**************************************************************************** File name: 3o1o.pdb no. of DNA/RNA chains: 2 [B=12,C=13] no. of nucleotides: 25 no. of atoms: 2332 no. of waters: 248 no. of metals: 1 [Mn=1] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 2YR-c 1 B.2YR10 2 MFT-t 1 B.MFT8 **************************************************************************** List of 10 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DA2 C.DT13 A-T WC 20-XX cWW cW-W 2 B.DG3 C.DC12 G-C WC 19-XIX cWW cW-W 3 B.DG4 C.DC11 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA10 T-A WC 20-XX cWW cW-W 5 B.DA6 C.DT9 A-T WC 20-XX cWW cW-W 6 B.DA9 C.DT6 A-T WC 20-XX cWW cW-W 7 B.2YR10 C.DG5 c-G WC 19-XIX cWW cW-W 8 B.DC11 C.DG4 C-G WC 19-XIX cWW cW-W 9 B.DG12 C.DC3 G-C WC 19-XIX cWW cW-W 10 B.DT13 C.DA2 T-A WC 20-XX 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=5 strand-1 5'-AGGTA-3' bp-type ||||| strand-2 3'-TCCAT-5' helix-form BBB. 1 B.DA2 C.DT13 A-T WC 20-XX cWW cW-W 2 B.DG3 C.DC12 G-C WC 19-XIX cWW cW-W 3 B.DG4 C.DC11 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA10 T-A WC 20-XX cWW cW-W 5 B.DA6 C.DT9 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=5 strand-1 5'-AcCGT-3' bp-type ||||| strand-2 3'-TGGCA-5' helix-form .BBB 1 B.DA9 C.DT6 A-T WC 20-XX cWW cW-W 2 B.2YR10 C.DG5 c-G WC 19-XIX cWW cW-W 3 B.DC11 C.DG4 C-G WC 19-XIX cWW cW-W 4 B.DG12 C.DC3 G-C WC 19-XIX cWW cW-W 5 B.DT13 C.DA2 T-A WC 20-XX 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=5 strand-1 5'-AGGTA-3' bp-type ||||| strand-2 3'-TCCAT-5' helix-form BBB. 1 B.DA2 C.DT13 A-T WC 20-XX cWW cW-W 2 B.DG3 C.DC12 G-C WC 19-XIX cWW cW-W 3 B.DG4 C.DC11 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA10 T-A WC 20-XX cWW cW-W 5 B.DA6 C.DT9 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=5 strand-1 5'-AcCGT-3' bp-type ||||| strand-2 3'-TGGCA-5' helix-form .BBB 1 B.DA9 C.DT6 A-T WC 20-XX cWW cW-W 2 B.2YR10 C.DG5 c-G WC 19-XIX cWW cW-W 3 B.DC11 C.DG4 C-G WC 19-XIX cWW cW-W 4 B.DG12 C.DC3 G-C WC 19-XIX cWW cW-W 5 B.DT13 C.DA2 T-A WC 20-XX 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 AA C.DA1,C.DA2 2 nts=3 YtH A.TYR76,B.MFT8,A.HIS131 3 nts=4 AAAT B.DA6,C.DA7,B.DA7,C.DT6 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@B.DA7 B.DA9 2.84 2 sugar O4'@C.DA7 C.DT9 2.85 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 1 internal loop 1 symmetric internal loop: nts=8; [2,2]; linked by [#1,#2] summary: [2] 2 2 [B.6 C.9 B.9 C.6] 5 5 nts=8 AAtATATT B.DA6,B.DA7,B.MFT8,B.DA9,C.DT6,C.DA7,C.DT8,C.DT9 nts=2 At B.DA7,B.MFT8 nts=2 AT C.DA7,C.DT8 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=1 A C.DA1 **************************************************************************** List of 2 splayed-apart dinucleotides 1 B.DA7 B.MFT8 angle=169 distance=19.1 ratio=1.00 2 B.MFT8 B.DA9 angle=116 distance=16.1 ratio=0.85 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=3 AtA B.DA7,B.MFT8,B.DA9 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >3o1o nts=25 [whole] AGGTAAtAcCGT&AACGGTATTACCT (((((..(((((&.)))))..))))) >3o1o-B #1 nts=12 3.17(1.22) [chain] DNA AGGTAAtAcCGT (((((..((((( >3o1o-C #2 nts=13 3.27(1.15) [chain] DNA AACGGTATTACCT .)))))..))))) **************************************************************************** Summary of structural features of 25 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 ( B.DA2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( B.DG3 0.005 anti,canonical,non-pair-contact,helix,stem 3 G ( B.DG4 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( B.DT5 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 5 A ( B.DA6 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop 6 A . B.DA7 0.010 anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor,phosphate,splayed-apart 7 t . B.MFT8 0.061 modified,turn,anti,~C2'-endo,internal-loop,phosphate,splayed-apart 8 A ( B.DA9 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop,cap-acceptor,phosphate,splayed-apart 9 c ( B.2YR10 0.009 modified,anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 C ( B.DC11 0.008 anti,BI,canonical,non-pair-contact,helix,stem 11 G ( B.DG12 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 T ( B.DT13 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 13 A . C.DA1 0.014 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 14 A ) C.DA2 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 15 C ) C.DC3 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 16 G ) C.DG4 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 17 G ) C.DG5 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 18 T ) C.DT6 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,internal-loop 19 A . C.DA7 0.003 turn,anti,~C2'-endo,non-pair-contact,internal-loop,cap-donor 20 T . C.DT8 --- turn,~C2'-endo,non-stack,internal-loop 21 T ) C.DT9 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,internal-loop,cap-acceptor 22 A ) C.DA10 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 C ) C.DC11 0.005 anti,canonical,non-pair-contact,helix,stem 24 C ) C.DC12 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 25 T ) C.DT13 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 15 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-iloops.pdb -- an ensemble of internal loops 5 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 6 dssr-2ndstrs.ct -- secondary structure in connectivity table format 7 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 8 dssr-torsions.txt -- backbone torsion angles and suite names 9 dssr-splays.pdb -- an ensemble of splayed-apart units 10 dssr-stacks.pdb -- an ensemble of base stacks 11 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 12 dssr-rotmat.txt -- position vector and rotation matrix 13 dssr-viewV.pdb -- vertical view of the principal moment of inertia 14 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 15 dssr-viewT.pdb -- top view of the principal moment of inertia