The binding sites of Platinum atom in the structure of Crystal Structure of DPO4 in Complex With Dna Containing the Major Cisplatin Lesion (pdb code 3m9n). This binding sites where shown with 5.0 Angstroms radius around Platinum atom.
The 3m9n structure was solved by J.H.Y.WONG, H.LING, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 27.6-1.9 | | Space group | P21212 | | a (A) | 98.227 | | b (A) | 103.233 | | c (A) | 52.259 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 24.3 | | Rfree (%) | 26.1 |
|
Platinum binding site 1 out of 2 in 3m9n
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 3m9n. 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: T: Dg4, T: Dg5, T: Cpt1005, | conact list:
| Atom | Atom | Distance (A) | | Pt | N9 T:Dg4 | 3.89 | | Pt | N9 T:Dg4 | 3.95 | | Pt | OP1 T:Dg4 | 4.66 | | Pt | OP1 T:Dg4 | 4.72 | | Pt | C8 T:Dg4 | 2.73 | | Pt | C8 T:Dg4 | 3.25 | | Pt | C6 T:Dg4 | 3.90 | | Pt | C6 T:Dg4 | 4.14 | | Pt | C5 T:Dg4 | 3.13 | | Pt | C5 T:Dg4 | 3.45 | | Pt | C1' T:Dg4 | 4.99 | | Pt | N7 T:Dg4 | 2.05 | | Pt | N7 T:Dg4 | 2.90 | | Pt | C4 T:Dg4 | 4.08 | | Pt | C4 T:Dg4 | 4.06 | | Pt | C2' T:Dg4 | 4.92 | | Pt | O6 T:Dg4 | 3.97 | | Pt | O6 T:Dg4 | 4.40 | | Pt | N9 T:Dg5 | 4.26 | | Pt | N9 T:Dg5 | 2.02 | | Pt | N3 T:Dg5 | 3.59 | | Pt | C8 T:Dg5 | 3.20 | | Pt | C8 T:Dg5 | 0.83 | | Pt | C2 T:Dg5 | 4.26 | | Pt | C6 T:Dg5 | 3.52 | | Pt | C6 T:Dg5 | 2.97 | | Pt | N1 T:Dg5 | 4.86 | | Pt | N1 T:Dg5 | 4.02 | | Pt | C5 T:Dg5 | 2.97 | | Pt | C5 T:Dg5 | 1.67 | | Pt | C1' T:Dg5 | 3.54 | | Pt | N7 T:Dg5 | 2.01 | | Pt | N7 T:Dg5 | 0.63 | | Pt | O4' T:Dg5 | 4.16 | | Pt | C4 T:Dg5 | 4.19 | | Pt | C4 T:Dg5 | 2.26 | | Pt | C2' T:Dg5 | 4.50 | | Pt | O6 T:Dg5 | 3.42 | | Pt | O6 T:Dg5 | 3.64 | | Pt | N1 T:Cpt1005 | 1.99 | | Pt | N1 T:Cpt1005 | 3.36 | | Pt | N2 T:Cpt1005 | 2.00 | | Pt | N2 T:Cpt1005 | 4.34 | | Pt | PT1 T:Cpt1005 | 0.00 | | Pt | PT1 T:Cpt1005 | 2.41 |
| interactive model:
| Platinum binding site 2 out of 2 in 3m9n
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 3m9n. 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: Gly58, T: Dg4, T: Dg5, T: Cpt1005, T: Hoh283, | conact list:
| Atom | Atom | Distance (A) | | Pt | O B:Gly58 | 4.33 | | Pt | C B:Gly58 | 4.92 | | Pt | CA B:Gly58 | 4.48 | | Pt | N9 T:Dg4 | 4.27 | | Pt | N9 T:Dg4 | 4.17 | | Pt | OP1 T:Dg4 | 4.42 | | Pt | OP1 T:Dg4 | 4.54 | | Pt | C8 T:Dg4 | 3.09 | | Pt | C8 T:Dg4 | 3.01 | | Pt | C6 T:Dg4 | 3.60 | | Pt | C6 T:Dg4 | 3.63 | | Pt | N1 T:Dg4 | 4.95 | | Pt | N1 T:Dg4 | 4.99 | | Pt | C5 T:Dg4 | 3.07 | | Pt | C5 T:Dg4 | 3.04 | | Pt | N7 T:Dg4 | 2.08 | | Pt | N7 T:Dg4 | 2.01 | | Pt | C4 T:Dg4 | 4.26 | | Pt | C4 T:Dg4 | 4.19 | | Pt | O6 T:Dg4 | 3.44 | | Pt | O6 T:Dg4 | 3.51 | | Pt | N9 T:Dg5 | 4.18 | | Pt | C8 T:Dg5 | 3.04 | | Pt | C6 T:Dg5 | 4.84 | | Pt | C6 T:Dg5 | 3.62 | | Pt | N1 T:Dg5 | 4.90 | | Pt | C5 T:Dg5 | 4.75 | | Pt | C5 T:Dg5 | 3.01 | | Pt | N7 T:Dg5 | 4.20 | | Pt | N7 T:Dg5 | 2.04 | | Pt | C4 T:Dg5 | 4.13 | | Pt | O6 T:Dg5 | 4.42 | | Pt | O6 T:Dg5 | 3.60 | | Pt | N1 T:Cpt1005 | 3.91 | | Pt | N1 T:Cpt1005 | 2.02 | | Pt | N2 T:Cpt1005 | 1.53 | | Pt | N2 T:Cpt1005 | 1.98 | | Pt | PT1 T:Cpt1005 | 2.41 | | Pt | PT1 T:Cpt1005 | 0.00 | | Pt | O T:Hoh283 | 4.78 |
| interactive model:
|
|