# 3q50.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 Jan 19 11:57:20 2024 File name: 3q50.pdb no. of DNA/RNA chains: 1 [A=34] no. of nucleotides: 34 no. of waters: 1 no. of metals: 0 **************************************************************************** List of 21 base pair(s) 1 A.C1 A.G20 [C-G] WC 19-XIX cWW cW-W -164.1(anti) C3'-endo lambda=56.4; -133.3(anti) C2'-endo lambda=52.1 d(C1'-C1')=10.70 d(N1-N9)=8.99 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-3.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.87]; N3-N1(imino)[2.94]; N4(amino)-O6(carbonyl)[2.94]" bp_pars: [0.30 -0.12 -0.09 0.92 -3.09 0.04] 2 A.U2 A.A19 [U-A] WC 20-XX cWW cW-W -163.8(anti) C3'-endo lambda=56.5; -171.6(anti) C3'-endo lambda=55.2 d(C1'-C1')=10.61 d(N1-N9)=8.96 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=-12.4 H-bonds[2]: "N3(imino)-N1[2.84]; O4(carbonyl)-N6(amino)[2.98]" bp_pars: [-0.18 -0.07 0.25 -0.29 -15.71 -0.26] 3 A.G3 A.C18 [G-C] WC 19-XIX cWW cW-W -158.4(anti) C3'-endo lambda=52.0; -161.3(anti) C3'-endo lambda=51.2 d(C1'-C1')=10.77 d(N1-N9)=8.95 d(C6-C8)=9.81 tor(N1-C1'-C1'-N9)=-9.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.74]; N1(imino)-N3[2.82]; N2(amino)-O2(carbonyl)[2.79]" bp_pars: [0.18 -0.19 0.22 -10.53 -12.32 -3.66] 4 A.G4 A.C17 [G-C] WC 19-XIX cWW cW-W -178.1(anti) C3'-endo lambda=53.1; -157.4(anti) C3'-endo lambda=52.8 d(C1'-C1')=10.61 d(N1-N9)=8.83 d(C6-C8)=9.76 tor(N1-C1'-C1'-N9)=-9.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.83]; N1(imino)-N3[2.78]; N2(amino)-O2(carbonyl)[2.64]" bp_pars: [-0.07 -0.25 0.30 -6.43 -8.16 -0.20] 5 A.G5 A.C16 [G-C] WC 19-XIX cWW cW-W -154.1(anti) C3'-endo lambda=53.6; -164.7(anti) C3'-endo lambda=52.7 d(C1'-C1')=10.67 d(N1-N9)=8.91 d(C6-C8)=9.80 tor(N1-C1'-C1'-N9)=-10.2 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.77]; N1(imino)-N3[2.81]; N2(amino)-O2(carbonyl)[2.87]" bp_pars: [0.00 -0.20 -0.12 -7.31 -10.94 -2.11] 6 A.G5 A.A27 [G+A] 00-n/a tSW tm+W -154.1(anti) C3'-endo lambda=118.6; -148.3(anti) C3'-endo lambda=10.9 d(C1'-C1')=9.48 d(N1-N9)=8.86 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=119.0 H-bonds[3]: "O2'(hydroxyl)-N6(amino)[2.60]; N2(amino)-N1[3.06]; N3-N6(amino)[3.22]" bp_pars: [3.34 -4.17 0.16 -11.98 10.57 -69.14] 7 A.U6 A.A28 [U+A] Hoogsteen 23-XXIII cWH cW+M -159.7(anti) C3'-endo lambda=64.1; -90.2(anti) C2'-endo lambda=47.2 d(C1'-C1')=8.43 d(N1-N9)=6.82 d(C6-C8)=6.36 tor(N1-C1'-C1'-N9)=-18.1 H-bonds[2]: "N3(imino)-N7[2.92]; O4(carbonyl)-N6(amino)[3.33]" bp_pars: [-0.21 3.47 1.19 -27.58 -18.29 -65.74] 8 A.C7 A.G11 [C-G] 00-n/a tWH tW-M -162.8(anti) C3'-endo lambda=28.3; -70.0(anti) C2'-endo lambda=6.3 d(C1'-C1')=11.22 d(N1-N9)=8.52 d(C6-C8)=7.60 tor(N1-C1'-C1'-N9)=166.3 H-bonds[2]: "N3*O6(carbonyl)[2.88]; N4(amino)-N7[3.35]" bp_pars: [3.13 -0.52 -0.29 0.42 1.19 -84.20] 9 A.C7 A.A29 [C+A] 00-n/a c.H c.+M -162.8(anti) C3'-endo lambda=113.0; -162.8(anti) C3'-endo lambda=24.6 d(C1'-C1')=8.77 d(N1-N9)=8.04 d(C6-C8)=8.25 tor(N1-C1'-C1'-N9)=-4.5 H-bonds[1]: "O2(carbonyl)-N6(amino)[3.26]" bp_pars: [4.84 0.06 2.06 -21.80 14.25 -40.68] 10 A.C7 A.C30 [C+C] 00-n/a tW. cW+. -162.8(anti) C3'-endo lambda=87.0; -165.1(anti) C3'-endo lambda=18.2 d(C1'-C1')=10.45 d(N1-N9)=9.06 d(C6-C8)=9.78 tor(N1-C1'-C1'-N9)=55.3 H-bonds[1]: "O2(carbonyl)-N4(amino)[3.26]" bp_pars: [2.79 -0.59 -1.05 -12.57 13.06 -84.98] 11 A.G8 A.A31 [G+A] 00-n/a tSW tm+W -163.4(anti) C3'-endo lambda=116.7; -158.4(anti) C3'-endo lambda=6.4 d(C1'-C1')=9.80 d(N1-N9)=9.12 d(C6-C8)=9.99 tor(N1-C1'-C1'-N9)=-178.0 H-bonds[2]: "N2(amino)-N1[3.31]; N3-N6(amino)[3.35]" bp_pars: [3.79 -3.97 -0.80 18.81 12.18 -66.73] 12 A.C9 A.G33 [C-G] WC 19-XIX cWW cW-W -177.8(anti) C3'-endo lambda=48.8; -179.2(anti) C3'-endo lambda=55.5 d(C1'-C1')=10.81 d(N1-N9)=9.02 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-6.0 H-bonds[4]: "O2(carbonyl)-N2(amino)[2.96]; N3-N1(imino)[2.87]; N3-N2(amino)[2.92]; N4(amino)-O6(carbonyl)[2.75]" bp_pars: [-0.93 -0.21 0.13 3.92 -6.06 -5.74] 13 A.A10 A.A32 [A-A] 00-n/a tSH cm-M -164.7(anti) C3'-endo lambda=82.7; -151.0(anti) C3'-endo lambda=4.4 d(C1'-C1')=10.00 d(N1-N9)=8.45 d(C6-C8)=8.67 tor(N1-C1'-C1'-N9)=17.8 H-bonds[2]: "O2'(hydroxyl)-N6(amino)[3.18]; N3-N6(amino)[2.89]" bp_pars: [6.33 -3.81 -0.77 -6.64 -18.63 -17.16] 14 A.G11 A.A14 [G+A] 00-n/a tSW cm+W -70.0(anti) C2'-endo lambda=115.7; 178.6(anti) C3'-endo lambda=1.1 d(C1'-C1')=9.27 d(N1-N9)=8.52 d(C6-C8)=9.27 tor(N1-C1'-C1'-N9)=-36.2 H-bonds[3]: "O4'-N6(amino)[3.31]; N2(amino)-N1[2.85]; N3-N6(amino)[2.67]" bp_pars: [3.57 -3.50 0.74 -13.75 -9.93 -61.87] 15 A.G11 A.C30 [G-C] WC 19-XIX cWW cW-W -70.0(anti) C2'-endo lambda=51.1; -165.1(anti) C3'-endo lambda=54.4 d(C1'-C1')=10.65 d(N1-N9)=8.88 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=-15.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.05]; N1(imino)-N3[2.83]; N2(amino)-O2(carbonyl)[2.64]" bp_pars: [-0.22 -0.20 0.50 -1.67 -17.53 0.60] 16 A.A13 A.A31 [A-A] 00-n/a c.S c.-m -168.5(anti) C3'-endo lambda=32.1; -158.4(anti) C3'-endo lambda=120.6 d(C1'-C1')=9.54 d(N1-N9)=9.04 d(C6-C8)=10.24 tor(N1-C1'-C1'-N9)=22.0 H-bonds[2]: "N6(amino)-N3[3.03]; N1-O2'(hydroxyl)[3.07]" bp_pars: [-6.58 -0.87 -0.85 23.97 16.51 45.95] 17 A.C15 A.PRF34 [C-g] WC 19-XIX .WW tW-W -166.1(anti) C3'-endo lambda=n/a; n/a(n/a) n/a lambda=n/a d(C1'-C1')=n/a d(N1-N9)=9.00 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=n/a H-bonds[3]: "O2(carbonyl)-N2(amino)[3.21]; N3-N1(imino)[2.89]; N4(amino)-O6(carbonyl)[2.70]" bp_pars: [0.50 -0.18 -0.46 19.59 -8.85 -7.86] 18 A.C16 A.A28 [C-A] 00-n/a cSW cm-W -164.7(anti) C3'-endo lambda=128.0; -90.2(anti) C2'-endo lambda=36.8 d(C1'-C1')=9.25 d(N1-N9)=8.99 d(C6-C8)=10.32 tor(N1-C1'-C1'-N9)=6.7 H-bonds[2]: "O2'(hydroxyl)-N1[2.76]; O2(carbonyl)-N6(amino)[2.89]" bp_pars: [6.74 -0.79 0.01 -21.43 4.43 54.01] 19 A.C17 A.A26 [C-A] 00-n/a cSW cm-W -157.4(anti) C3'-endo lambda=129.4; -175.8(anti) C3'-endo lambda=31.8 d(C1'-C1')=9.30 d(N1-N9)=9.00 d(C6-C8)=10.27 tor(N1-C1'-C1'-N9)=-8.3 H-bonds[2]: "O2'(hydroxyl)-N1[2.73]; O2(carbonyl)-N6(amino)[2.91]" bp_pars: [7.17 -1.45 -0.25 -7.50 -3.94 53.17] 20 A.G20 A.U21 [G+U] Platform 00-n/a cSH cm+M -133.3(anti) C2'-endo lambda=130.7; -137.1(anti) C2'-endo lambda=61.5 d(C1'-C1')=6.60 d(N1-N9)=6.91 d(C6-C8)=7.07 tor(N1-C1'-C1'-N9)=42.1 H-bonds[1]: "N2(amino)-O4(carbonyl)[3.17]" bp_pars: [7.56 2.21 -1.75 1.91 42.86 12.88] 21 A.A29 A.PRF34 [A+g] 00-n/a .WS tW+m -162.8(anti) C3'-endo lambda=n/a; n/a(n/a) n/a lambda=n/a d(C1'-C1')=n/a d(N1-N9)=9.03 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=n/a H-bonds[2]: "N6(amino)-N3[3.13]; N1-N2(amino)[2.67]" bp_pars: [-3.34 3.78 -0.28 27.00 -9.98 72.29] **************************************************************************** List of 6 multiplet(s) 1 nts=3 A.C1+A.G20+A.U21 [CGU] 2 nts=3 A.G4+A.C17+A.A26 [GCA] 3 nts=3 A.G8+A.A13+A.A31 [GAA] 4 nts=3 A.C15+A.A29+A.PRF34 [CAg] 5 nts=4 A.G5+A.C16+A.A27+A.A28 [GCAA] 6 nts=4 A.C7+A.G11+A.A14+A.C30 [CGAC] **************************************************************************** List of 2 helices helix=1[1] bps=5 1 A.C1 A.G20 [C-G] WC 19-XIX cWW cW-W 2 A.U2 A.A19 [U-A] WC 20-XX cWW cW-W 3 A.G3 A.C18 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C17 [G-C] WC 19-XIX cWW cW-W 5 A.G5 A.C16 [G-C] WC 19-XIX cWW cW-W helix=2[0] bps=6 1 A.U6 A.A28 [U+A] Hoogsteen 23-XXIII cWH cW+M 2 A.A29 A.C7 [A+C] 00-n/a cH. cM+. 3 A.C30 A.G11 [C-G] WC 19-XIX cWW cW-W 4 A.A31 A.G8 [A+G] 00-n/a tWS tW+m 5 A.A32 A.A10 [A-A] 00-n/a tHS cM-m 6 A.G33 A.C9 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 1 stem stem=1[#1] bps=5 1 A.C1 A.G20 [C-G] WC 19-XIX cWW cW-W 2 A.U2 A.A19 [U-A] WC 20-XX cWW cW-W 3 A.G3 A.C18 [G-C] WC 19-XIX cWW cW-W 4 A.G4 A.C17 [G-C] WC 19-XIX cWW cW-W 5 A.G5 A.C16 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 3 lone WC/wobble pair(s) -1 A.C9 A.G33 [C-G] WC 19-XIX cWW cW-W -2 A.G11 A.C30 [G-C] WC 19-XIX cWW cW-W -3 A.C15 A.PRF34 [C-g] WC 19-XIX .WW tW-W **************************************************************************** List of 2 hairpin loop(s) 1 nts=10 UCGCAGUAAC closed by pair {A.G5+A.C16 [GC], #1} A.G5+A.U6+A.C7+A.G8+A.C9+A.A10+A.G11+A.U12+A.A13+A.A14+A.C15+A.C16 [GUCGCAGUAACC] 2 nts=18 UAACCCCAGUUAACAAAA closed by pair {A.G11+A.C30 [GC], #-2} A.G11+A.U12+A.A13+A.A14+A.C15+A.C16+A.C17+A.C18+A.A19+A.G20+A.U21+A.U22+A.A23+A.A24+A.C25+A.A26+A.A27+A.A28+A.A29+A.C30 [GUAACCCCAGUUAACAAAAC] **************************************************************************** List of 1 internal loop(s) 1 asymmetric internal loop: 7 nts; [1x2]; linked by [#-1, #-2] A.C9+A.A10+A.G11+A.C30+A.A31+A.A32+A.G33 [CAGCAAG] This structure contains pseudo-knot(s). **************************************************************************** List of 1 A-minor motif(s) 1 type=I A/U-A A.A23 vs A.U2+A.A19 [WC] +A.U2 H-bonds[1]: "N1-O2'(hydroxyl)[2.79]" -A.A19 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.53]; O2'(hydroxyl)-N3[2.86]" **************************************************************************** >chain-A #1 RNA[33]/1* with 34 nts CUGGGUCGCAGUAACCCCAGUUAACAAAACAAGg (((((...[.[...[))))).........]..]] DONE!