**************************************************************************** File name: 5guh.pdb no. of DNA/RNA chains: 1 [B=8] no. of nucleotides: 8 no. of atoms: 6078 no. of waters: 84 no. of metals: 2 [Mg=2] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 OMU-u 1 B.OMU28 **************************************************************************** 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=2 YU A.TYR607,B.U1 2 nts=4 FuUU A.PHE370,B.OMU28,B.U27,B.U26 3 nts=4 AUUU B.A2,B.U3,B.U4,B.U5 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=8* UAUUUUUu B.U1,B.A2,B.U3,B.U4,B.U5,B.U26,B.U27,B.OMU28 **************************************************************************** List of 1 splayed-apart dinucleotide 1 B.U1 B.A2 angle=134 distance=17.1 ratio=0.92 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 UA B.U1,B.A2 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5guh nts=8 [whole] UAUUU&UUu .....&... >5guh-B #1 nts=8 0.31(0.93) [chain] RNA* UAUUU&UUu .....&... **************************************************************************** Summary of structural features of 8 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 . B.U1 0.002 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 2 A . B.A2 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 3 U . B.U3 0.001 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 4 U . B.U4 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 5 U . B.U5 0.002 break,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 6 U . B.U26 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 7 U . B.U27 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 8 u . B.OMU28 0.053 modified,anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate **************************************************************************** List of 10 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-rotmat.txt -- position vector and rotation matrix 8 dssr-viewV.pdb -- vertical view of the principal moment of inertia 9 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 10 dssr-viewT.pdb -- top view of the principal moment of inertia