The binding sites of Platinum atom in the structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1). (pdb code 4dl4). This binding sites where shown with 5.0 Angstroms radius around Platinum atom.
The 4dl4 structure was solved by YE ZHAO, CHRISTIAN BIERTUMPFEL, MARK GREGORY, YUE-JIN HUA, FUMIO HANAOKA, WEI YANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 30.0-2.0 | | Space group | P61 | | a (A) | 99.210 | | b (A) | 99.210 | | c (A) | 82.150 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 120.00 | | Rfactor (%) | 19.4 | | Rfree (%) | 21.7 |
|
Platinum binding site 1 out of 2 in 4dl4
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 4dl4. 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: Dg3, T: Dg4, T: Dc5, T: Cpt101, T: Hoh201, T: Hoh212, | conact list:
| Atom | Atom | Distance (A) | | Pt | N9 T:Dg3 | 4.20 | | Pt | N9 T:Dg3 | 3.77 | | Pt | N3 T:Dg3 | 4.98 | | Pt | C8 T:Dg3 | 3.05 | | Pt | C8 T:Dg3 | 2.65 | | Pt | C6 T:Dg3 | 3.43 | | Pt | C6 T:Dg3 | 3.20 | | Pt | N1 T:Dg3 | 4.81 | | Pt | N1 T:Dg3 | 4.56 | | Pt | C5 T:Dg3 | 3.00 | | Pt | C5 T:Dg3 | 2.58 | | Pt | N7 T:Dg3 | 2.03 | | Pt | N7 T:Dg3 | 1.60 | | Pt | C4 T:Dg3 | 4.17 | | Pt | C4 T:Dg3 | 3.73 | | Pt | O6 T:Dg3 | 3.12 | | Pt | O6 T:Dg3 | 3.09 | | Pt | N9 T:Dg4 | 4.21 | | Pt | N9 T:Dg4 | 4.17 | | Pt | C8 T:Dg4 | 3.05 | | Pt | C8 T:Dg4 | 2.97 | | Pt | C6 T:Dg4 | 3.60 | | Pt | C6 T:Dg4 | 3.67 | | Pt | N1 T:Dg4 | 4.97 | | Pt | C5 T:Dg4 | 3.10 | | Pt | C5 T:Dg4 | 3.13 | | Pt | N7 T:Dg4 | 2.11 | | Pt | N7 T:Dg4 | 2.12 | | Pt | C4 T:Dg4 | 4.25 | | Pt | C4 T:Dg4 | 4.24 | | Pt | O6 T:Dg4 | 3.38 | | Pt | O6 T:Dg4 | 3.50 | | Pt | N4 T:Dc5 | 4.63 | | Pt | N1 T:Cpt101 | 2.08 | | Pt | N1 T:Cpt101 | 2.27 | | Pt | N2 T:Cpt101 | 2.02 | | Pt | N2 T:Cpt101 | 2.57 | | Pt | PT1 T:Cpt101 | 0.00 | | Pt | PT1 T:Cpt101 | 0.61 | | Pt | O T:Hoh201 | 4.39 | | Pt | O T:Hoh212 | 4.47 |
| interactive model:
| Platinum binding site 2 out of 2 in 4dl4
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 4dl4. 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: Dg3, T: Dg4, T: Dc5, T: Cpt101, T: Hoh201, T: Hoh212, | conact list:
| Atom | Atom | Distance (A) | | Pt | N9 T:Dg3 | 4.76 | | Pt | N9 T:Dg3 | 4.30 | | Pt | C8 T:Dg3 | 3.57 | | Pt | C8 T:Dg3 | 3.12 | | Pt | C6 T:Dg3 | 3.95 | | Pt | C6 T:Dg3 | 3.62 | | Pt | C5 T:Dg3 | 3.59 | | Pt | C5 T:Dg3 | 3.11 | | Pt | N7 T:Dg3 | 2.62 | | Pt | N7 T:Dg3 | 2.11 | | Pt | C4 T:Dg3 | 4.77 | | Pt | C4 T:Dg3 | 4.29 | | Pt | O6 T:Dg3 | 3.52 | | Pt | O6 T:Dg3 | 3.35 | | Pt | N9 T:Dg4 | 4.29 | | Pt | N9 T:Dg4 | 4.24 | | Pt | C8 T:Dg4 | 3.13 | | Pt | C8 T:Dg4 | 3.03 | | Pt | C6 T:Dg4 | 3.55 | | Pt | C6 T:Dg4 | 3.62 | | Pt | N1 T:Dg4 | 4.94 | | Pt | C5 T:Dg4 | 3.11 | | Pt | C5 T:Dg4 | 3.13 | | Pt | N7 T:Dg4 | 2.14 | | Pt | N7 T:Dg4 | 2.11 | | Pt | C4 T:Dg4 | 4.29 | | Pt | C4 T:Dg4 | 4.28 | | Pt | O6 T:Dg4 | 3.29 | | Pt | O6 T:Dg4 | 3.39 | | Pt | N4 T:Dc5 | 4.16 | | Pt | N1 T:Cpt101 | 2.19 | | Pt | N1 T:Cpt101 | 2.07 | | Pt | N2 T:Cpt101 | 1.46 | | Pt | N2 T:Cpt101 | 2.02 | | Pt | PT1 T:Cpt101 | 0.61 | | Pt | PT1 T:Cpt101 | 0.00 | | Pt | O T:Hoh201 | 4.39 | | Pt | O T:Hoh212 | 3.93 |
| interactive model:
|
|