The binding sites of Platinum atom in the structure of 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(Ammine)(Cyclohexylamine)}2+ Bound to A Dodecamer Dna Duplex (pdb code 1lu5). This binding sites where shown with 5.0 Angstroms radius around Platinum atom. The 1lu5 structure was solved by A.P.SILVERMAN, W.BU, S.M.COHEN, S.J.LIPPARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 50.0-2.4 | Space group | P1 | a (A) | 31.644 | b (A) | 35.638 | c (A) | 46.556 | alpha (°) | 79.53 | beta (°) | 83.02 | gamma (°) | 81.36 | Rfactor (%) | 23.4 | Rfree (%) | 29.4 |
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Platinum binding site 1 out of 2 in 1lu5
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 1lu5. 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: Lpt49, A: Hoh204, A: Hoh222, A: Hoh224, | conact list:
Atom | Atom | Distance (A) | Pt | N3 A:Dt5 | 4.96 | Pt | C4 A:Dt5 | 4.88 | Pt | N9 A:Dg6 | 3.96 | Pt | C8 A:Dg6 | 2.85 | Pt | C6 A:Dg6 | 3.53 | Pt | N1 A:Dg6 | 4.82 | Pt | C5 A:Dg6 | 2.93 | Pt | N7 A:Dg6 | 1.97 | Pt | C4 A:Dg6 | 4.00 | Pt | OP2 A:Dg6 | 4.08 | Pt | O6 A:Dg6 | 3.45 | Pt | N9 A:Dg7 | 4.11 | Pt | C8 A:Dg7 | 2.93 | Pt | C6 A:Dg7 | 3.54 | Pt | N1 A:Dg7 | 4.89 | Pt | C5 A:Dg7 | 2.99 | Pt | N7 A:Dg7 | 1.96 | Pt | C4 A:Dg7 | 4.14 | Pt | O6 A:Dg7 | 3.38 | Pt | N1 A:Lpt49 | 2.01 | Pt | C5 A:Lpt49 | 4.48 | Pt | N2 A:Lpt49 | 2.05 | Pt | C4 A:Lpt49 | 3.03 | Pt | C3 A:Lpt49 | 3.00 | Pt | PT A:Lpt49 | 0.00 | Pt | C8 A:Lpt49 | 4.27 | Pt | O A:Hoh204 | 3.86 | Pt | O A:Hoh222 | 4.41 | Pt | O A:Hoh224 | 3.27 |
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| Platinum binding site 2 out of 2 in 1lu5
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 1lu5. 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: Lpt50, C: Hoh201, | conact list:
Atom | Atom | Distance (A) | Pt | N3 C:Dt29 | 4.98 | Pt | C4 C:Dt29 | 4.92 | Pt | N9 C:Dg30 | 4.02 | Pt | C8 C:Dg30 | 2.94 | Pt | C6 C:Dg30 | 3.35 | Pt | N1 C:Dg30 | 4.67 | Pt | C5 C:Dg30 | 2.84 | Pt | N7 C:Dg30 | 1.96 | Pt | C4 C:Dg30 | 3.97 | Pt | OP2 C:Dg30 | 3.99 | Pt | O6 C:Dg30 | 3.22 | Pt | N9 C:Dg31 | 4.01 | Pt | C8 C:Dg31 | 2.85 | Pt | C6 C:Dg31 | 3.63 | Pt | N1 C:Dg31 | 4.95 | Pt | C5 C:Dg31 | 3.00 | Pt | N7 C:Dg31 | 1.96 | Pt | C4 C:Dg31 | 4.09 | Pt | O6 C:Dg31 | 3.56 | Pt | N1 C:Lpt50 | 2.01 | Pt | C5 C:Lpt50 | 4.55 | Pt | N2 C:Lpt50 | 2.05 | Pt | C4 C:Lpt50 | 3.06 | Pt | C3 C:Lpt50 | 3.05 | Pt | PT C:Lpt50 | 0.00 | Pt | C8 C:Lpt50 | 4.19 | Pt | O C:Hoh201 | 3.60 |
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