 H-bonds[1]: "N3(imino)-OP2[2.80]" bp_pars: [6.01 -9.48 1.18 12.36 20.63 -53.95] 29 A.5MC49 A.G65 [c-G] WC 19-XIX cWW cW-W -173.6(anti) C3'-endo lambda=56.4; -172.8(anti) C3'-endo lambda=54.8 d(C1'-C1')=10.77 d(N1-N9)=9.10 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-2.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.92]; N3-N1(imino)[3.04]; N4(amino)-O6(carbonyl)[3.01]" bp_pars: [0.27 0.02 0.04 1.61 -11.93 0.87] 30 A.U50 A.A64 [U-A] WC 20-XX cWW cW-W -165.3(anti) C3'-endo lambda=54.3; -161.8(anti) C3'-endo lambda=54.7 d(C1'-C1')=10.60 d(N1-N9)=8.89 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-4.6 H-bonds[2]: "N3(imino)-N1[2.79]; O4(carbonyl)-N6(amino)[2.81]" bp_pars: [-0.13 -0.17 -0.11 -1.83 -6.15 -2.40] 31 A.G51 A.C63 [G-C] WC 19-XIX cWW cW-W -156.6(anti) C3'-endo lambda=55.2; -152.6(anti) C3'-endo lambda=55.8 d(C1'-C1')=10.58 d(N1-N9)=8.90 d(C6-C8)=9.88 tor(N1-C1'-C1'-N9)=-5.4 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.89]; N1(imino)-N3[2.80]; N2(amino)-O2(carbonyl)[2.74]" bp_pars: [-0.14 -0.17 -0.26 -6.20 -13.77 2.27] 32 A.U52 A.A62 [U-A] WC 20-XX cWW cW-W -164.0(anti) C3'-endo lambda=55.1; -158.7(anti) C3'-endo lambda=55.6 d(C1'-C1')=10.55 d(N1-N9)=8.87 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-10.1 H-bonds[2]: "N3(imino)-N1[2.82]; O4(carbonyl)-N6(amino)[2.96]" bp_pars: [-0.27 -0.09 0.03 -1.47 -10.84 2.55] 33 A.G53 A.C61 [G-C] WC 19-XIX cWW cW-W -169.2(anti) C3'-endo lambda=54.7; -166.7(anti) C3'-endo lambda=54.3 d(C1'-C1')=10.63 d(N1-N9)=8.92 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=-5.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.95]; N1(imino)-N3[2.87]; N2(amino)-O2(carbonyl)[2.80]" bp_pars: [-0.28 -0.15 -0.14 -10.86 -9.92 0.24] 34 A.5MU54 A.1MA58 [u-a] rHoogsteen 24-XXIV tWH tW-M -161.5(anti) C3'-endo lambda=28.0; -86.3(anti) C2'-endo lambda=22.3 d(C1'-C1')=9.83 d(N1-N9)=7.27 d(C6-C8)=6.20 tor(N1-C1'-C1'-N9)=178.2 H-bonds[2]: "N3(imino)-N7[2.92]; O2(carbonyl)-N6(amino)[3.25]" bp_pars: [4.21 -1.63 0.24 -5.07 6.43 -103.97] **************************************************************************** List of 4 multiplet(s) 1 nts=3 A.U8+A.A14+A.A21 [UAA] 2 nts=3 A.A9+A.U12+A.A23 [AUA] 3 nts=3 A.2MG10+A.C25+A.G45 [gCG] 4 nts=3 A.C13+A.G22+A.7MG46 [CGg] **************************************************************************** List of 2 helices helix=1[2] bps=15 1 A.G1 A.C72 [G-C] WC 19-XIX cWW cW-W 2 A.C2 A.G71 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C70 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.U69 [G-U] Wobble 28-XXVIII cWW cW-W 5 A.A5 A.U68 [A-U] WC 20-XX cWW cW-W 6 A.U6 A.A67 [U-A] WC 20-XX cWW cW-W 7 A.U7 A.A66 [U-A] WC 20-XX cWW cW-W 8 A.5MC49 A.G65 [c-G] WC 19-XIX cWW cW-W 9 A.U50 A.A64 [U-A] WC 20-XX cWW cW-W 10 A.G51 A.C63 [G-C] WC 19-XIX cWW cW-W 11 A.U52 A.A62 [U-A] WC 20-XX cWW cW-W 12 A.G53 A.C61 [G-C] WC 19-XIX cWW cW-W 13 A.5MU54 A.1MA58 [u-a] rHoogsteen 24-XXIV tWH tW-M 14 A.PSU55 A.G18 [P+G] 00-n/a tSW tm+W 15 A.C56 A.G19 [C-G] WC 19-XIX cWW cW-W helix=2[2] bps=15 1 A.A36 A.U33 [A-U] 00-n/a ... t... 2 A.A38 A.OMC32 [A-c] 00-n/a c.. c.-. 3 A.PSU39 A.A31 [P-A] 00-n/a ... c... 4 A.5MC40 A.G30 [c-G] WC 19-XIX cWW cW-W 5 A.U41 A.A29 [U-A] WC 20-XX cWW cW-W 6 A.G42 A.C28 [G-C] WC 19-XIX cWW cW-W 7 A.G43 A.C27 [G-C] WC 19-XIX cWW cW-W 8 A.A44 A.M2G26 [A-g] Imino 08-VIII cWW cW-W 9 A.2MG10 A.C25 [g-C] WC 19-XIX cWW cW-W 10 A.C11 A.G24 [C-G] WC 19-XIX cWW cW-W 11 A.U12 A.A23 [U-A] WC 20-XX cWW cW-W 12 A.C13 A.G22 [C-G] WC 19-XIX cWW cW-W 13 A.A14 A.U8 [A-U] rHoogsteen 24-XXIV tHW tM-W 14 A.G15 A.C48 [G+C] rWC 22-XXII tWW tW+W 15 A.H2U16 A.U59 [u+U] 00-n/a tSW tm+W **************************************************************************** List of 4 stems stem=1[#1] bps=7 1 A.G1 A.C72 [G-C] WC 19-XIX cWW cW-W 2 A.C2 A.G71 [C-G] WC 19-XIX cWW cW-W 3 A.G3 A.C70 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.U69 [G-U] Wobble 28-XXVIII cWW cW-W 5 A.A5 A.U68 [A-U] WC 20-XX cWW cW-W 6 A.U6 A.A67 [U-A] WC 20-XX cWW cW-W 7 A.U7 A.A66 [U-A] WC 20-XX cWW cW-W stem=2[#2] bps=4 1 A.2MG10 A.C25 [g-C] WC 19-XIX cWW cW-W 2 A.C11 A.G24 [C-G] WC 19-XIX cWW cW-W 3 A.U12 A.A23 [U-A] WC 20-XX cWW cW-W 4 A.C13 A.G22 [C-G] WC 19-XIX cWW cW-W stem=3[#2] bps=4 1 A.C27 A.G43 [C-G] WC 19-XIX cWW cW-W 2 A.C28 A.G42 [C-G] WC 19-XIX cWW cW-W 3 A.A29 A.U41 [A-U] WC 20-XX cWW cW-W 4 A.G30 A.5MC40 [G-c] WC 19-XIX cWW cW-W stem=4[#1] bps=5 1 A.5MC49 A.G65 [c-G] WC 19-XIX cWW cW-W 2 A.U50 A.A64 [U-A] WC 20-XX cWW cW-W 3 A.G51 A.C63 [G-C] WC 19-XIX cWW cW-W 4 A.U52 A.A62 [U-A] WC 20-XX cWW cW-W 5 A.G53 A.C61 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 1 lone WC/wobble pair(s) -1 A.G19 A.C56 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 2 coaxial stack(s) 1 Helix#1 contains 2 stems: [#1, #4] 2 Helix#2 contains 2 stems: [#2, #3] **************************************************************************** List of 3 hairpin loop(s) 1 nts=8 AGuuGGGA closed by pair {A.C13+A.G22 [CG], #2} A.C13+A.A14+A.G15+A.H2U16+A.H2U17+A.G18+A.G19+A.G20+A.A21+A.G22 [CAGuuGGGAG] 2 nts=9 AcUgAAgAP closed by pair {A.G30+A.5MC40 [Gc], #3} A.G30+A.A31+A.OMC32+A.U33+A.OMG34+A.A35+A.A36+A.YYG37+A.A38+A.PSU39+A.5MC40 [GAcUgAAgAPc] 3 nts=7 uPCGaUC closed by pair {A.G53+A.C61 [GC], #4} A.G53+A.5MU54+A.PSU55+A.C56+A.G57+A.1MA58+A.U59+A.C60+A.C61 [GuPCGaUCC] **************************************************************************** List of 1 junction(s) 1 4-way junctions: 16 nts; [2x1x5x0]; linked by [#1, #2, #3, #4] A.U7+A.U8+A.A9+A.2MG10+A.C25+A.M2G26+A.C27+A.G43+A.A44+A.G45+A.7MG46+A.U47+A.C48+A.5MC49+A.G65+A.A66 [UUAgCgCGAGgUCcGA] This structure contains pseudo-knot(s). **************************************************************************** >chain-A #1 RNA with 76 nts GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAPcUGGAGgUCcUGUGuPCGaUCCACAGAAUUCGCACCA (((((((..((((.....[..)))).((((.........)))).....(((((..]....)))))))))))).... DONE!