**************************************************************************** File name: 5o7t.pdb no. of DNA/RNA chains: 2 [B=12,C=16] no. of nucleotides: 29 no. of atoms: 9842 no. of waters: 265 no. of metals: 3 [Mg=3] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 DCP-c 1 A.DCP903 2 DDG-g 1 B.DDG112 **************************************************************************** List of 13 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DG101 C.DC216 G-C WC 19-XIX cWW cW-W 2 B.DA102 C.DT215 A-T WC 20-XX cWW cW-W 3 B.DC103 C.DG214 C-G WC 19-XIX cWW cW-W 4 B.DC104 C.DG213 C-G WC 19-XIX cWW cW-W 5 B.DA105 C.DT212 A-T WC 20-XX cWW cW-W 6 B.DC106 C.DG211 C-G WC 19-XIX cWW cW-W 7 B.DG107 C.DC210 G-C WC 19-XIX cWW cW-W 8 B.DG108 C.DC209 G-C WC 19-XIX cWW cW-W 9 B.DC109 C.DG208 C-G WC 19-XIX cWW cW-W 10 B.DG110 C.DC207 G-C WC 19-XIX cWW cW-W 11 B.DC111 C.DG206 C-G WC 19-XIX cWW cW-W 12 B.DDG112 C.DC205 g-C WC 19-XIX cWW cW-W 13 C.DG204 A.DCP903 G-c WC 19-XIX cWW cW-W **************************************************************************** List of 1 helix 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=13 strand-1 5'-GACCACGGCGCgc-3' bp-type ||||||||||||| strand-2 3'-CTGGTGCCGCGCG-5' helix-form B.BBBBB.B..x 1 B.DG101 C.DC216 G-C WC 19-XIX cWW cW-W 2 B.DA102 C.DT215 A-T WC 20-XX cWW cW-W 3 B.DC103 C.DG214 C-G WC 19-XIX cWW cW-W 4 B.DC104 C.DG213 C-G WC 19-XIX cWW cW-W 5 B.DA105 C.DT212 A-T WC 20-XX cWW cW-W 6 B.DC106 C.DG211 C-G WC 19-XIX cWW cW-W 7 B.DG107 C.DC210 G-C WC 19-XIX cWW cW-W 8 B.DG108 C.DC209 G-C WC 19-XIX cWW cW-W 9 B.DC109 C.DG208 C-G WC 19-XIX cWW cW-W 10 B.DG110 C.DC207 G-C WC 19-XIX cWW cW-W 11 B.DC111 C.DG206 C-G WC 19-XIX cWW cW-W 12 B.DDG112 C.DC205 g-C WC 19-XIX cWW cW-W 13 A.DCP903 C.DG204 c-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 stem 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=12 strand-1 5'-GACCACGGCGCg-3' bp-type |||||||||||| strand-2 3'-CTGGTGCCGCGC-5' helix-form B.BBBBB.B.. 1 B.DG101 C.DC216 G-C WC 19-XIX cWW cW-W 2 B.DA102 C.DT215 A-T WC 20-XX cWW cW-W 3 B.DC103 C.DG214 C-G WC 19-XIX cWW cW-W 4 B.DC104 C.DG213 C-G WC 19-XIX cWW cW-W 5 B.DA105 C.DT212 A-T WC 20-XX cWW cW-W 6 B.DC106 C.DG211 C-G WC 19-XIX cWW cW-W 7 B.DG107 C.DC210 G-C WC 19-XIX cWW cW-W 8 B.DG108 C.DC209 G-C WC 19-XIX cWW cW-W 9 B.DC109 C.DG208 C-G WC 19-XIX cWW cW-W 10 B.DG110 C.DC207 G-C WC 19-XIX cWW cW-W 11 B.DC111 C.DG206 C-G WC 19-XIX cWW cW-W 12 B.DDG112 C.DC205 g-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#1] -1 C.DG204 A.DCP903 G-c WC 19-XIX cWW cW-W **************************************************************************** List of 3 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 AA C.DA201,C.DA202 2 nts=2 GC C.DG204,C.DC205 3 nts=3 Fcg A.PHE667,A.DCP903,B.DDG112 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 A C.DA203 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=3 AAA C.DA201,C.DA202,C.DA203 **************************************************************************** List of 2 splayed-apart dinucleotides 1 C.DA202 C.DA203 angle=100 distance=14.5 ratio=0.77 2 C.DA203 C.DG204 angle=118 distance=16.7 ratio=0.86 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=3 AAG C.DA202,C.DA203,C.DG204 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5o7t nts=29 [whole] GACCACGGCGCg&AAAGCGCGCCGTGGTC&c ((((((((((((&....))))))))))))&. >5o7t-B #1 nts=12 3.19(0.48) [chain] DNA GACCACGGCGCg (((((((((((( >5o7t-C #2 nts=16 2.18(1.99) [chain] DNA AAAGCGCGCCGTGGTC ....)))))))))))) **************************************************************************** Summary of structural features of 29 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 G ( B.DG101 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 A ( B.DA102 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 3 C ( B.DC103 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 C ( B.DC104 0.018 anti,BI,canonical,non-pair-contact,helix,stem 5 A ( B.DA105 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 C ( B.DC106 0.017 anti,BI,canonical,non-pair-contact,helix,stem 7 G ( B.DG107 0.026 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 G ( B.DG108 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 9 C ( B.DC109 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 10 G ( B.DG110 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 C ( B.DC111 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 g ( B.DDG112 0.030 modified,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,phosphate 13 A . C.DA201 0.007 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 14 A . C.DA202 0.016 syn,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 15 A . C.DA203 0.006 anti,~C3'-endo,BI,non-stack,ss-non-loop,splayed-apart 16 G . C.DG204 0.017 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,phosphate,splayed-apart 17 C ) C.DC205 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 18 G ) C.DG206 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 19 C ) C.DC207 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 20 G ) C.DG208 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 21 C ) C.DC209 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 22 C ) C.DC210 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 23 G ) C.DG211 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 T ) C.DT212 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ) C.DG213 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 G ) C.DG214 0.016 anti,BI,canonical,non-pair-contact,helix,stem 27 T ) C.DT215 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 C ) C.DC216 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 29 c . A.DCP903 0.010 modified,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end **************************************************************************** List of 13 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-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks 10 dssr-rotmat.txt -- position vector and rotation matrix 11 dssr-viewV.pdb -- vertical view of the principal moment of inertia 12 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 13 dssr-viewT.pdb -- top view of the principal moment of inertia