**************************************************************************** File name: 4g4n.pdb no. of DNA/RNA chains: 2 [B=15,C=13] no. of nucleotides: 28 no. of atoms: 2834 no. of waters: 265 no. of metals: 1 [Zn=1] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 TX2-c 1 C.TX2/11 **************************************************************************** List of 13 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DG3 C.DC15 G-C WC 19-XIX cWW cW-W 2 B.DT4 C.DA14 T-A WC 20-XX cWW cW-W 3 B.DA5 C.DT13 A-T WC 20-XX cWW cW-W 4 B.DG6 C.DC12 G-C WC 19-XIX cWW cW-W 5 B.DA7 C.TX2/11 A-c -- -- cWW cW-W 6 B.DC8 C.DG10 C-G WC 19-XIX cWW cW-W 7 B.DT9 C.DA9 T-A WC 20-XX cWW cW-W 8 B.DC10 C.DG8 C-G WC 19-XIX cWW cW-W 9 B.DG11 C.DC7 G-C WC 19-XIX cWW cW-W 10 B.DG12 C.DC6 G-C WC 19-XIX cWW cW-W 11 B.DA13 C.DT5 A-T WC 20-XX cWW cW-W 12 B.DC14 C.DG4 C-G WC 19-XIX cWW cW-W 13 B.DG15 C.DC3 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=13 strand-1 5'-GTAGACTCGGACG-3' bp-type ||||.|||||||| strand-2 3'-CATCcGAGCCTGC-5' helix-form BBBBBB..BBBB 1 B.DG3 C.DC15 G-C WC 19-XIX cWW cW-W 2 B.DT4 C.DA14 T-A WC 20-XX cWW cW-W 3 B.DA5 C.DT13 A-T WC 20-XX cWW cW-W 4 B.DG6 C.DC12 G-C WC 19-XIX cWW cW-W 5 B.DA7 C.TX2/11 A-c -- -- cWW cW-W 6 B.DC8 C.DG10 C-G WC 19-XIX cWW cW-W 7 B.DT9 C.DA9 T-A WC 20-XX cWW cW-W 8 B.DC10 C.DG8 C-G WC 19-XIX cWW cW-W 9 B.DG11 C.DC7 G-C WC 19-XIX cWW cW-W 10 B.DG12 C.DC6 G-C WC 19-XIX cWW cW-W 11 B.DA13 C.DT5 A-T WC 20-XX cWW cW-W 12 B.DC14 C.DG4 C-G WC 19-XIX cWW cW-W 13 B.DG15 C.DC3 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=4 strand-1 5'-GTAG-3' bp-type |||| strand-2 3'-CATC-5' helix-form BBB 1 B.DG3 C.DC15 G-C WC 19-XIX cWW cW-W 2 B.DT4 C.DA14 T-A WC 20-XX cWW cW-W 3 B.DA5 C.DT13 A-T WC 20-XX cWW cW-W 4 B.DG6 C.DC12 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=8 strand-1 5'-CTCGGACG-3' bp-type |||||||| strand-2 3'-GAGCCTGC-5' helix-form B..BBBB 1 B.DC8 C.DG10 C-G WC 19-XIX cWW cW-W 2 B.DT9 C.DA9 T-A WC 20-XX cWW cW-W 3 B.DC10 C.DG8 C-G WC 19-XIX cWW cW-W 4 B.DG11 C.DC7 G-C WC 19-XIX cWW cW-W 5 B.DG12 C.DC6 G-C WC 19-XIX cWW cW-W 6 B.DA13 C.DT5 A-T WC 20-XX cWW cW-W 7 B.DC14 C.DG4 C-G WC 19-XIX cWW cW-W 8 B.DG15 C.DC3 G-C WC 19-XIX 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 AGG B.DA1,B.DG2,B.DG3 2 nts=3 GAC B.DG6,B.DA7,B.DC8 3 nts=3 GcC C.DG10,C.TX2/11,C.DC12 **************************************************************************** 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 [B.6 C.12 B.8 C.10] 4 8 nts=6 GACGcC B.DG6,B.DA7,B.DC8,C.DG10,C.TX2/11,C.DC12 nts=1 A B.DA7 nts=1 c C.TX2/11 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=2 AG B.DA1,B.DG2 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4g4n nts=28 [whole] AGGTAGACTCGGACG&CGTCCGAGcCTAC ..((((.((((((((&)))))))).)))) >4g4n-B #1 nts=15 3.11(1.18) [chain] DNA AGGTAGACTCGGACG ..((((.(((((((( >4g4n-C #2 nts=13 2.89(0.81) [chain] DNA CGTCCGAGcCTAC )))))))).)))) **************************************************************************** Summary of structural features of 28 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 . B.DA1 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 G . B.DG2 0.004 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 3 G ( B.DG3 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 4 T ( B.DT4 0.007 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 5 A ( B.DA5 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 G ( B.DG6 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 7 A . B.DA7 0.006 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 8 C ( B.DC8 0.004 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 9 T ( B.DT9 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 C ( B.DC10 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 G ( B.DG11 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 12 G ( B.DG12 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 A ( B.DA13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 C ( B.DC14 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 G ( B.DG15 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 16 C ) C.DC3 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 17 G ) C.DG4 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 T ) C.DT5 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 C ) C.DC6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 C ) C.DC7 0.005 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 G ) C.DG8 0.008 ~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 22 A ) C.DA9 0.008 ~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 23 G ) C.DG10 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 24 c . C.TX2/11 0.034 modified,anti,BI,non-canonical,non-pair-contact,helix,internal-loop 25 C ) C.DC12 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 26 T ) C.DT13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 A ) C.DA14 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 28 C ) C.DC15 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** 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