Platinum in the structure of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link (pdb 3lpv)

The binding sites of Platinum atom in the structure of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link (pdb code 3lpv). This binding sites where shown with 5.0 Angstroms radius around Platinum atom. The 3lpv structure was solved by R.C.TODD, S.J.LIPPARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 44.3-1.8 Space group P1 a (A) 31.303 b (A) 35.425 c (A) 45.128 alpha (°) 80.06 beta (°) 84.09 gamma (°) 81.77 Rfactor (%) 17.2 Rfree (%) 19.8 Platinum Binding Sites: Platinum binding site 1 out of 2 in 3lpv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 3lpv. 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: Dt5, A: Dg6, A: Dg7, A: Cpt49, A: Hoh1005, A: Hoh1053, A: Hoh1074, A: Hoh1075, A: Hoh1076, A: Hoh1077, A: Hoh1078, conact list: Atom Atom Distance (A) Pt N3 A:Dt5 4.98 Pt C4 A:Dt5 4.86 Pt N9 A:Dg6 4.11 Pt C8 A:Dg6 3.00 Pt C6 A:Dg6 3.52 Pt N1 A:Dg6 4.84 Pt C5 A:Dg6 3.01 Pt N7 A:Dg6 2.07 Pt C4 A:Dg6 4.10 Pt OP2 A:Dg6 3.98 Pt O6 A:Dg6 3.35 Pt N9 A:Dg7 4.17 Pt C8 A:Dg7 2.96 Pt C6 A:Dg7 3.73 Pt C5 A:Dg7 3.16 Pt N7 A:Dg7 2.11 Pt C4 A:Dg7 4.25 Pt O6 A:Dg7 3.60 Pt N1 A:Cpt49 2.07 Pt N2 A:Cpt49 2.01 Pt PT1 A:Cpt49 0.00 Pt O A:Hoh1005 3.66 Pt O A:Hoh1053 4.18 Pt O A:Hoh1074 4.69 Pt O A:Hoh1075 4.13 Pt O A:Hoh1076 4.19 Pt O A:Hoh1077 4.23 Pt O A:Hoh1078 3.43 interactive model: Platinum binding site 2 out of 2 in 3lpv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 3lpv. 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: C: Dt29, C: Dg30, C: Dg31, C: Cpt50, C: Hoh1002, C: Hoh1003, C: Hoh1020, C: Hoh1073, C: Hoh1116, C: Hoh1121, conact list: Atom Atom Distance (A) Pt C4 C:Dt29 4.87 Pt N9 C:Dg30 4.10 Pt C8 C:Dg30 2.96 Pt C6 C:Dg30 3.55 Pt N1 C:Dg30 4.87 Pt C5 C:Dg30 3.01 Pt N7 C:Dg30 1.99 Pt C4 C:Dg30 4.12 Pt OP2 C:Dg30 3.91 Pt O5' C:Dg30 4.89 Pt O6 C:Dg30 3.36 Pt N9 C:Dg31 4.18 Pt C8 C:Dg31 2.97 Pt C6 C:Dg31 3.72 Pt C5 C:Dg31 3.15 Pt N7 C:Dg31 2.10 Pt C4 C:Dg31 4.25 Pt O6 C:Dg31 3.56 Pt N1 C:Cpt50 2.07 Pt N2 C:Cpt50 1.93 Pt PT1 C:Cpt50 0.00 Pt O C:Hoh1002 3.75 Pt O C:Hoh1003 3.64 Pt O C:Hoh1020 4.11 Pt O C:Hoh1073 3.82 Pt O C:Hoh1116 4.86 Pt O C:Hoh1121 4.73 interactive model: