**************************************************************************** File name: 9qn8.pdb no. of DNA/RNA chains: 1 [Z=21] no. of nucleotides: 28 no. of atoms: 15950 no. of waters: 0 no. of metals: 14 [K=7,Ca=7] **************************************************************************** List of 1 type of 7 modified nucleotides nt count list 1 ATP-a 7 A.ATP401,C.ATP401,E.ATP401,G.ATP401,I.ATP401,K.ATP401,K.ATP402 **************************************************************************** List of 12 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 Ra A.ARG170,A.ATP401 2 nts=2 Qa C.GLN135,C.ATP401 3 nts=2 Qa E.GLN135,E.ATP401 4 nts=2 Qa G.GLN135,G.ATP401 5 nts=2 Qa I.GLN135,I.ATP401 6 nts=2 Qa K.GLN135,K.ATP401 7 nts=3 TTT Z.DT2,Z.DT3,Z.DT4 8 nts=3 TTT Z.DT5,Z.DT6,Z.DT7 9 nts=3 TTT Z.DT8,Z.DT9,Z.DT10 10 nts=3 TTT Z.DT11,Z.DT12,Z.DT13 11 nts=3 TTT Z.DT14,Z.DT15,Z.DT16 12 nts=3 TTT Z.DT17,Z.DT18,Z.DT19 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 TTT Z.DT1,Z.DT20,Z.DT21 **************************************************************************** List of 7 non-loop single-stranded segments 1 nts=21 TTTTTTTTTTTTTTTTTTTTT Z.DT1,Z.DT2,Z.DT3,Z.DT4,Z.DT5,Z.DT6,Z.DT7,Z.DT8,Z.DT9,Z.DT10,Z.DT11,Z.DT12,Z.DT13,Z.DT14,Z.DT15,Z.DT16,Z.DT17,Z.DT18,Z.DT19,Z.DT20,Z.DT21 2 nts=1 a A.ATP401 3 nts=1 a C.ATP401 4 nts=1 a E.ATP401 5 nts=1 a G.ATP401 6 nts=1 a I.ATP401 7 nts=2* aa K.ATP401,K.ATP402 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >9qn8 nts=28 [whole] TTTTTTTTTTTTTTTTTTTTT&a&a&a&a&a&a&a .....................&.&.&.&.&.&.&. >9qn8-Z #1 nts=21 0.04(1.18) [chain] DNA TTTTTTTTTTTTTTTTTTTTT ..................... **************************************************************************** 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 T . Z.DT1 0.002 anti,~C2'-endo,BII,non-stack,ss-non-loop 2 T . Z.DT2 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 3 T . Z.DT3 0.002 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate 4 T . Z.DT4 0.002 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 5 T . Z.DT5 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 6 T . Z.DT6 0.002 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate 7 T . Z.DT7 0.002 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 8 T . Z.DT8 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 9 T . Z.DT9 0.003 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate 10 T . Z.DT10 0.002 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 11 T . Z.DT11 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 12 T . Z.DT12 0.002 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop,phosphate 13 T . Z.DT13 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop 14 T . Z.DT14 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 15 T . Z.DT15 0.003 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 16 T . Z.DT16 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 17 T . Z.DT17 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 18 T . Z.DT18 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 19 T . Z.DT19 0.002 anti,non-pair-contact,ss-non-loop 20 T . Z.DT20 0.002 ~C2'-endo,non-stack,non-pair-contact,ss-non-loop,phosphate 21 T . Z.DT21 0.002 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop 22 a . A.ATP401 0.004 modified,anti,ss-non-loop 23 a . C.ATP401 0.004 modified,anti,ss-non-loop 24 a . E.ATP401 0.004 modified,anti,ss-non-loop 25 a . G.ATP401 0.004 modified,anti,ss-non-loop 26 a . I.ATP401 0.004 modified,anti,ss-non-loop 27 a . K.ATP401 0.004 modified,break,anti,ss-non-loop 28 a . K.ATP402 0.004 modified,anti,ss-non-loop **************************************************************************** List of 9 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-stacks.pdb -- an ensemble of base stacks 6 dssr-rotmat.txt -- position vector and rotation matrix 7 dssr-viewV.pdb -- vertical view of the principal moment of inertia 8 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 9 dssr-viewT.pdb -- top view of the principal moment of inertia