**************************************************************************** File name: 5w0u.pdb no. of DNA/RNA chains: 2 [D=12,G=12] no. of nucleotides: 26 no. of atoms: 9130 no. of waters: 2 no. of metals: 4 [Ca=2,Zn=2] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 DCM-c 2 B.DCM2002,A.DCM2002 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 D.DG1 G.DC12 G-C WC 19-XIX cWW cW-W 2 D.DT2 G.DA11 T-A WC 20-XX cWW cW-W 3 D.DT3 G.DA10 T-A WC 20-XX cWW cW-W 4 D.DC4 G.DG9 C-G WC 19-XIX cWW cW-W 5 D.DA5 G.DT8 A-T WC 20-XX cWW cW-W 6 D.DA6 G.DT7 A-T WC 20-XX cWW cW-W 7 D.DG7 G.DC6 G-C WC 19-XIX cWW cW-W 8 D.DG8 G.DC5 G-C WC 19-XIX cWW cW-W 9 D.DC9 G.DG4 C-G WC 19-XIX cWW cW-W 10 D.DC10 G.DG3 C-G WC 19-XIX cWW cW-W 11 D.DA11 G.DT2 A-T WC 20-XX cWW cW-W 12 D.DG12 G.DC1 G-C 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=12 strand-1 5'-GTTCAAGGCCAG-3' bp-type |||||||||||| strand-2 3'-CAAGTTCCGGTC-5' helix-form .BBB.BBBBB. 1 D.DG1 G.DC12 G-C WC 19-XIX cWW cW-W 2 D.DT2 G.DA11 T-A WC 20-XX cWW cW-W 3 D.DT3 G.DA10 T-A WC 20-XX cWW cW-W 4 D.DC4 G.DG9 C-G WC 19-XIX cWW cW-W 5 D.DA5 G.DT8 A-T WC 20-XX cWW cW-W 6 D.DA6 G.DT7 A-T WC 20-XX cWW cW-W 7 D.DG7 G.DC6 G-C WC 19-XIX cWW cW-W 8 D.DG8 G.DC5 G-C WC 19-XIX cWW cW-W 9 D.DC9 G.DG4 C-G WC 19-XIX cWW cW-W 10 D.DC10 G.DG3 C-G WC 19-XIX cWW cW-W 11 D.DA11 G.DT2 A-T WC 20-XX cWW cW-W 12 D.DG12 G.DC1 G-C 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=12 strand-1 5'-GTTCAAGGCCAG-3' bp-type |||||||||||| strand-2 3'-CAAGTTCCGGTC-5' helix-form .BBB.BBBBB. 1 D.DG1 G.DC12 G-C WC 19-XIX cWW cW-W 2 D.DT2 G.DA11 T-A WC 20-XX cWW cW-W 3 D.DT3 G.DA10 T-A WC 20-XX cWW cW-W 4 D.DC4 G.DG9 C-G WC 19-XIX cWW cW-W 5 D.DA5 G.DT8 A-T WC 20-XX cWW cW-W 6 D.DA6 G.DT7 A-T WC 20-XX cWW cW-W 7 D.DG7 G.DC6 G-C WC 19-XIX cWW cW-W 8 D.DG8 G.DC5 G-C WC 19-XIX cWW cW-W 9 D.DC9 G.DG4 C-G WC 19-XIX cWW cW-W 10 D.DC10 G.DG3 C-G WC 19-XIX cWW cW-W 11 D.DA11 G.DT2 A-T WC 20-XX cWW cW-W 12 D.DG12 G.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 base stack 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 Hc A.HIS1056,A.DCM2002 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 c B.DCM2002 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 c B.DCM2002 2 nts=1 c A.DCM2002 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5w0u nts=26 [whole] GTTCAAGGCCAG&CTGGCCTTGAAC&c&c ((((((((((((&))))))))))))&.&. >5w0u-D #1 nts=12 3.28(0.19) [chain] DNA GTTCAAGGCCAG (((((((((((( >5w0u-G #2 nts=12 3.30(0.23) [chain] DNA CTGGCCTTGAAC )))))))))))) **************************************************************************** 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 G ( D.DG1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 T ( D.DT2 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 T ( D.DT3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 C ( D.DC4 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 5 A ( D.DA5 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 A ( D.DA6 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 7 G ( D.DG7 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 8 G ( D.DG8 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 9 C ( D.DC9 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 C ( D.DC10 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 11 A ( D.DA11 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 G ( D.DG12 0.017 anti,canonical,non-pair-contact,helix-end,stem-end 13 C ) G.DC1 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 14 T ) G.DT2 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 G ) G.DG3 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 G ) G.DG4 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 C ) G.DC5 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 C ) G.DC6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 T ) G.DT7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 T ) G.DT8 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 21 G ) G.DG9 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 A ) G.DA10 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 A ) G.DA11 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 C ) G.DC12 0.003 anti,canonical,non-pair-contact,helix-end,stem-end 25 c . B.DCM2002 0.027 modified,anti,~C2'-endo,non-stack,ss-non-loop 26 c . A.DCM2002 0.027 modified,anti,~C2'-endo,ss-non-loop,phosphate **************************************************************************** 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