**************************************************************************** File name: 8fng.pdb no. of DNA/RNA chains: 4 [E=19,F=17,K=19,L=17] no. of nucleotides: 72 no. of atoms: 12476 no. of waters: 1186 no. of metals: 6 [Mg=4,Zn=2] **************************************************************************** List of 32 base pairs nt1 nt2 bp name Saenger LW DSSR 1 E.DG18 F.DC20 G-C WC 19-XIX cWW cW-W 2 E.DC19 F.DG19 C-G WC 19-XIX cWW cW-W 3 E.DT20 F.DA18 T-A WC 20-XX cWW cW-W 4 E.DA21 F.DT17 A-T WC 20-XX cWW cW-W 5 E.DG22 F.DC16 G-C WC 19-XIX cWW cW-W 6 E.DA23 F.DT15 A-T WC 20-XX cWW cW-W 7 E.DG24 F.DC14 G-C WC 19-XIX cWW cW-W 8 E.DA25 F.DT13 A-T WC 20-XX cWW cW-W 9 E.DT26 F.DA12 T-A WC 20-XX cWW cW-W 10 E.DT27 F.DA11 T-A WC 20-XX cWW cW-W 11 E.DT28 F.DA10 T-A WC 20-XX cWW cW-W 12 E.DT29 F.DA9 T-A WC 20-XX cWW cW-W 13 E.DC30 F.DG8 C-G WC 19-XIX cWW cW-W 14 E.DC31 F.DG7 C-G WC 19-XIX cWW cW-W 15 E.DC32 F.DG6 C-G WC 19-XIX cWW cW-W 16 E.DG33 F.DC5 G-C WC 19-XIX cWW cW-W 17 K.DG18 L.DC20 G-C WC 19-XIX cWW cW-W 18 K.DC19 L.DG19 C-G WC 19-XIX cWW cW-W 19 K.DT20 L.DA18 T-A WC 20-XX cWW cW-W 20 K.DA21 L.DT17 A-T WC 20-XX cWW cW-W 21 K.DG22 L.DC16 G-C WC 19-XIX cWW cW-W 22 K.DA23 L.DT15 A-T WC 20-XX cWW cW-W 23 K.DG24 L.DC14 G-C WC 19-XIX cWW cW-W 24 K.DA25 L.DT13 A-T WC 20-XX cWW cW-W 25 K.DT26 L.DA12 T-A WC 20-XX cWW cW-W 26 K.DT27 L.DA11 T-A WC 20-XX cWW cW-W 27 K.DT28 L.DA10 T-A WC 20-XX cWW cW-W 28 K.DT29 L.DA9 T-A WC 20-XX cWW cW-W 29 K.DC30 L.DG8 C-G WC 19-XIX cWW cW-W 30 K.DC31 L.DG7 C-G WC 19-XIX cWW cW-W 31 K.DC32 L.DG6 C-G WC 19-XIX cWW cW-W 32 K.DG33 L.DC5 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 helices 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=16 strand-1 5'-GCTAGAGATTTTCCCG-3' bp-type |||||||||||||||| strand-2 3'-CGATCTCTAAAAGGGC-5' helix-form BBBBBBBBBBBBBBB 1 E.DG18 F.DC20 G-C WC 19-XIX cWW cW-W 2 E.DC19 F.DG19 C-G WC 19-XIX cWW cW-W 3 E.DT20 F.DA18 T-A WC 20-XX cWW cW-W 4 E.DA21 F.DT17 A-T WC 20-XX cWW cW-W 5 E.DG22 F.DC16 G-C WC 19-XIX cWW cW-W 6 E.DA23 F.DT15 A-T WC 20-XX cWW cW-W 7 E.DG24 F.DC14 G-C WC 19-XIX cWW cW-W 8 E.DA25 F.DT13 A-T WC 20-XX cWW cW-W 9 E.DT26 F.DA12 T-A WC 20-XX cWW cW-W 10 E.DT27 F.DA11 T-A WC 20-XX cWW cW-W 11 E.DT28 F.DA10 T-A WC 20-XX cWW cW-W 12 E.DT29 F.DA9 T-A WC 20-XX cWW cW-W 13 E.DC30 F.DG8 C-G WC 19-XIX cWW cW-W 14 E.DC31 F.DG7 C-G WC 19-XIX cWW cW-W 15 E.DC32 F.DG6 C-G WC 19-XIX cWW cW-W 16 E.DG33 F.DC5 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=16 strand-1 5'-GCTAGAGATTTTCCCG-3' bp-type |||||||||||||||| strand-2 3'-CGATCTCTAAAAGGGC-5' helix-form BBBBBBBBBBBBBBB 1 K.DG18 L.DC20 G-C WC 19-XIX cWW cW-W 2 K.DC19 L.DG19 C-G WC 19-XIX cWW cW-W 3 K.DT20 L.DA18 T-A WC 20-XX cWW cW-W 4 K.DA21 L.DT17 A-T WC 20-XX cWW cW-W 5 K.DG22 L.DC16 G-C WC 19-XIX cWW cW-W 6 K.DA23 L.DT15 A-T WC 20-XX cWW cW-W 7 K.DG24 L.DC14 G-C WC 19-XIX cWW cW-W 8 K.DA25 L.DT13 A-T WC 20-XX cWW cW-W 9 K.DT26 L.DA12 T-A WC 20-XX cWW cW-W 10 K.DT27 L.DA11 T-A WC 20-XX cWW cW-W 11 K.DT28 L.DA10 T-A WC 20-XX cWW cW-W 12 K.DT29 L.DA9 T-A WC 20-XX cWW cW-W 13 K.DC30 L.DG8 C-G WC 19-XIX cWW cW-W 14 K.DC31 L.DG7 C-G WC 19-XIX cWW cW-W 15 K.DC32 L.DG6 C-G WC 19-XIX cWW cW-W 16 K.DG33 L.DC5 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems 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=16 strand-1 5'-GCTAGAGATTTTCCCG-3' bp-type |||||||||||||||| strand-2 3'-CGATCTCTAAAAGGGC-5' helix-form BBBBBBBBBBBBBBB 1 E.DG18 F.DC20 G-C WC 19-XIX cWW cW-W 2 E.DC19 F.DG19 C-G WC 19-XIX cWW cW-W 3 E.DT20 F.DA18 T-A WC 20-XX cWW cW-W 4 E.DA21 F.DT17 A-T WC 20-XX cWW cW-W 5 E.DG22 F.DC16 G-C WC 19-XIX cWW cW-W 6 E.DA23 F.DT15 A-T WC 20-XX cWW cW-W 7 E.DG24 F.DC14 G-C WC 19-XIX cWW cW-W 8 E.DA25 F.DT13 A-T WC 20-XX cWW cW-W 9 E.DT26 F.DA12 T-A WC 20-XX cWW cW-W 10 E.DT27 F.DA11 T-A WC 20-XX cWW cW-W 11 E.DT28 F.DA10 T-A WC 20-XX cWW cW-W 12 E.DT29 F.DA9 T-A WC 20-XX cWW cW-W 13 E.DC30 F.DG8 C-G WC 19-XIX cWW cW-W 14 E.DC31 F.DG7 C-G WC 19-XIX cWW cW-W 15 E.DC32 F.DG6 C-G WC 19-XIX cWW cW-W 16 E.DG33 F.DC5 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=16 strand-1 5'-GCTAGAGATTTTCCCG-3' bp-type |||||||||||||||| strand-2 3'-CGATCTCTAAAAGGGC-5' helix-form BBBBBBBBBBBBBBB 1 K.DG18 L.DC20 G-C WC 19-XIX cWW cW-W 2 K.DC19 L.DG19 C-G WC 19-XIX cWW cW-W 3 K.DT20 L.DA18 T-A WC 20-XX cWW cW-W 4 K.DA21 L.DT17 A-T WC 20-XX cWW cW-W 5 K.DG22 L.DC16 G-C WC 19-XIX cWW cW-W 6 K.DA23 L.DT15 A-T WC 20-XX cWW cW-W 7 K.DG24 L.DC14 G-C WC 19-XIX cWW cW-W 8 K.DA25 L.DT13 A-T WC 20-XX cWW cW-W 9 K.DT26 L.DA12 T-A WC 20-XX cWW cW-W 10 K.DT27 L.DA11 T-A WC 20-XX cWW cW-W 11 K.DT28 L.DA10 T-A WC 20-XX cWW cW-W 12 K.DT29 L.DA9 T-A WC 20-XX cWW cW-W 13 K.DC30 L.DG8 C-G WC 19-XIX cWW cW-W 14 K.DC31 L.DG7 C-G WC 19-XIX cWW cW-W 15 K.DC32 L.DG6 C-G WC 19-XIX cWW cW-W 16 K.DG33 L.DC5 G-C 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 CT E.DC16,E.DT17 2 nts=2 CT K.DC16,K.DT17 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 CACA F.DC5,F.DA21,L.DC5,L.DA21 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 other FAF@A.DLU304 E.DG18 2.84 2 other FAF@G.DLU304 K.DG18 2.84 **************************************************************************** List of 4 non-loop single-stranded segments 1 nts=3 ACT E.DA15,E.DC16,E.DT17 2 nts=1 A F.DA21 3 nts=3 ACT K.DA15,K.DC16,K.DT17 4 nts=1 A L.DA21 **************************************************************************** List of 6 splayed-apart dinucleotides 1 E.DA15 E.DC16 angle=97 distance=14.6 ratio=0.75 2 E.DT17 E.DG18 angle=131 distance=18.2 ratio=0.91 3 F.DC20 F.DA21 angle=113 distance=14.9 ratio=0.84 4 K.DA15 K.DC16 angle=97 distance=14.6 ratio=0.75 5 K.DT17 K.DG18 angle=131 distance=18.2 ratio=0.91 6 L.DC20 L.DA21 angle=113 distance=14.9 ratio=0.84 ---------------------------------------------------------------- Summary of 6 splayed-apart units 1 nts=2 AC E.DA15,E.DC16 2 nts=2 TG E.DT17,E.DG18 3 nts=2 CA F.DC20,F.DA21 4 nts=2 AC K.DA15,K.DC16 5 nts=2 TG K.DT17,K.DG18 6 nts=2 CA L.DC20,L.DA21 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >8fng nts=72 [whole] ACTGCTAGAGATTTTCCCG&CGGGAAAATCTCTAGCA&ACTGCTAGAGATTTTCCCG&CGGGAAAATCTCTAGCA ...((((((((((((((((&)))))))))))))))).&...((((((((((((((((&)))))))))))))))). >8fng-E #1 nts=19 3.28(0.70) [chain] DNA ACTGCTAGAGATTTTCCCG ...(((((((((((((((( >8fng-F #2 nts=17 3.56(1.41) [chain] DNA CGGGAAAATCTCTAGCA )))))))))))))))). >8fng-K #3 nts=19 3.28(0.70) [chain] DNA ACTGCTAGAGATTTTCCCG ...(((((((((((((((( >8fng-L #4 nts=17 3.56(1.41) [chain] DNA CGGGAAAATCTCTAGCA )))))))))))))))). **************************************************************************** Summary of structural features of 72 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 . E.DA15 0.003 anti,~C2'-endo,ss-non-loop,splayed-apart 2 C . E.DC16 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 3 T . E.DT17 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 4 G ( E.DG18 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,cap-acceptor,phosphate,splayed-apart 5 C ( E.DC19 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 T ( E.DT20 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 7 A ( E.DA21 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 8 G ( E.DG22 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 A ( E.DA23 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 G ( E.DG24 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 A ( E.DA25 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 T ( E.DT26 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 T ( E.DT27 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 14 T ( E.DT28 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 T ( E.DT29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ( E.DC30 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 17 C ( E.DC31 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 18 C ( E.DC32 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 G ( E.DG33 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 20 C ) F.DC5 0.003 anti,~C2'-endo,non-stack,canonical,helix-end,stem-end 21 G ) F.DG6 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 22 G ) F.DG7 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 G ) F.DG8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 A ) F.DA9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 25 A ) F.DA10 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 A ) F.DA11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 27 A ) F.DA12 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 T ) F.DT13 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 C ) F.DC14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 T ) F.DT15 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 C ) F.DC16 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 32 T ) F.DT17 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 33 A ) F.DA18 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 34 G ) F.DG19 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 35 C ) F.DC20 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 36 A . F.DA21 0.004 syn,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 37 A . K.DA15 0.003 anti,~C2'-endo,ss-non-loop,splayed-apart 38 C . K.DC16 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 39 T . K.DT17 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 40 G ( K.DG18 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,cap-acceptor,phosphate,splayed-apart 41 C ( K.DC19 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 42 T ( K.DT20 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 43 A ( K.DA21 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 44 G ( K.DG22 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 45 A ( K.DA23 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 46 G ( K.DG24 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 47 A ( K.DA25 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 48 T ( K.DT26 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 49 T ( K.DT27 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 50 T ( K.DT28 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 51 T ( K.DT29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 52 C ( K.DC30 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 53 C ( K.DC31 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 54 C ( K.DC32 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 55 G ( K.DG33 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 56 C ) L.DC5 0.003 anti,~C2'-endo,non-stack,canonical,helix-end,stem-end 57 G ) L.DG6 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 58 G ) L.DG7 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 59 G ) L.DG8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 60 A ) L.DA9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 61 A ) L.DA10 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 62 A ) L.DA11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 63 A ) L.DA12 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 64 T ) L.DT13 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 65 C ) L.DC14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 66 T ) L.DT15 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 67 C ) L.DC16 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 68 T ) L.DT17 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 69 A ) L.DA18 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 70 G ) L.DG19 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 71 C ) L.DC20 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 72 A . L.DA21 0.004 syn,~C2'-endo,non-stack,ss-non-loop,phosphate,splayed-apart **************************************************************************** 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