**************************************************************************** File name: 313d.pdb no. of DNA/RNA chains: 2 [A=7,B=7] no. of nucleotides: 14 no. of atoms: 349 no. of waters: 55 no. of metals: 2 [Mg=1,Co=1] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 A.5CM2,B.5CM9 **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.5CM2 B.DG14 c-G WC 19-XIX cWW cW-W 2 A.DG3 B.DC13 G-C WC 19-XIX cWW cW-W 3 A.DC4 B.DG12 C-G WC 19-XIX cWW cW-W 4 A.DG5 B.DC11 G-C WC 19-XIX cWW cW-W 5 A.DC6 B.DG10 C-G WC 19-XIX cWW cW-W 6 A.DG7 B.5CM9 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=6 strand-1 5'-cGCGCG-3' bp-type |||||| strand-2 3'-GCGCGc-5' helix-form ZZZZZ 1 A.5CM2 B.DG14 c-G WC 19-XIX cWW cW-W 2 A.DG3 B.DC13 G-C WC 19-XIX cWW cW-W 3 A.DC4 B.DG12 C-G WC 19-XIX cWW cW-W 4 A.DG5 B.DC11 G-C WC 19-XIX cWW cW-W 5 A.DC6 B.DG10 C-G WC 19-XIX cWW cW-W 6 A.DG7 B.5CM9 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=6 strand-1 5'-cGCGCG-3' bp-type |||||| strand-2 3'-GCGCGc-5' helix-form ZZZZZ 1 A.5CM2 B.DG14 c-G WC 19-XIX cWW cW-W 2 A.DG3 B.DC13 G-C WC 19-XIX cWW cW-W 3 A.DC4 B.DG12 C-G WC 19-XIX cWW cW-W 4 A.DG5 B.DC11 G-C WC 19-XIX cWW cW-W 5 A.DC6 B.DG10 C-G WC 19-XIX cWW cW-W 6 A.DG7 B.5CM9 G-c WC 19-XIX cWW cW-W **************************************************************************** List of 1 base stack 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 A.DG1,A.5CM2 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 GGG A.DG7,B.DG8,B.DG14 **************************************************************************** List of 6 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@A.5CM2 A.DG3 2.82 2 sugar O4'@A.DC4 A.DG5 2.80 3 sugar O4'@A.DC6 A.DG7 2.88 4 sugar O4'@B.5CM9 B.DG10 2.88 5 sugar O4'@B.DC11 B.DG12 2.92 6 sugar O4'@B.DC13 B.DG14 2.87 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 G A.DG1 2 nts=1 G B.DG8 **************************************************************************** List of 1 splayed-apart dinucleotide 1 B.DG8 B.5CM9 angle=137 distance=17.1 ratio=0.93 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 Gc B.DG8,B.5CM9 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >313d nts=14 [whole] GcGCGCG&GcGCGCG .((((((&.)))))) >313d-A #1 nts=7 3.54(0.23) [chain] DNA GcGCGCG .(((((( >313d-B #2 nts=7 3.64(0.26) [chain] DNA GcGCGCG .)))))) **************************************************************************** Summary of structural features of 14 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 . A.DG1 0.014 syn,~C2'-endo,non-pair-contact,ss-non-loop 2 c ( A.5CM2 0.003 modified,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,cap-donor 3 G ( A.DG3 0.014 turn,syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 4 C ( A.DC4 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor,phosphate 5 G ( A.DG5 0.017 turn,syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 6 C ( A.DC6 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor 7 G ( A.DG7 0.010 syn,~C2'-endo,non-stack,canonical,helix-end,stem-end,cap-acceptor 8 G . B.DG8 0.014 anti,~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 9 c ) B.5CM9 0.008 modified,turn,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,cap-donor,splayed-apart 10 G ) B.DG10 0.051 turn,syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 11 C ) B.DC11 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor 12 G ) B.DG12 0.014 syn,~C3'-endo,canonical,non-pair-contact,helix,stem,cap-acceptor 13 C ) B.DC13 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,cap-donor 14 G ) B.DG14 0.021 syn,~C2'-endo,non-stack,canonical,helix-end,stem-end,cap-acceptor **************************************************************************** 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-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-atom2bases.pdb -- an ensemble of atom-base stacking interactions 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