**************************************************************************** File name: 1t3n.pdb no. of DNA/RNA chains: 2 [P=13,T=14] no. of nucleotides: 28 no. of atoms: 6769 no. of waters: 438 no. of metals: 1 [Mg=1] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 DOC-c 1 P.DOC13 2 TTP-t 1 B.TTP902 **************************************************************************** List of 14 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DA5 B.TTP902 A+t Hoogsteen 23-XXIII cHW cM+W 2 T.DG6 P.DOC13 G-c WC 19-XIX cWW cW-W 3 T.DG7 P.DC12 G-C WC 19-XIX cWW cW-W 4 T.DG8 P.DC11 G-C WC 19-XIX cWW cW-W 5 T.DT9 P.DA10 T-A WC 20-XX cWW cW-W 6 T.DC10 P.DG9 C-G WC 19-XIX cWW cW-W 7 T.DC11 P.DG8 C-G WC 19-XIX cWW cW-W 8 T.DT12 P.DA7 T-A WC 20-XX cWW cW-W 9 T.DT13 P.DA6 T-A WC 20-XX cWW cW-W 10 T.DC14 P.DG5 C-G WC 19-XIX cWW cW-W 11 T.DC15 P.DG4 C-G WC 19-XIX cWW cW-W 12 T.DC16 P.DG3 C-G WC 19-XIX cWW cW-W 13 T.DC17 P.DG2 C-G WC 19-XIX cWW cW-W 14 T.DC18 P.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=14 strand-1 5'-AGGGTCCTTCCCCC-3' bp-type .||||||||||||| strand-2 3'-tcCCAGGAAGGGGG-5' helix-form x...BBBB.B... 1 T.DA5 B.TTP902 A+t Hoogsteen 23-XXIII cHW cM+W 2 T.DG6 P.DOC13 G-c WC 19-XIX cWW cW-W 3 T.DG7 P.DC12 G-C WC 19-XIX cWW cW-W 4 T.DG8 P.DC11 G-C WC 19-XIX cWW cW-W 5 T.DT9 P.DA10 T-A WC 20-XX cWW cW-W 6 T.DC10 P.DG9 C-G WC 19-XIX cWW cW-W 7 T.DC11 P.DG8 C-G WC 19-XIX cWW cW-W 8 T.DT12 P.DA7 T-A WC 20-XX cWW cW-W 9 T.DT13 P.DA6 T-A WC 20-XX cWW cW-W 10 T.DC14 P.DG5 C-G WC 19-XIX cWW cW-W 11 T.DC15 P.DG4 C-G WC 19-XIX cWW cW-W 12 T.DC16 P.DG3 C-G WC 19-XIX cWW cW-W 13 T.DC17 P.DG2 C-G WC 19-XIX cWW cW-W 14 T.DC18 P.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=13 strand-1 5'-GGGTCCTTCCCCC-3' bp-type ||||||||||||| strand-2 3'-cCCAGGAAGGGGG-5' helix-form ...BBBB.B... 1 T.DG6 P.DOC13 G-c WC 19-XIX cWW cW-W 2 T.DG7 P.DC12 G-C WC 19-XIX cWW cW-W 3 T.DG8 P.DC11 G-C WC 19-XIX cWW cW-W 4 T.DT9 P.DA10 T-A WC 20-XX cWW cW-W 5 T.DC10 P.DG9 C-G WC 19-XIX cWW cW-W 6 T.DC11 P.DG8 C-G WC 19-XIX cWW cW-W 7 T.DT12 P.DA7 T-A WC 20-XX cWW cW-W 8 T.DT13 P.DA6 T-A WC 20-XX cWW cW-W 9 T.DC14 P.DG5 C-G WC 19-XIX cWW cW-W 10 T.DC15 P.DG4 C-G WC 19-XIX cWW cW-W 11 T.DC16 P.DG3 C-G WC 19-XIX cWW cW-W 12 T.DC17 P.DG2 C-G WC 19-XIX cWW cW-W 13 T.DC18 P.DG1 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=2 AG T.DA5,T.DG6 2 nts=2 ct P.DOC13,B.TTP902 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 A T.DA5 2 nts=1 t B.TTP902 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1t3n nts=28 [whole] AGGGTCCTTCCCCC&GGGGGAAGGACCc&t .(((((((((((((&)))))))))))))&. >1t3n-T #1 nts=14 3.42(0.28) [chain] DNA AGGGTCCTTCCCCC .((((((((((((( >1t3n-P #2 nts=13 3.41(0.50) [chain] DNA GGGGGAAGGACCc ))))))))))))) **************************************************************************** Summary of structural features of 28 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 A . T.DA5 0.020 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 2 G ( T.DG6 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 3 G ( T.DG7 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 G ( T.DG8 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 T ( T.DT9 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 C ( T.DC10 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 7 C ( T.DC11 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 T ( T.DT12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 9 T ( T.DT13 0.007 anti,canonical,non-pair-contact,helix,stem,phosphate 10 C ( T.DC14 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 C ( T.DC15 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 12 C ( T.DC16 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ( T.DC17 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 14 C ( T.DC18 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 15 G ) P.DG1 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 16 G ) P.DG2 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 17 G ) P.DG3 0.008 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 18 G ) P.DG4 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 19 G ) P.DG5 0.012 anti,BI,canonical,non-pair-contact,helix,stem 20 A ) P.DA6 0.008 anti,canonical,non-pair-contact,helix,stem 21 A ) P.DA7 0.007 anti,canonical,non-pair-contact,helix,stem,phosphate 22 G ) P.DG8 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 23 G ) P.DG9 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 24 A ) P.DA10 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 25 C ) P.DC11 0.011 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 26 C ) P.DC12 0.013 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 27 c ) P.DOC13 0.025 modified,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,phosphate 28 t . B.TTP902 0.064 modified,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop **************************************************************************** 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