**************************************************************************** File name: 3bkz.pdb no. of DNA/RNA chains: 2 [B=13,C=13] no. of nucleotides: 26 no. of atoms: 2402 no. of waters: 292 no. of metals: 1 [Mn=1] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 2YR-c 1 B.2YR8 **************************************************************************** List of 11 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.DA7 C.DA7 A-A -- 05-V tHW tM-W 7 B.DA9 C.DT6 A-T WC 20-XX cWW cW-W 8 B.DT10 C.DA5 T-A WC 20-XX cWW cW-W 9 B.DC11 C.DG4 C-G WC 19-XIX cWW cW-W 10 B.DG12 C.DC3 G-C WC 19-XIX cWW cW-W 11 B.DT13 C.DA2 T-A WC 20-XX 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[2] bps=11 strand-1 5'-AGGTAAATCGT-3' bp-type |||||.||||| strand-2 3'-TCCATATAGCA-5' helix-form BBBBxx.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 6 B.DA7 C.DA7 A-A -- 05-V tHW tM-W 7 B.DA9 C.DT6 A-T WC 20-XX cWW cW-W 8 B.DT10 C.DA5 T-A WC 20-XX cWW cW-W 9 B.DC11 C.DG4 C-G WC 19-XIX cWW cW-W 10 B.DG12 C.DC3 G-C WC 19-XIX cWW cW-W 11 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 BBBB 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[#1] bps=5 strand-1 5'-ATCGT-3' bp-type ||||| strand-2 3'-TAGCA-5' helix-form .BBB 1 B.DA9 C.DT6 A-T WC 20-XX cWW cW-W 2 B.DT10 C.DA5 T-A WC 20-XX 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 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 5 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 TA B.DT1,B.DA2 2 nts=2 AA B.DA6,C.DA7 3 nts=2 AT B.DA7,C.DT6 4 nts=2 AA C.DA1,C.DA2 5 nts=3 YcH A.TYR76,B.2YR8,A.HIS131 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 T C.DT8 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'.A@B.DA7 B.DA9 3.04 2 sugar O4'.A@C.DA7 C.DT9 2.93 **************************************************************************** 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 AAcATATT B.DA6,B.DA7,B.2YR8,B.DA9,C.DT6,C.DA7,C.DT8,C.DT9 nts=2 Ac B.DA7,B.2YR8 nts=2 AT C.DA7,C.DT8 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 T B.DT1 2 nts=1 A C.DA1 **************************************************************************** List of 4 splayed-apart dinucleotides 1 B.DA7 B.2YR8 angle=143 distance=17.0 ratio=0.95 2 B.2YR8 B.DA9 angle=107 distance=15.9 ratio=0.80 3 C.DA7 C.DT8 angle=146 distance=18.2 ratio=0.96 4 C.DT8 C.DT9 angle=107 distance=16.8 ratio=0.80 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=3 AcA B.DA7,B.2YR8,B.DA9 2 nts=3 ATT C.DA7,C.DT8,C.DT9 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >3bkz nts=26 [whole] TAGGTAAcATCGT&AACGATATTACCT .(((((..(((((&.)))))..))))) >3bkz-B #1 nts=13 3.22(1.09) [chain] DNA TAGGTAAcATCGT .(((((..((((( >3bkz-C #2 nts=13 3.23(1.37) [chain] DNA AACGATATTACCT .)))))..))))) **************************************************************************** Summary of structural features of 26 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 T . B.DT1 0.006 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 A ( B.DA2 0.006 ~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 3 G ( B.DG3 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 G ( B.DG4 0.010 anti,canonical,non-pair-contact,helix,stem,coaxial-stack 5 T ( B.DT5 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 6 A ( B.DA6 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 7 A . B.DA7 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-donor,splayed-apart 8 c . B.2YR8 0.007 modified,turn,anti,~C2'-endo,internal-loop,phosphate,splayed-apart 9 A ( B.DA9 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-acceptor,phosphate,splayed-apart 10 T ( B.DT10 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 11 C ( B.DC11 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 G ( B.DG12 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 T ( B.DT13 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 14 A . C.DA1 0.007 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 15 A ) C.DA2 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 16 C ) C.DC3 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 17 G ) C.DG4 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 A ) C.DA5 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 T ) C.DT6 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 20 A . C.DA7 0.008 ~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,cap-donor,splayed-apart 21 T . C.DT8 0.006 turn,anti,non-stack,internal-loop,splayed-apart 22 T ) C.DT9 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-acceptor,splayed-apart 23 A ) C.DA10 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 C ) C.DC11 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 25 C ) C.DC12 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 26 T ) C.DT13 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** 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