**************************************************************************** File name: 4fk2.pdb no. of DNA/RNA chains: 2 [P=13,T=17] no. of nucleotides: 31 no. of atoms: 8595 no. of waters: 608 no. of metals: 5 [Ca=5] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 DOC-c 1 P.DOC115 2 TTP-t 1 A.TTP1001 **************************************************************************** List of 14 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DG4 A.TTP1001 G-t Wobble 28-XXVIII cWW cW-W 2 T.DG5 P.DOC115 G-c WC 19-XIX cWW cW-W 3 T.DT6 P.DA114 T-A WC 20-XX cWW cW-W 4 T.DA7 P.DT113 A-T WC 20-XX cWW cW-W 5 T.DA8 P.DT112 A-T WC 20-XX cWW cW-W 6 T.DG9 P.DC111 G-C WC 19-XIX cWW cW-W 7 T.DC10 P.DG110 C-G WC 19-XIX cWW cW-W 8 T.DA11 P.DT109 A-T WC 20-XX cWW cW-W 9 T.DG12 P.DC108 G-C WC 19-XIX cWW cW-W 10 T.DT13 P.DA107 T-A WC 20-XX cWW cW-W 11 T.DC14 P.DG106 C-G WC 19-XIX cWW cW-W 12 T.DC15 P.DG105 C-G WC 19-XIX cWW cW-W 13 T.DG16 P.DC104 G-C WC 19-XIX cWW cW-W 14 T.DC17 P.DG103 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'-GGTAAGCAGTCCGC-3' bp-type |||||||||||||| strand-2 3'-tcATTCGTCAGGCG-5' helix-form x.B.B..BBBBBB 1 T.DG4 A.TTP1001 G-t Wobble 28-XXVIII cWW cW-W 2 T.DG5 P.DOC115 G-c WC 19-XIX cWW cW-W 3 T.DT6 P.DA114 T-A WC 20-XX cWW cW-W 4 T.DA7 P.DT113 A-T WC 20-XX cWW cW-W 5 T.DA8 P.DT112 A-T WC 20-XX cWW cW-W 6 T.DG9 P.DC111 G-C WC 19-XIX cWW cW-W 7 T.DC10 P.DG110 C-G WC 19-XIX cWW cW-W 8 T.DA11 P.DT109 A-T WC 20-XX cWW cW-W 9 T.DG12 P.DC108 G-C WC 19-XIX cWW cW-W 10 T.DT13 P.DA107 T-A WC 20-XX cWW cW-W 11 T.DC14 P.DG106 C-G WC 19-XIX cWW cW-W 12 T.DC15 P.DG105 C-G WC 19-XIX cWW cW-W 13 T.DG16 P.DC104 G-C WC 19-XIX cWW cW-W 14 T.DC17 P.DG103 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'-GTAAGCAGTCCGC-3' bp-type ||||||||||||| strand-2 3'-cATTCGTCAGGCG-5' helix-form .B.B..BBBBBB 1 T.DG5 P.DOC115 G-c WC 19-XIX cWW cW-W 2 T.DT6 P.DA114 T-A WC 20-XX cWW cW-W 3 T.DA7 P.DT113 A-T WC 20-XX cWW cW-W 4 T.DA8 P.DT112 A-T WC 20-XX cWW cW-W 5 T.DG9 P.DC111 G-C WC 19-XIX cWW cW-W 6 T.DC10 P.DG110 C-G WC 19-XIX cWW cW-W 7 T.DA11 P.DT109 A-T WC 20-XX cWW cW-W 8 T.DG12 P.DC108 G-C WC 19-XIX cWW cW-W 9 T.DT13 P.DA107 T-A WC 20-XX cWW cW-W 10 T.DC14 P.DG106 C-G WC 19-XIX cWW cW-W 11 T.DC15 P.DG105 C-G WC 19-XIX cWW cW-W 12 T.DG16 P.DC104 G-C WC 19-XIX cWW cW-W 13 T.DC17 P.DG103 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#1] -1 T.DG4 A.TTP1001 G-t Wobble 28-XXVIII cWW cW-W **************************************************************************** List of 3 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 GG T.DG4,T.DG5 2 nts=3 FAC A.PHE359,T.DA3,T.DC2 3 nts=3 Ntc A.ASN564,A.TTP1001,P.DOC115 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 G T.DG18 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=2 CA T.DC2,T.DA3 2 nts=1 G T.DG18 **************************************************************************** List of 2 splayed-apart dinucleotides 1 T.DA3 T.DG4 angle=113 distance=17.8 ratio=0.83 2 T.DC17 T.DG18 angle=117 distance=15.9 ratio=0.85 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 AG T.DA3,T.DG4 2 nts=2 CG T.DC17,T.DG18 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4fk2 nts=31 [whole] CAGGTAAGCAGTCCGCG&GCGGACTGCTTAc&t ...(((((((((((((.&)))))))))))))&. >4fk2-T #1 nts=17 2.98(1.67) [chain] DNA CAGGTAAGCAGTCCGCG ...(((((((((((((. >4fk2-P #2 nts=13 2.89(0.34) [chain] DNA GCGGACTGCTTAc ))))))))))))) **************************************************************************** Summary of structural features of 31 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 C . T.DC2 0.002 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 2 A . T.DA3 0.004 ~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 3 G . T.DG4 0.005 anti,~C3'-endo,BI,isolated-canonical,non-pair-contact,helix-end,phosphate,splayed-apart 4 G ( T.DG5 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,phosphate 5 T ( T.DT6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 A ( T.DA7 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 7 A ( T.DA8 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 8 G ( T.DG9 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 9 C ( T.DC10 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 A ( T.DA11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 G ( T.DG12 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 T ( T.DT13 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 C ( T.DC14 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 14 C ( T.DC15 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 15 G ( T.DG16 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ( T.DC17 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 17 G . T.DG18 0.006 syn,~C2'-endo,non-stack,ss-non-loop,splayed-apart 18 G ) P.DG103 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end 19 C ) P.DC104 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 20 G ) P.DG105 0.005 anti,canonical,non-pair-contact,helix,stem 21 G ) P.DG106 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 A ) P.DA107 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 C ) P.DC108 0.005 anti,BI,canonical,non-pair-contact,helix,stem 24 T ) P.DT109 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 25 G ) P.DG110 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 C ) P.DC111 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 27 T ) P.DT112 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 28 T ) P.DT113 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 29 A ) P.DA114 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 30 c ) P.DOC115 0.006 modified,anti,canonical,non-pair-contact,helix,stem-end,phosphate 31 t . A.TTP1001 0.058 modified,anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-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