**************************************************************************** File name: 5ke8.pdb no. of DNA/RNA chains: 2 [B=10,C=10] no. of nucleotides: 20 no. of atoms: 2008 no. of waters: 9 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 B.5CM5,C.5CM5 **************************************************************************** List of 10 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DG1 C.DC10 G-C WC 19-XIX cWW cW-W 2 B.DA2 C.DT9 A-T WC 20-XX cWW cW-W 3 B.DG3 C.DC8 G-C WC 19-XIX cWW cW-W 4 B.DG4 C.DC7 G-C WC 19-XIX cWW cW-W 5 B.5CM5 C.DG6 c-G WC 19-XIX cWW cW-W 6 B.DG6 C.5CM5 G-c WC 19-XIX cWW cW-W 7 B.DT7 C.DA4 T-A WC 20-XX cWW cW-W 8 B.DG8 C.DC3 G-C WC 19-XIX cWW cW-W 9 B.DG9 C.DC2 G-C WC 19-XIX cWW cW-W 10 B.DC10 C.DG1 C-G 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=10 strand-1 5'-GAGGcGTGGC-3' bp-type |||||||||| strand-2 3'-CTCCGcACCG-5' helix-form BBB.BBBBB 1 B.DG1 C.DC10 G-C WC 19-XIX cWW cW-W 2 B.DA2 C.DT9 A-T WC 20-XX cWW cW-W 3 B.DG3 C.DC8 G-C WC 19-XIX cWW cW-W 4 B.DG4 C.DC7 G-C WC 19-XIX cWW cW-W 5 B.5CM5 C.DG6 c-G WC 19-XIX cWW cW-W 6 B.DG6 C.5CM5 G-c WC 19-XIX cWW cW-W 7 B.DT7 C.DA4 T-A WC 20-XX cWW cW-W 8 B.DG8 C.DC3 G-C WC 19-XIX cWW cW-W 9 B.DG9 C.DC2 G-C WC 19-XIX cWW cW-W 10 B.DC10 C.DG1 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=10 strand-1 5'-GAGGcGTGGC-3' bp-type |||||||||| strand-2 3'-CTCCGcACCG-5' helix-form BBB.BBBBB 1 B.DG1 C.DC10 G-C WC 19-XIX cWW cW-W 2 B.DA2 C.DT9 A-T WC 20-XX cWW cW-W 3 B.DG3 C.DC8 G-C WC 19-XIX cWW cW-W 4 B.DG4 C.DC7 G-C WC 19-XIX cWW cW-W 5 B.5CM5 C.DG6 c-G WC 19-XIX cWW cW-W 6 B.DG6 C.5CM5 G-c WC 19-XIX cWW cW-W 7 B.DT7 C.DA4 T-A WC 20-XX cWW cW-W 8 B.DG8 C.DC3 G-C WC 19-XIX cWW cW-W 9 B.DG9 C.DC2 G-C WC 19-XIX cWW cW-W 10 B.DC10 C.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5ke8 nts=20 [whole] GAGGcGTGGC&GCCAcGCCTC ((((((((((&)))))))))) >5ke8-B #1 nts=10 3.22(0.24) [chain] DNA GAGGcGTGGC (((((((((( >5ke8-C #2 nts=10 3.24(0.46) [chain] DNA GCCAcGCCTC )))))))))) **************************************************************************** Summary of structural features of 20 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.DG1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 A ( B.DA2 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 G ( B.DG3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 G ( B.DG4 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 c ( B.5CM5 0.013 modified,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 G ( B.DG6 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 7 T ( B.DT7 0.002 anti,BI,canonical,non-pair-contact,helix,stem 8 G ( B.DG8 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 9 G ( B.DG9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 C ( B.DC10 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 11 G ) C.DG1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 12 C ) C.DC2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 C ) C.DC3 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 14 A ) C.DA4 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 15 c ) C.5CM5 0.016 modified,anti,BI,canonical,non-pair-contact,helix,stem,phosphate 16 G ) C.DG6 0.003 anti,BI,canonical,non-pair-contact,helix,stem 17 C ) C.DC7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 C ) C.DC8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 T ) C.DT9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 C ) C.DC10 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 11 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-rotmat.txt -- position vector and rotation matrix 9 dssr-viewV.pdb -- vertical view of the principal moment of inertia 10 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 11 dssr-viewT.pdb -- top view of the principal moment of inertia