**************************************************************************** File name: 1nz1.pdb no. of DNA/RNA chains: 1 [A=24] no. of nucleotides: 24 no. of atoms: 767 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 SSU-u 1 A.SSU19 **************************************************************************** List of 10 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1 A.C24 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C23 G-C WC 19-XIX cWW cW-W 3 A.U3 A.A22 U-A WC 20-XX cWW cW-W 4 A.U4 A.A21 U-A WC 20-XX cWW cW-W 5 A.C5 A.G20 C-G WC 19-XIX cWW cW-W 6 A.C6 A.A18 C-A ~Wobble -- cWW cW-W 7 A.C7 A.G17 C-G WC 19-XIX cWW cW-W 8 A.C8 A.G16 C-G WC 19-XIX cWW cW-W 9 A.U9 A.A15 U-A WC 20-XX cWW cW-W 10 A.G10 A.A14 G-A Sheared 11-XI tSH tm-M **************************************************************************** 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[2] bps=10 strand-1 5'-GGUUCCCCUG-3' bp-type |||||.|||. strand-2 3'-CCAAGAGGAA-5' helix-form .AAAx.... 1 A.G1 A.C24 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C23 G-C WC 19-XIX cWW cW-W 3 A.U3 A.A22 U-A WC 20-XX cWW cW-W 4 A.U4 A.A21 U-A WC 20-XX cWW cW-W 5 A.C5 A.G20 C-G WC 19-XIX cWW cW-W 6 A.C6 A.A18 C-A ~Wobble -- cWW cW-W 7 A.C7 A.G17 C-G WC 19-XIX cWW cW-W 8 A.C8 A.G16 C-G WC 19-XIX cWW cW-W 9 A.U9 A.A15 U-A WC 20-XX cWW cW-W 10 A.G10 A.A14 G-A Sheared 11-XI tSH tm-M **************************************************************************** List of 2 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=5 strand-1 5'-GGUUC-3' bp-type ||||| strand-2 3'-CCAAG-5' helix-form .AAA 1 A.G1 A.C24 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C23 G-C WC 19-XIX cWW cW-W 3 A.U3 A.A22 U-A WC 20-XX cWW cW-W 4 A.U4 A.A21 U-A WC 20-XX cWW cW-W 5 A.C5 A.G20 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=3 strand-1 5'-CCU-3' bp-type ||| strand-2 3'-GGA-5' helix-form .. 1 A.C7 A.G17 C-G WC 19-XIX cWW cW-W 2 A.C8 A.G16 C-G WC 19-XIX cWW cW-W 3 A.U9 A.A15 U-A WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 4 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 UG A.U9,A.G10 2 nts=3 CCC A.C5,A.C6,A.C7 3 nts=3 AAA A.A12,A.A14,A.A15 4 nts=4 GAuG A.G17,A.A18,A.SSU19,A.G20 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 CUC A.C11,A.U13,A.C24 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate OP1@A.A12 A.G10 3.29 **************************************************************************** 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 1 hairpin loop 1 hairpin loop: nts=7; [5]; linked by [#2] summary: [1] 5 [A.9 A.15] 3 nts=7 UGCAUAA A.U9,A.G10,A.C11,A.A12,A.U13,A.A14,A.A15 nts=5 GCAUA A.G10,A.C11,A.A12,A.U13,A.A14 **************************************************************************** List of 1 internal loop 1 asymmetric internal loop: nts=7; [1,2]; linked by [#1,#2] summary: [2] 1 2 [A.5 A.20 A.7 A.17] 5 3 nts=7 CCCGAuG A.C5,A.C6,A.C7,A.G17,A.A18,A.SSU19,A.G20 nts=1 C A.C6 nts=2 Au A.A18,A.SSU19 **************************************************************************** List of 1 splayed-apart dinucleotide 1 A.G10 A.C11 angle=95 distance=13.1 ratio=0.74 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 GC A.G10,A.C11 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1nz1 nts=24 [whole] GGUUCCCCUGCAUAAGGAuGAACC (((((.(((.....)))..))))) >1nz1-A #1 nts=24 0.33(2.73) [chain] RNA GGUUCCCCUGCAUAAGGAuGAACC (((((.(((.....)))..))))) **************************************************************************** Summary of structural features of 24 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 G ( A.G1 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 G ( A.G2 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 U ( A.U3 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 U ( A.U4 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 C ( A.C5 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 6 C . A.C6 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 7 C ( A.C7 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 8 C ( A.C8 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 U ( A.U9 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 10 G . A.G10 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,splayed-apart 11 C . A.C11 0.009 anti,~C3'-endo,BI,non-stack,non-pair-contact,hairpin-loop,splayed-apart 12 A . A.A12 0.019 anti,~C2'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate 13 U . A.U13 0.015 turn,anti,non-stack,hairpin-loop 14 A . A.A14 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 15 A ) A.A15 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 16 G ) A.G16 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 G ) A.G17 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 18 A . A.A18 0.018 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 19 u . A.SSU19 0.016 modified,anti,~C3'-endo,BI,non-pair-contact,internal-loop 20 G ) A.G20 0.019 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 21 A ) A.A21 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 A ) A.A22 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 C ) A.C23 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 C ) A.C24 0.009 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 16 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-hairpins.pdb -- an ensemble of hairpin loops 5 dssr-iloops.pdb -- an ensemble of internal loops 6 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 7 dssr-2ndstrs.ct -- secondary structure in connectivity table format 8 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 dssr-torsions.txt -- backbone torsion angles and suite names 10 dssr-splays.pdb -- an ensemble of splayed-apart units 11 dssr-stacks.pdb -- an ensemble of base stacks 12 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions 13 dssr-rotmat.txt -- position vector and rotation matrix 14 dssr-viewV.pdb -- vertical view of the principal moment of inertia 15 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 16 dssr-viewT.pdb -- top view of the principal moment of inertia