**************************************************************************** File name: 5bte.pdb no. of DNA/RNA chains: 2 [C=6,D=6] no. of nucleotides: 12 no. of atoms: 6550 no. of waters: 357 no. of metals: 6 [Mn=6] **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 U37-u 4 D.U37/3,D.U37/4,C.U37/3,C.U37/4 **************************************************************************** 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 YU B.TYR163,D.U2 2 nts=2 UY C.U2,A.TYR163 3 nts=3 QUU B.GLN253,D.U7,D.U6 4 nts=3 uuU D.U37/3,D.U37/4,D.U5 5 nts=3 uuU C.U37/3,C.U37/4,C.U5 6 nts=3 UUQ C.U6,C.U7,A.GLN253 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@D.U6 D.U7 2.82 2 sugar O4'@C.U6 C.U7 2.71 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=6 UuuUUU D.U2,D.U37/3,D.U37/4,D.U5,D.U6,D.U7 2 nts=6 UuuUUU C.U2,C.U37/3,C.U37/4,C.U5,C.U6,C.U7 **************************************************************************** List of 2 splayed-apart dinucleotides 1 D.U5 D.U6 angle=128 distance=17.6 ratio=0.90 2 C.U5 C.U6 angle=128 distance=17.5 ratio=0.90 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 UU D.U5,D.U6 2 nts=2 UU C.U5,C.U6 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5bte nts=12 [whole] UuuUUU&UuuUUU ......&...... >5bte-D #1 nts=6 2.06(1.12) [chain] RNA UuuUUU ...... >5bte-C #2 nts=6 1.98(1.12) [chain] RNA UuuUUU ...... **************************************************************************** Summary of structural features of 12 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 U . D.U2 0.008 anti,~C3'-endo,BI,ss-non-loop,phosphate 2 u . D.U37/3 0.050 modified,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 3 u . D.U37/4 0.047 modified,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 4 U . D.U5 0.012 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 5 U . D.U6 0.005 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,splayed-apart 6 U . D.U7 0.005 ~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor 7 U . C.U2 0.006 anti,~C3'-endo,BI,ss-non-loop,phosphate 8 u . C.U37/3 0.059 modified,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 9 u . C.U37/4 0.054 modified,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 10 U . C.U5 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 11 U . C.U6 0.005 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor,splayed-apart 12 U . C.U7 0.006 ~C3'-endo,non-pair-contact,ss-non-loop,cap-acceptor **************************************************************************** List of 11 additional files 1 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 2 dssr-2ndstrs.ct -- secondary structure in connectivity table format 3 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 4 dssr-torsions.txt -- backbone torsion angles and suite names 5 dssr-splays.pdb -- an ensemble of splayed-apart units 6 dssr-stacks.pdb -- an ensemble of base stacks 7 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 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