The binding sites of Platinum atom in the structure of Nucleosome Core Particle Modified With A Cisplatin 1,3-Cis-{Pt(NH3) 2}2+-D(Gptpg) Intrastrand Cross-Link (pdb code 3o62). This binding sites where shown with 5.0 Angstroms radius around Platinum atom.
The 3o62 structure was solved by S.J.LIPPARD, R.C.TODD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 42.0-3.2 | | Space group | P212121 | | a (A) | 106.095 | | b (A) | 109.551 | | c (A) | 177.176 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 24.9 | | Rfree (%) | 30.6 |
|
Platinum binding site 1 out of 1 in 3o62
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 3o62. 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: I: Dg70, I: Dg72, I: Da73, I: Cpt147, | conact list:
| Atom | Atom | Distance (A) | | Pt | N9 I:Dg70 | 4.19 | | Pt | C8 I:Dg70 | 2.95 | | Pt | C6 I:Dg70 | 3.69 | | Pt | C5 I:Dg70 | 3.13 | | Pt | N7 I:Dg70 | 2.04 | | Pt | C4 I:Dg70 | 4.27 | | Pt | O6 I:Dg70 | 3.53 | | Pt | N9 I:Dg72 | 4.24 | | Pt | OP1 I:Dg72 | 4.48 | | Pt | C8 I:Dg72 | 2.97 | | Pt | C6 I:Dg72 | 3.89 | | Pt | C5 I:Dg72 | 3.22 | | Pt | P I:Dg72 | 4.72 | | Pt | N7 I:Dg72 | 2.07 | | Pt | C4 I:Dg72 | 4.35 | | Pt | OP2 I:Dg72 | 4.32 | | Pt | O5' I:Dg72 | 4.87 | | Pt | O6 I:Dg72 | 3.79 | | Pt | C8 I:Da73 | 4.98 | | Pt | C6 I:Da73 | 4.47 | | Pt | C5 I:Da73 | 4.41 | | Pt | N6 I:Da73 | 4.40 | | Pt | N7 I:Da73 | 4.36 | | Pt | N1 I:Cpt147 | 2.02 | | Pt | N2 I:Cpt147 | 2.06 | | Pt | PT1 I:Cpt147 | 0.00 |
| interactive model:
|
|