**************************************************************************** File name: 5kn9.pdb no. of DNA/RNA chains: 2 [C=10,D=10] no. of nucleotides: 20 no. of atoms: 2377 no. of waters: 165 no. of metals: 6 [Ca=2,Fe=4] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 8OG-g 1 C.8OG7 **************************************************************************** List of 10 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DA3 D.DT22 A+T rWC 21-XXI tWW tW+W 2 C.DT4 D.DT22 T+T -- 12-XII tWW tW+W 3 C.DC5 D.DG20 C-G WC 19-XIX cWW cW-W 4 C.DC6 D.DG19 C-G WC 19-XIX cWW cW-W 5 C.8OG7 D.DA18 g+A -- 09-IX cHW cM+W 6 C.DG8 D.DC17 G-C WC 19-XIX cWW cW-W 7 C.DT9 D.DA16 T-A WC 20-XX cWW cW-W 8 C.DG10 D.DC15 G-C WC 19-XIX cWW cW-W 9 C.DC11 D.DG14 C-G WC 19-XIX cWW cW-W 10 C.DT12 D.DA13 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=8 strand-1 5'-CCgGTGCT-3' bp-type ||.||||| strand-2 3'-GGACACGA-5' helix-form B..BBBB 1 C.DC5 D.DG20 C-G WC 19-XIX cWW cW-W 2 C.DC6 D.DG19 C-G WC 19-XIX cWW cW-W 3 C.8OG7 D.DA18 g+A -- 09-IX cHW cM+W 4 C.DG8 D.DC17 G-C WC 19-XIX cWW cW-W 5 C.DT9 D.DA16 T-A WC 20-XX cWW cW-W 6 C.DG10 D.DC15 G-C WC 19-XIX cWW cW-W 7 C.DC11 D.DG14 C-G WC 19-XIX cWW cW-W 8 C.DT12 D.DA13 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=2 strand-1 5'-CC-3' bp-type || strand-2 3'-GG-5' helix-form B 1 C.DC5 D.DG20 C-G WC 19-XIX cWW cW-W 2 C.DC6 D.DG19 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=5 strand-1 5'-GTGCT-3' bp-type ||||| strand-2 3'-CACGA-5' helix-form BBBB 1 C.DG8 D.DC17 G-C WC 19-XIX cWW cW-W 2 C.DT9 D.DA16 T-A WC 20-XX cWW cW-W 3 C.DG10 D.DC15 G-C WC 19-XIX cWW cW-W 4 C.DC11 D.DG14 C-G WC 19-XIX cWW cW-W 5 C.DT12 D.DA13 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** 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=3 CgG C.DC6,C.8OG7,C.DG8 2 nts=3 CAG D.DC17,D.DA18,D.DG19 3 nts=4 ATAG C.DA3,C.DT4,D.DA21,D.DG20 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 T D.DT22 **************************************************************************** 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=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [C.6 D.19 C.8 D.17] 2 5 nts=6 CgGCAG C.DC6,C.8OG7,C.DG8,D.DC17,D.DA18,D.DG19 nts=1 g C.8OG7 nts=1 A D.DA18 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=2 AT C.DA3,C.DT4 2 nts=2 AT D.DA21,D.DT22 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5kn9 nts=20 [whole] ATCCgGTGCT&AGCACAGGAT ..((.(((((&))))).)).. >5kn9-C #1 nts=10 3.66(0.79) [chain] DNA ATCCgGTGCT ..((.((((( >5kn9-D #2 nts=10 3.19(0.88) [chain] DNA AGCACAGGAT ))))).)).. **************************************************************************** Summary of structural features of 20 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 . C.DA3 0.009 anti,~C2'-endo,BI,non-canonical,non-pair-contact,ss-non-loop 2 T . C.DT4 0.013 anti,~C2'-endo,BI,non-canonical,non-pair-contact,ss-non-loop,phosphate 3 C ( C.DC5 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 4 C ( C.DC6 0.007 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 5 g . C.8OG7 0.028 modified,syn,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop,phosphate 6 G ( C.DG8 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 7 T ( C.DT9 0.005 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 8 G ( C.DG10 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 C ( C.DC11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 T ( C.DT12 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 11 A ) D.DA13 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 12 G ) D.DG14 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 C ) D.DC15 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 A ) D.DA16 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 C ) D.DC17 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 16 A . D.DA18 0.011 ~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 17 G ) D.DG19 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 18 G ) D.DG20 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 19 A . D.DA21 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 20 T . D.DT22 0.006 anti,~C2'-endo,non-stack,non-canonical,ss-non-loop **************************************************************************** List of 13 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-stacks.pdb -- an ensemble of base stacks 10 dssr-rotmat.txt -- position vector and rotation matrix 11 dssr-viewV.pdb -- vertical view of the principal moment of inertia 12 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 13 dssr-viewT.pdb -- top view of the principal moment of inertia