Platinum in the structure of A Backbone Binding Dna Complex (pdb 2dyw)

The binding sites of Platinum atom in the structure of A Backbone Binding Dna Complex (pdb code 2dyw). This binding sites where shown with 5.0 Angstroms radius around Platinum atom. The 2dyw structure was solved by S.KOMEDA, T.MOULAEI, K.K.WOODS, M.CHIKUMA, N.P.FARRELL, L.D.WILLIAMS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 5.5-1.1 Space group P212121 a (A) 23.675 b (A) 41.692 c (A) 65.651 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) 23.2 Platinum Binding Sites: Platinum binding site 1 out of 4 in 2dyw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 2dyw. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg4, A: A71301, A: Hoh2106, conact list: Atom Atom Distance (A) Pt OP1 A:Dg4 3.81 Pt P A:Dg4 4.92 Pt C5' A:Dg4 4.50 Pt C6 A:A71301 4.25 Pt N10 A:A71301 1.98 Pt N9 A:A71301 1.99 Pt C7 A:A71301 2.87 Pt N8 A:A71301 1.96 Pt N11 A:A71301 2.05 Pt PT A:A71301 0.00 Pt O A:Hoh2106 4.45 interactive model: Platinum binding site 2 out of 4 in 2dyw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 2dyw. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Dc3, B: A71201, B: A72202, B: Hoh2006, B: Hoh2046, conact list: Atom Atom Distance (A) Pt OP1 B:Dc3 4.99 Pt C6 B:A71201 3.18 Pt N10 B:A71201 1.98 Pt N9 B:A71201 1.95 Pt C5 B:A71201 4.24 Pt C7 B:A71201 2.90 Pt N8 B:A71201 1.99 Pt N11 B:A71201 1.99 Pt PT B:A71201 0.00 Pt C12 B:A72202 2.95 Pt C14 B:A72202 4.80 Pt C13 B:A72202 3.37 Pt O B:Hoh2006 3.95 Pt O B:Hoh2046 4.17 interactive model: Platinum binding site 3 out of 4 in 2dyw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Platinum in the PDB 2dyw. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Dg4, B: A72202, B: Hoh2086, conact list: Atom Atom Distance (A) Pt OP1 B:Dg4 3.96 Pt P B:Dg4 4.97 Pt C5' B:Dg4 4.26 Pt N19 B:A72202 1.97 Pt N20 B:A72202 1.98 Pt N18 B:A72202 1.96 Pt PT B:A72202 0.00 Pt C16 B:A72202 4.36 Pt C17 B:A72202 2.96 Pt C23 B:A72202 4.20 Pt C22 B:A72202 2.86 Pt N21 B:A72202 1.96 Pt O B:Hoh2086 4.54 interactive model: Platinum binding site 4 out of 4 in 2dyw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Platinum in the PDB 2dyw. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Da5, B: A72202, B: A71203, conact list: Atom Atom Distance (A) Pt OP1 B:Da5 3.86 Pt C25 B:A72202 4.79 Pt C27 B:A72202 2.86 Pt C26 B:A72202 4.08 Pt C6 B:A71203 4.23 Pt N10 B:A71203 1.99 Pt N9 B:A71203 1.98 Pt C7 B:A71203 2.86 Pt N8 B:A71203 2.00 Pt N11 B:A71203 1.98 Pt PT B:A71203 0.00 interactive model: