**************************************************************************** File name: 5d8t.pdb no. of DNA/RNA chains: 2 [A=8,B=8] no. of nucleotides: 16 no. of atoms: 740 no. of waters: 126 no. of metals: 4 [Co=4] **************************************************************************** List of 2 types of 4 modified nucleotides nt count list 1 CBV-c 2 A.CBV1,B.CBV1 2 U5M-u 2 A.U5M5,B.U5M5 **************************************************************************** List of 8 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.CBV1 B.G8 c-G WC 19-XIX cWW cW-W 2 A.G2 B.C7 G-C WC 19-XIX cWW cW-W 3 A.A3 B.U6 A-U WC 20-XX cWW cW-W 4 A.A4 B.U5M5 A-u WC 20-XX cWW cW-W 5 A.U5M5 B.A4 u-A WC 20-XX cWW cW-W 6 A.U6 B.A3 U-A WC 20-XX cWW cW-W 7 A.C7 B.G2 C-G WC 19-XIX cWW cW-W 8 A.G8 B.CBV1 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=8 strand-1 5'-cGAAuUCG-3' bp-type |||||||| strand-2 3'-GCUuAAGc-5' helix-form AAA.AAA 1 A.CBV1 B.G8 c-G WC 19-XIX cWW cW-W 2 A.G2 B.C7 G-C WC 19-XIX cWW cW-W 3 A.A3 B.U6 A-U WC 20-XX cWW cW-W 4 A.A4 B.U5M5 A-u WC 20-XX cWW cW-W 5 A.U5M5 B.A4 u-A WC 20-XX cWW cW-W 6 A.U6 B.A3 U-A WC 20-XX cWW cW-W 7 A.C7 B.G2 C-G WC 19-XIX cWW cW-W 8 A.G8 B.CBV1 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=8 strand-1 5'-cGAAuUCG-3' bp-type |||||||| strand-2 3'-GCUuAAGc-5' helix-form AAA.AAA 1 A.CBV1 B.G8 c-G WC 19-XIX cWW cW-W 2 A.G2 B.C7 G-C WC 19-XIX cWW cW-W 3 A.A3 B.U6 A-U WC 20-XX cWW cW-W 4 A.A4 B.U5M5 A-u WC 20-XX cWW cW-W 5 A.U5M5 B.A4 u-A WC 20-XX cWW cW-W 6 A.U6 B.A3 U-A WC 20-XX cWW cW-W 7 A.C7 B.G2 C-G WC 19-XIX cWW cW-W 8 A.G8 B.CBV1 G-c WC 19-XIX cWW cW-W **************************************************************************** Nucleotides not involved in stacking interactions nts=2 cc A.CBV1,B.CBV1 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5d8t nts=16 [whole] cGAAuUCG&cGAAuUCG ((((((((&)))))))) >5d8t-A #1 nts=8 2.18(0.44) [chain] RNA cGAAuUCG (((((((( >5d8t-B #2 nts=8 2.12(0.35) [chain] RNA cGAAuUCG )))))))) **************************************************************************** Summary of structural features of 16 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 ( A.CBV1 0.024 modified,anti,~C3'-endo,BI,non-stack,canonical,helix-end,stem-end 2 G ( A.G2 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 3 A ( A.A3 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 A ( A.A4 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 u ( A.U5M5 0.031 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 U ( A.U6 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 7 C ( A.C7 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 8 G ( A.G8 0.026 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 9 c ) B.CBV1 0.022 modified,anti,~C3'-endo,BI,non-stack,canonical,helix-end,stem-end 10 G ) B.G2 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 A ) B.A3 0.025 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 A ) B.A4 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 u ) B.U5M5 0.021 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 14 U ) B.U6 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 15 C ) B.C7 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 G ) B.G8 0.025 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 11 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-rotmat.txt -- position vector and rotation matrix 9 dssr-viewV.pdb -- vertical view of the principal moment of inertia 10 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 11 dssr-viewT.pdb -- top view of the principal moment of inertia