**************************************************************************** File name: 9ig7.pdb no. of DNA/RNA chains: 2 [P=13,T=16] no. of nucleotides: 29 no. of atoms: 6979 no. of waters: 140 no. of metals: 2 [Mg=1,Mn=1] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 A6G-g 1 T.A6G5 2 A6U-u 1 T.A6U4 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 P.DG1 T.DC16 G-C WC 19-XIX cWW cW-W 2 P.DA2 T.DT15 A-T WC 20-XX cWW cW-W 3 P.DC3 T.DG14 C-G WC 19-XIX cWW cW-W 4 P.DC4 T.DG13 C-G WC 19-XIX cWW cW-W 5 P.DA5 T.DT12 A-T WC 20-XX cWW cW-W 6 P.DC6 T.DG11 C-G WC 19-XIX cWW cW-W 7 P.DG7 T.DC10 G-C WC 19-XIX cWW cW-W 8 P.DG8 T.DC9 G-C WC 19-XIX cWW cW-W 9 P.DC9 T.DG8 C-G WC 19-XIX cWW cW-W 10 P.DC10 T.DG7 C-G WC 19-XIX cWW cW-W 11 P.DA11 T.DT6 A-T WC 20-XX cWW cW-W 12 P.DC12 T.A6G5 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=12 strand-1 5'-GACCACGGCCAC-3' bp-type |||||||||||| strand-2 3'-CTGGTGCCGGTg-5' helix-form .BBBB.BBB.. 1 P.DG1 T.DC16 G-C WC 19-XIX cWW cW-W 2 P.DA2 T.DT15 A-T WC 20-XX cWW cW-W 3 P.DC3 T.DG14 C-G WC 19-XIX cWW cW-W 4 P.DC4 T.DG13 C-G WC 19-XIX cWW cW-W 5 P.DA5 T.DT12 A-T WC 20-XX cWW cW-W 6 P.DC6 T.DG11 C-G WC 19-XIX cWW cW-W 7 P.DG7 T.DC10 G-C WC 19-XIX cWW cW-W 8 P.DG8 T.DC9 G-C WC 19-XIX cWW cW-W 9 P.DC9 T.DG8 C-G WC 19-XIX cWW cW-W 10 P.DC10 T.DG7 C-G WC 19-XIX cWW cW-W 11 P.DA11 T.DT6 A-T WC 20-XX cWW cW-W 12 P.DC12 T.A6G5 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'-GACCACGGCCAC-3' bp-type |||||||||||| strand-2 3'-CTGGTGCCGGTg-5' helix-form .BBBB.BBB.. 1 P.DG1 T.DC16 G-C WC 19-XIX cWW cW-W 2 P.DA2 T.DT15 A-T WC 20-XX cWW cW-W 3 P.DC3 T.DG14 C-G WC 19-XIX cWW cW-W 4 P.DC4 T.DG13 C-G WC 19-XIX cWW cW-W 5 P.DA5 T.DT12 A-T WC 20-XX cWW cW-W 6 P.DC6 T.DG11 C-G WC 19-XIX cWW cW-W 7 P.DG7 T.DC10 G-C WC 19-XIX cWW cW-W 8 P.DG8 T.DC9 G-C WC 19-XIX cWW cW-W 9 P.DC9 T.DG8 C-G WC 19-XIX cWW cW-W 10 P.DC10 T.DG7 C-G WC 19-XIX cWW cW-W 11 P.DA11 T.DT6 A-T WC 20-XX cWW cW-W 12 P.DC12 T.A6G5 C-g 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=3 Cug T.DC3,T.A6U4,T.A6G5 2 nts=4 CAAA P.DC12,P.DA13,T.DA2,T.DA1 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 A P.DA13 2 nts=4 AACu T.DA1,T.DA2,T.DC3,T.A6U4 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >9ig7 nts=29 [whole] GACCACGGCCACA&AACugTGGCCGTGGTC ((((((((((((.&....)))))))))))) >9ig7-P #1 nts=13 3.49(0.52) [chain] DNA GACCACGGCCACA ((((((((((((. >9ig7-T #2 nts=16 3.19(0.77) [chain] DNA[14]/RNA[2] AACugTGGCCGTGGTC ....)))))))))))) **************************************************************************** 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 ( P.DG1 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end 2 A ( P.DA2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 C ( P.DC3 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 C ( P.DC4 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 5 A ( P.DA5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 C ( P.DC6 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 7 G ( P.DG7 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 G ( P.DG8 0.003 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 9 C ( P.DC9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 C ( P.DC10 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 A ( P.DA11 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 C ( P.DC12 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 13 A . P.DA13 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 14 A . T.DA1 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 15 A . T.DA2 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop 16 C . T.DC3 0.002 turn,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 17 u . T.A6U4 0.107 modified,non-pair-contact,ss-non-loop,phosphate 18 g ) T.A6G5 0.124 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 19 T ) T.DT6 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 20 G ) T.DG7 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 21 G ) T.DG8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 C ) T.DC9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 23 C ) T.DC10 0.002 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 24 G ) T.DG11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 T ) T.DT12 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 26 G ) T.DG13 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 27 G ) T.DG14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 T ) T.DT15 0.002 anti,canonical,non-pair-contact,helix,stem 29 C ) T.DC16 0.003 ~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 12 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-stacks.pdb -- an ensemble of base stacks 9 dssr-rotmat.txt -- position vector and rotation matrix 10 dssr-viewV.pdb -- vertical view of the principal moment of inertia 11 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 12 dssr-viewT.pdb -- top view of the principal moment of inertia