**************************************************************************** File name: 3c7r.pdb no. of DNA/RNA chains: 2 [A=23,B=23] no. of nucleotides: 46 no. of atoms: 1162 no. of waters: 96 no. of metals: 2 [K=2] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 UMS-u 2 A.UMS3,B.UMS3 **************************************************************************** List of 20 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.C1 B.G23 C-G WC 19-XIX cWW cW-W 2 A.U2 B.A22 U-A WC 20-XX cWW cW-W 3 A.UMS3 B.A21 u-A WC 20-XX cWW cW-W 4 A.G4 B.C20 G-C WC 19-XIX cWW cW-W 5 A.C5 B.G19 C-G WC 19-XIX cWW cW-W 6 A.U6 B.A18 U-A WC 20-XX cWW cW-W 7 A.G7 B.C17 G-C WC 19-XIX cWW cW-W 8 A.G10 B.C15 G-C WC 19-XIX cWW cW-W 9 A.U11 B.A14 U-A WC 20-XX cWW cW-W 10 A.G12 B.C13 G-C WC 19-XIX cWW cW-W 11 A.C13 B.G12 C-G WC 19-XIX cWW cW-W 12 A.A14 B.U11 A-U WC 20-XX cWW cW-W 13 A.C15 B.G10 C-G WC 19-XIX cWW cW-W 14 A.C17 B.G7 C-G WC 19-XIX cWW cW-W 15 A.A18 B.U6 A-U WC 20-XX cWW cW-W 16 A.G19 B.C5 G-C WC 19-XIX cWW cW-W 17 A.C20 B.G4 C-G WC 19-XIX cWW cW-W 18 A.A21 B.UMS3 A-u WC 20-XX cWW cW-W 19 A.A22 B.U2 A-U WC 20-XX cWW cW-W 20 A.G23 B.C1 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[3] bps=20 strand-1 5'-CUuGCUGGUGCACCAGCAAG-3' bp-type |||||||||||||||||||| strand-2 3'-GAACGACCACGUGGUCGuUC-5' helix-form AAAAAAxAAAAAxAAAAAA 1 A.C1 B.G23 C-G WC 19-XIX cWW cW-W 2 A.U2 B.A22 U-A WC 20-XX cWW cW-W 3 A.UMS3 B.A21 u-A WC 20-XX cWW cW-W 4 A.G4 B.C20 G-C WC 19-XIX cWW cW-W 5 A.C5 B.G19 C-G WC 19-XIX cWW cW-W 6 A.U6 B.A18 U-A WC 20-XX cWW cW-W 7 A.G7 B.C17 G-C WC 19-XIX cWW cW-W 8 A.G10 B.C15 G-C WC 19-XIX cWW cW-W 9 A.U11 B.A14 U-A WC 20-XX cWW cW-W 10 A.G12 B.C13 G-C WC 19-XIX cWW cW-W 11 A.C13 B.G12 C-G WC 19-XIX cWW cW-W 12 A.A14 B.U11 A-U WC 20-XX cWW cW-W 13 A.C15 B.G10 C-G WC 19-XIX cWW cW-W 14 A.C17 B.G7 C-G WC 19-XIX cWW cW-W 15 A.A18 B.U6 A-U WC 20-XX cWW cW-W 16 A.G19 B.C5 G-C WC 19-XIX cWW cW-W 17 A.C20 B.G4 C-G WC 19-XIX cWW cW-W 18 A.A21 B.UMS3 A-u WC 20-XX cWW cW-W 19 A.A22 B.U2 A-U WC 20-XX cWW cW-W 20 A.G23 B.C1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 3 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=7 strand-1 5'-CUuGCUG-3' bp-type ||||||| strand-2 3'-GAACGAC-5' helix-form AAAAAA 1 A.C1 B.G23 C-G WC 19-XIX cWW cW-W 2 A.U2 B.A22 U-A WC 20-XX cWW cW-W 3 A.UMS3 B.A21 u-A WC 20-XX cWW cW-W 4 A.G4 B.C20 G-C WC 19-XIX cWW cW-W 5 A.C5 B.G19 C-G WC 19-XIX cWW cW-W 6 A.U6 B.A18 U-A WC 20-XX cWW cW-W 7 A.G7 B.C17 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=6 strand-1 5'-GUGCAC-3' bp-type |||||| strand-2 3'-CACGUG-5' helix-form AAAAA 1 A.G10 B.C15 G-C WC 19-XIX cWW cW-W 2 A.U11 B.A14 U-A WC 20-XX cWW cW-W 3 A.G12 B.C13 G-C WC 19-XIX cWW cW-W 4 A.C13 B.G12 C-G WC 19-XIX cWW cW-W 5 A.A14 B.U11 A-U WC 20-XX cWW cW-W 6 A.C15 B.G10 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=7 strand-1 5'-CAGCAAG-3' bp-type ||||||| strand-2 3'-GUCGuUC-5' helix-form AAAAAA 1 A.C17 B.G7 C-G WC 19-XIX cWW cW-W 2 A.A18 B.U6 A-U WC 20-XX cWW cW-W 3 A.G19 B.C5 G-C WC 19-XIX cWW cW-W 4 A.C20 B.G4 C-G WC 19-XIX cWW cW-W 5 A.A21 B.UMS3 A-u WC 20-XX cWW cW-W 6 A.A22 B.U2 A-U WC 20-XX cWW cW-W 7 A.G23 B.C1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 3 stems: [#1,#2,#3] **************************************************************************** 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 AAA A.A8,B.A9,B.A8 2 nts=3 GAC A.G10,B.A16,B.C17 3 nts=3 CAG A.C17,A.A16,B.G10 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 A A.A9 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 other O3@A.NMY24 A.G7 3.18 2 other O3@B.NMY24 B.G7 3.45 **************************************************************************** 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 2 internal loops 1 asymmetric internal loop: nts=7; [2,1]; linked by [#1,#2] summary: [2] 2 1 [A.7 B.17 A.10 B.15] 7 6 nts=7 GAAGCAC A.G7,A.A8,A.A9,A.G10,B.C15,B.A16,B.C17 nts=2 AA A.A8,A.A9 nts=1 A B.A16 2 asymmetric internal loop: nts=7; [1,2]; linked by [#2,#3] summary: [2] 1 2 [A.15 B.10 A.17 B.7] 6 7 nts=7 CACGAAG A.C15,A.A16,A.C17,B.G7,B.A8,B.A9,B.G10 nts=1 A A.A16 nts=2 AA B.A8,B.A9 **************************************************************************** List of 1 ribose zipper 1 nts=4 AAAA A.A8,A.A9,B.A8,B.A9 **************************************************************************** List of 5 splayed-apart dinucleotides 1 A.G7 A.A8 angle=132 distance=18.1 ratio=0.92 2 A.A8 A.A9 angle=96 distance=14.0 ratio=0.75 3 A.A9 A.G10 angle=103 distance=13.9 ratio=0.79 4 B.G7 B.A8 angle=115 distance=17.4 ratio=0.85 5 B.A9 B.G10 angle=153 distance=17.6 ratio=0.97 ---------------------------------------------------------------- Summary of 3 splayed-apart units 1 nts=4 GAAG A.G7,A.A8,A.A9,A.G10 2 nts=2 GA B.G7,B.A8 3 nts=2 AG B.A9,B.G10 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >3c7r nts=46 [whole] CUuGCUGAAGUGCACACAGCAAG&CUuGCUGAAGUGCACACAGCAAG (((((((..((((((.(((((((&)))))))..)))))).))))))) >3c7r-A #1 nts=23 2.36(1.57) [chain] RNA CUuGCUGAAGUGCACACAGCAAG (((((((..((((((.((((((( >3c7r-B #2 nts=23 2.32(1.70) [chain] RNA CUuGCUGAAGUGCACACAGCAAG )))))))..)))))).))))))) **************************************************************************** Summary of structural features of 46 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 C ( A.C1 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 U ( A.U2 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 u ( A.UMS3 0.013 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 G ( A.G4 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 C ( A.C5 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 U ( A.U6 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 G ( A.G7 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-acceptor,splayed-apart 8 A . A.A8 0.009 anti,non-pair-contact,internal-loop,ribose-zipper,phosphate,splayed-apart 9 A . A.A9 0.006 anti,~C3'-endo,non-stack,non-pair-contact,internal-loop,ribose-zipper,phosphate,splayed-apart 10 G ( A.G10 0.011 ~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 11 U ( A.U11 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 G ( A.G12 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 C ( A.C13 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 14 A ( A.A14 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 15 C ( A.C15 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 16 A . A.A16 0.008 anti,~C3'-endo,BI,non-pair-contact,internal-loop 17 C ( A.C17 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 18 A ( A.A18 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 G ( A.G19 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 C ( A.C20 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 A ( A.A21 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 A ( A.A22 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 G ( A.G23 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 24 C ) B.C1 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 25 U ) B.U2 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 u ) B.UMS3 0.025 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 G ) B.G4 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 28 C ) B.C5 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 29 U ) B.U6 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 G ) B.G7 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-acceptor,splayed-apart 31 A . B.A8 0.013 anti,~C3'-endo,BI,non-pair-contact,internal-loop,ribose-zipper,phosphate,splayed-apart 32 A . B.A9 0.005 anti,~C3'-endo,BII,non-pair-contact,internal-loop,ribose-zipper,phosphate,splayed-apart 33 G ) B.G10 0.015 ~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 34 U ) B.U11 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 35 G ) B.G12 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 36 C ) B.C13 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 37 A ) B.A14 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 38 C ) B.C15 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 39 A . B.A16 0.009 anti,~C3'-endo,BI,non-pair-contact,internal-loop 40 C ) B.C17 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 41 A ) B.A18 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 G ) B.G19 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 43 C ) B.C20 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 44 A ) B.A21 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 45 A ) B.A22 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 46 G ) B.G23 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 15 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-splays.pdb -- an ensemble of splayed-apart units 10 dssr-stacks.pdb -- an ensemble of base stacks 11 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 12 dssr-rotmat.txt -- position vector and rotation matrix 13 dssr-viewV.pdb -- vertical view of the principal moment of inertia 14 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 15 dssr-viewT.pdb -- top view of the principal moment of inertia