**************************************************************************** File name: 3r2d.pdb no. of DNA/RNA chains: 2 [R=12,S=8] no. of nucleotides: 20 no. of atoms: 4032 no. of waters: 98 no. of metals: 0 **************************************************************************** List of 7 base pairs nt1 nt2 bp name Saenger LW DSSR 1 R.G2 S.C11 G-C WC 19-XIX cWW cW-W 2 R.C5 S.G10 C-G WC 19-XIX cWW cW-W 3 R.C6 S.G9 C-G WC 19-XIX cWW cW-W 4 R.U7 S.U8 U-U -- 16-XVI cWW cW-W 5 R.U8 S.U7 U-U -- 16-XVI cWW cW-W 6 R.G9 S.C6 G-C WC 19-XIX cWW cW-W 7 R.G10 S.C5 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[2] bps=7 strand-1 5'-GCCUUGG-3' bp-type |||..|| strand-2 3'-CGGUUCC-5' helix-form x....A 1 R.G2 S.C11 G-C WC 19-XIX cWW cW-W 2 R.C5 S.G10 C-G WC 19-XIX cWW cW-W 3 R.C6 S.G9 C-G WC 19-XIX cWW cW-W 4 R.U7 S.U8 U-U -- 16-XVI cWW cW-W 5 R.U8 S.U7 U-U -- 16-XVI cWW cW-W 6 R.G9 S.C6 G-C WC 19-XIX cWW cW-W 7 R.G10 S.C5 G-C WC 19-XIX 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 . 1 R.C5 S.G10 C-G WC 19-XIX cWW cW-W 2 R.C6 S.G9 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=2 strand-1 5'-GG-3' bp-type || strand-2 3'-CC-5' helix-form A 1 R.G9 S.C6 G-C WC 19-XIX cWW cW-W 2 R.G10 S.C5 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#1] -1 R.G2 S.C11 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 6 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 CU R.C6,R.U7 2 nts=2 CU S.C6,S.U7 3 nts=3 GGC R.G1,R.G2,R.C5 4 nts=3 GCA R.G10,R.C11,R.A12 5 nts=3 GCA S.G10,S.C11,S.A12 6 nts=4 GUUG R.G9,R.U8,S.U8,S.G9 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 CU R.C3,R.U4 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@R.A12 R.C11 3.48 **************************************************************************** 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 bulge 1 bulge: nts=6; [2,0]; linked by [#-1,#1] summary: [2] 2 0 [R.2 S.11 R.5 S.10] 1 2 nts=6 GCUCGC R.G2,R.C3,R.U4,R.C5,S.G10,S.C11 nts=2 CU R.C3,R.U4 nts=0 **************************************************************************** List of 1 internal loop 1 symmetric internal loop: nts=8; [2,2]; linked by [#1,#2] summary: [2] 2 2 [R.6 S.9 R.9 S.6] 2 2 nts=8 CUUGCUUG R.C6,R.U7,R.U8,R.G9,S.C6,S.U7,S.U8,S.G9 nts=2 UU R.U7,R.U8 nts=2 UU S.U7,S.U8 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=1 G R.G1 2 nts=2 CA R.C11,R.A12 3 nts=1 A S.A12 **************************************************************************** List of 3 splayed-apart dinucleotides 1 R.G2 R.C3 angle=110 distance=15.0 ratio=0.82 2 R.C3 R.U4 angle=110 distance=15.8 ratio=0.82 3 R.U4 R.C5 angle=100 distance=16.3 ratio=0.77 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=4 GCUC R.G2,R.C3,R.U4,R.C5 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >3r2d nts=20 [whole] GGCUCCUUGGCA&CCUUGGCA .(..((..((..&))..))). >3r2d-R #1 nts=12 1.27(1.94) [chain] RNA GGCUCCUUGGCA .(..((..((.. >3r2d-S #2 nts=8 3.37(0.46) [chain] RNA CCUUGGCA ))..))). **************************************************************************** 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 G . R.G1 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 2 G ( R.G2 0.011 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix-end,bulge,phosphate,splayed-apart 3 C . R.C3 0.005 turn,syn,~C2'-endo,non-stack,non-pair-contact,bulge,phosphate,splayed-apart 4 U . R.U4 0.003 turn,anti,~C2'-endo,non-stack,non-pair-contact,bulge,splayed-apart 5 C ( R.C5 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 6 C ( R.C6 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 7 U . R.U7 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 8 U . R.U8 0.006 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 9 G ( R.G9 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 10 G ( R.G10 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 11 C . R.C11 0.008 anti,~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor 12 A . R.A12 0.006 anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor 13 C ) S.C5 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 14 C ) S.C6 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 15 U . S.U7 0.004 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 16 U . S.U8 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 17 G ) S.G9 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 18 G ) S.G10 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 19 C ) S.C11 0.003 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,bulge,phosphate 20 A . S.A12 0.006 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate **************************************************************************** List of 16 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-bulges.pdb -- an ensemble of bulges 5 dssr-iloops.pdb -- an ensemble of internal loops 6 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 7 dssr-2ndstrs.ct -- secondary structure in connectivity table format 8 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 dssr-torsions.txt -- backbone torsion angles and suite names 10 dssr-splays.pdb -- an ensemble of splayed-apart units 11 dssr-stacks.pdb -- an ensemble of base stacks 12 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 13 dssr-rotmat.txt -- position vector and rotation matrix 14 dssr-viewV.pdb -- vertical view of the principal moment of inertia 15 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 16 dssr-viewT.pdb -- top view of the principal moment of inertia