**************************************************************************** File name: 7b0g.pdb no. of DNA/RNA chains: 2 [P=11,T=11] no. of nucleotides: 22 no. of atoms: 6535 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 6HC-c 2 P.6HC13,P.6HC14 **************************************************************************** List of 9 base pairs nt1 nt2 bp name Saenger LW DSSR 1 P.DG4 T.DC13 G-C WC 19-XIX cWW cW-W 2 P.DG5 T.DC12 G-C WC 19-XIX cWW cW-W 3 P.DA6 T.DT11 A-T WC 20-XX cWW cW-W 4 P.DG7 T.DC10 G-C WC 19-XIX cWW cW-W 5 P.DG8 T.DC9 G-C WC 19-XIX cWW cW-W 6 P.DG9 T.DC8 G-C WC 19-XIX cWW cW-W 7 P.DC10 T.DG7 C-G WC 19-XIX cWW cW-W 8 P.DA11 T.DT6 A-T WC 20-XX cWW cW-W 9 P.DG12 T.DC5 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=9 strand-1 5'-GGAGGGCAG-3' bp-type ||||||||| strand-2 3'-CCTCCCGTC-5' helix-form BB..BBB. 1 P.DG4 T.DC13 G-C WC 19-XIX cWW cW-W 2 P.DG5 T.DC12 G-C WC 19-XIX cWW cW-W 3 P.DA6 T.DT11 A-T WC 20-XX cWW cW-W 4 P.DG7 T.DC10 G-C WC 19-XIX cWW cW-W 5 P.DG8 T.DC9 G-C WC 19-XIX cWW cW-W 6 P.DG9 T.DC8 G-C WC 19-XIX cWW cW-W 7 P.DC10 T.DG7 C-G WC 19-XIX cWW cW-W 8 P.DA11 T.DT6 A-T WC 20-XX cWW cW-W 9 P.DG12 T.DC5 G-C 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=9 strand-1 5'-GGAGGGCAG-3' bp-type ||||||||| strand-2 3'-CCTCCCGTC-5' helix-form BB..BBB. 1 P.DG4 T.DC13 G-C WC 19-XIX cWW cW-W 2 P.DG5 T.DC12 G-C WC 19-XIX cWW cW-W 3 P.DA6 T.DT11 A-T WC 20-XX cWW cW-W 4 P.DG7 T.DC10 G-C WC 19-XIX cWW cW-W 5 P.DG8 T.DC9 G-C WC 19-XIX cWW cW-W 6 P.DG9 T.DC8 G-C WC 19-XIX cWW cW-W 7 P.DC10 T.DG7 C-G WC 19-XIX cWW cW-W 8 P.DA11 T.DT6 A-T WC 20-XX cWW cW-W 9 P.DG12 T.DC5 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 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 Gc P.DG12,P.6HC13 2 nts=2 GC T.DG4,T.DC5 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 cG P.6HC14,T.DG3 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=2 cc P.6HC13,P.6HC14 2 nts=2 GG T.DG3,T.DG4 **************************************************************************** List of 2 splayed-apart dinucleotides 1 P.6HC13 P.6HC14 angle=161 distance=19.8 ratio=0.99 2 T.DG3 T.DG4 angle=165 distance=18.8 ratio=0.99 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 cc P.6HC13,P.6HC14 2 nts=2 GG T.DG3,T.DG4 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7b0g nts=22 [whole] GGAGGGCAGcc&GGCTGCCCTCC (((((((((..&..))))))))) >7b0g-P #1 nts=11 3.53(0.99) [chain] DNA GGAGGGCAGcc (((((((((.. >7b0g-T #2 nts=11 2.49(1.53) [chain] DNA GGCTGCCCTCC ..))))))))) **************************************************************************** Summary of structural features of 22 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 ( P.DG4 0.010 anti,canonical,non-pair-contact,helix-end,stem-end 2 G ( P.DG5 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 A ( P.DA6 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 G ( P.DG7 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 5 G ( P.DG8 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 G ( P.DG9 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 7 C ( P.DC10 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 8 A ( P.DA11 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 9 G ( P.DG12 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 10 c . P.6HC13 0.007 modified,anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 11 c . P.6HC14 0.014 modified,~C3'-endo,non-stack,ss-non-loop,splayed-apart 12 G . T.DG3 0.008 ~C3'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 13 G . T.DG4 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 14 C ) T.DC5 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 15 T ) T.DT6 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 16 G ) T.DG7 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 17 C ) T.DC8 0.005 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 18 C ) T.DC9 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 19 C ) T.DC10 0.009 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 20 T ) T.DT11 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ) T.DC12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 C ) T.DC13 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-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