**************************************************************************** File name: 7s9j.pdb no. of DNA/RNA chains: 3 [D=5,P=10,T=16] no. of nucleotides: 31 no. of atoms: 3694 no. of waters: 464 no. of metals: 4 [Na=4] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 8NI-u 1 T.8NI13 **************************************************************************** List of 15 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W 6 T.DG7 P.DC10 G-C WC 19-XIX cWW cW-W 7 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 8 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 9 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 10 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 11 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 12 T.8NI13 P.DC4 u+C -- -- cSW cm+W 13 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 14 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 15 T.DC16 P.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 helices Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[1] bps=5 strand-1 5'-CCGAC-3' bp-type ||||| strand-2 3'-GGCTG-5' helix-form BBBB 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[2] bps=10 strand-1 5'-GCGCATuAGC-3' bp-type ||||||.||| strand-2 3'-CGCGTACTCG-5' helix-form BBBBB..B. 1 T.DG7 P.DC10 G-C WC 19-XIX cWW cW-W 2 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 3 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 4 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 5 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 6 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 7 T.8NI13 P.DC4 u+C -- -- cSW cm+W 8 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 9 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 10 T.DC16 P.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 3 stems Note: A stem is defined as a helix consisting strictly of canonical WC/wobble pairs with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=5 strand-1 5'-CCGAC-3' bp-type ||||| strand-2 3'-GGCTG-5' helix-form BBBB 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=6 strand-1 5'-GCGCAT-3' bp-type |||||| strand-2 3'-CGCGTA-5' helix-form BBBBB 1 T.DG7 P.DC10 G-C WC 19-XIX cWW cW-W 2 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 3 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 4 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 5 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 6 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=3 strand-1 5'-AGC-3' bp-type ||| strand-2 3'-TCG-5' helix-form B. 1 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 2 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 3 T.DC16 P.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#2 contains 2 stems: [#2,#3] **************************************************************************** List of 4 base stacks Note: A stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 HC A.HIS34,T.DC5 2 nts=2 GG T.DG6,T.DG7 3 nts=3 TuA T.DT12,T.8NI13,T.DA14 4 nts=3 TCA P.DT3,P.DC4,P.DA5 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 1 internal loop 1 symmetric internal loop: nts=6; [1,1]; linked by [#2,#3] summary: [2] 1 1 [T.12 P.5 T.14 P.3] 6 3 nts=6 TuATCA T.DT12,T.8NI13,T.DA14,P.DT3,P.DC4,P.DA5 nts=1 u T.8NI13 nts=1 C P.DC4 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=1 G T.DG6 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DC5 T.DG6 angle=139 distance=17.1 ratio=0.94 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 CG T.DC5,T.DG6 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7s9j nts=31 [whole] CCGACGGCGCATuAGC&GCTCATGCGC>CGG (((((.((((((.(((&))).))))))&))))) >7s9j-T #1 nts=16 2.52(1.46) [chain] DNA CCGACGGCGCATuAGC (((((.((((((.((( >7s9j-P #2 nts=10 3.55(0.37) [chain] DNA GCTCATGCGC ))).)))))) >7s9j-D #3 nts=5 4.23(0.24) [chain] DNA GTCGG ))))) **************************************************************************** Summary of structural features of 31 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 C ( T.DC1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( T.DC2 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 3 G ( T.DG3 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 A ( T.DA4 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 C ( T.DC5 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 6 G . T.DG6 0.007 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 7 G ( T.DG7 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 8 C ( T.DC8 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 9 G ( T.DG9 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 C ( T.DC10 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 11 A ( T.DA11 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 12 T ( T.DT12 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 13 u . T.8NI13 0.059 modified,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop 14 A ( T.DA14 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 15 G ( T.DG15 0.025 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 16 C ( T.DC16 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 17 G ) P.DG1 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 18 C ) P.DC2 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 T ) P.DT3 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 20 C . P.DC4 0.007 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,internal-loop 21 A ) P.DA5 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 22 T ) P.DT6 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 G ) P.DG7 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 C ) P.DC8 0.010 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 25 G ) P.DG9 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 26 C ) P.DC10 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 27 G ) D.DG1 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 28 T ) D.DT2 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 29 C ) D.DC3 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 30 G ) D.DG4 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 31 G ) D.DG5 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 14 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-stems.pdb -- an ensemble of stems 3 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 4 dssr-iloops.pdb -- an ensemble of internal loops 5 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 6 dssr-2ndstrs.ct -- secondary structure in connectivity table format 7 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 8 dssr-torsions.txt -- backbone torsion angles and suite names 9 dssr-splays.pdb -- an ensemble of splayed-apart units 10 dssr-stacks.pdb -- an ensemble of base stacks 11 dssr-rotmat.txt -- position vector and rotation matrix 12 dssr-viewV.pdb -- vertical view of the principal moment of inertia 13 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 14 dssr-viewT.pdb -- top view of the principal moment of inertia