Platinum in the structure of The Primary Mode Of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G (pdb 5bna)

The binding sites of Platinum atom in the structure of The Primary Mode Of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G (pdb code 5bna). This binding sites where shown with 5.0 Angstroms radius around Platinum atom. The 5bna structure was solved by R.M.WING, P.PJURA, H.R.DREW, R.E.DICKERSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.6 Space group P212121 a (A) 24.160 b (A) 39.930 c (A) 66.120 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 10.2 Rfree (%) n/a Platinum Binding Sites: Platinum binding site 1 out of 3 in 5bna Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 5bna. 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: Dt8, B: Dc15, B: Dg16, B: Da17, A: Ptn25, A: Hoh33, A: Hoh71, A: Hoh137, A: Hoh152, B: Hoh57, conact list: Atom Atom Distance (A) Pt O4 A:Dt8 4.85 Pt C6 B:Dc15 4.72 Pt C5 B:Dc15 4.82 Pt N9 B:Dg16 4.35 Pt C8 B:Dg16 3.15 Pt C6 B:Dg16 3.73 Pt C5 B:Dg16 3.19 Pt N7 B:Dg16 2.16 Pt C4 B:Dg16 4.37 Pt OP2 B:Dg16 4.45 Pt O6 B:Dg16 3.52 Pt N6 B:Da17 4.45 Pt N1 A:Ptn25 2.02 Pt N3 A:Ptn25 2.00 Pt PT A:Ptn25 0.00 Pt N2 A:Ptn25 1.81 Pt O A:Hoh33 3.56 Pt O A:Hoh71 4.96 Pt O A:Hoh137 4.02 Pt O A:Hoh152 4.93 Pt O B:Hoh57 4.56 interactive model: Platinum binding site 2 out of 3 in 5bna Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 5bna. 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: Dc3, A: Dg4, A: Da5, A: Ptn26, A: Hoh109, conact list: Atom Atom Distance (A) Pt C6 A:Dc3 4.24 Pt N1 A:Dc3 4.72 Pt C5 A:Dc3 4.38 Pt C4 A:Dc3 4.98 Pt C2' A:Dc3 4.25 Pt N9 A:Dg4 4.47 Pt C8 A:Dg4 3.23 Pt C6 A:Dg4 3.95 Pt C5 A:Dg4 3.38 Pt N7 A:Dg4 2.31 Pt C4 A:Dg4 4.52 Pt OP2 A:Dg4 4.73 Pt O6 A:Dg4 3.74 Pt N6 A:Da5 4.73 Pt N1 A:Ptn26 1.75 Pt N3 A:Ptn26 2.23 Pt PT A:Ptn26 0.00 Pt N2 A:Ptn26 2.25 Pt O A:Hoh109 4.45 interactive model: Platinum binding site 3 out of 3 in 5bna Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Platinum in the PDB 5bna. 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: Dg10, B: Ptn27, A: Hoh139, B: Hoh99, conact list: Atom Atom Distance (A) Pt N9 A:Dg10 4.17 Pt C8 A:Dg10 2.96 Pt C6 A:Dg10 4.02 Pt C5 A:Dg10 3.33 Pt N7 A:Dg10 2.23 Pt C4 A:Dg10 4.35 Pt O6 A:Dg10 3.93 Pt N1 B:Ptn27 1.83 Pt N3 B:Ptn27 2.14 Pt PT B:Ptn27 0.00 Pt N2 B:Ptn27 2.10 Pt O A:Hoh139 3.89 Pt O B:Hoh99 4.61 interactive model: