**************************************************************************** File name: 3r8f.pdb no. of DNA/RNA chains: 1 [E=12] no. of nucleotides: 16 no. of atoms: 10874 no. of waters: 22 no. of metals: 4 [Mg=4] **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 ACP-a 4 A.ACP700,B.ACP700,C.ACP700,D.ACP700 **************************************************************************** List of 8 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 Ha A.HIS127,A.ACP700 2 nts=2 Ha B.HIS127,B.ACP700 3 nts=2 Ha C.HIS127,C.ACP700 4 nts=2 Ha D.HIS127,D.ACP700 5 nts=3 AAA E.DA1,E.DA2,E.DA3 6 nts=3 AAA E.DA4,E.DA5,E.DA6 7 nts=3 AAA E.DA7,E.DA8,E.DA9 8 nts=3 AAA E.DA10,E.DA11,E.DA12 **************************************************************************** List of 5 non-loop single-stranded segments 1 nts=12 AAAAAAAAAAAA E.DA1,E.DA2,E.DA3,E.DA4,E.DA5,E.DA6,E.DA7,E.DA8,E.DA9,E.DA10,E.DA11,E.DA12 2 nts=1 a A.ACP700 3 nts=1 a B.ACP700 4 nts=1 a C.ACP700 5 nts=1 a D.ACP700 **************************************************************************** List of 1 splayed-apart dinucleotide 1 E.DA9 E.DA10 angle=87 distance=14.7 ratio=0.69 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 AA E.DA9,E.DA10 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >3r8f nts=16 [whole] AAAAAAAAAAAA&a&a&a&a ............&.&.&.&. >3r8f-E #1 nts=12 3.89(0.44) [chain] DNA AAAAAAAAAAAA ............ **************************************************************************** Summary of structural features of 16 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 . E.DA1 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 2 A . E.DA2 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 3 A . E.DA3 0.003 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate 4 A . E.DA4 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 5 A . E.DA5 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 6 A . E.DA6 0.003 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate 7 A . E.DA7 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 8 A . E.DA8 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 9 A . E.DA9 0.003 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 10 A . E.DA10 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 11 A . E.DA11 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 12 A . E.DA12 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 13 a . A.ACP700 0.072 modified,anti,~C2'-endo,ss-non-loop 14 a . B.ACP700 0.072 modified,anti,ss-non-loop 15 a . C.ACP700 0.072 modified,anti,~C2'-endo,ss-non-loop 16 a . D.ACP700 0.072 modified,anti,~C2'-endo,ss-non-loop **************************************************************************** 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