Chemical elements
  Platinum
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    Chemical Properties
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    PDB 1a2e-2bho
    PDB 2ch8-3un9
    PDB 3vdk-5bna
      3vdk
      4dd4
      4dd6
      4dd7
      4dd9
      4ddb
      4ddc
      4dl4
      4dl5
      4dl6
      4dl7
      4eey
      5bna

Platinum in the structure of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). (pdb 4dl6)






The binding sites of Platinum atom in the structure of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). (pdb code 4dl6). This binding sites where shown with 5.0 Angstroms radius around Platinum atom.
The 4dl6 structure was solved by Y.ZHAO, C.BIERTUMPFEL, M.GREGORY, Y.HUA, F.HANAOKA, W.YANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)30.0-2.5
Space groupP61
a (A)98.780
b (A)98.780
c (A)81.510
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)20.2
Rfree (%)22


Platinum Binding Sites:

Platinum binding site 1 out of 2 in 4dl6


Platinum binding site 1 out of 2 in 4dl6
Click to enlarge
stereopicture of Platinum binding site 1 out of 2 in 4dl6
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 4dl6. 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: Dg5, T: Dg6, T: Dc7, T: Cpt101, T: Hoh202,

conact list:


AtomAtomDistance (A)
PtN9 T:Dg53.99
PtN9 T:Dg54.31
PtC8 T:Dg52.96
PtC8 T:Dg53.55
PtC6 T:Dg53.46
PtC6 T:Dg54.18
PtN1 T:Dg54.73
PtC5 T:Dg52.95
PtC5 T:Dg53.65
PtN7 T:Dg52.08
PtN7 T:Dg53.07
PtC4 T:Dg53.97
PtC4 T:Dg54.36
PtO6 T:Dg53.35
PtO6 T:Dg54.25
PtN9 T:Dg64.19
PtN9 T:Dg62.99
PtN3 T:Dg64.50
PtC8 T:Dg63.01
PtC8 T:Dg61.77
PtC2 T:Dg64.97
PtC6 T:Dg63.62
PtC6 T:Dg63.24
PtN1 T:Dg64.98
PtN1 T:Dg64.48
PtC5 T:Dg63.10
PtC5 T:Dg62.26
PtC1' T:Dg64.36
PtN7 T:Dg62.05
PtN7 T:Dg61.00
PtO4' T:Dg64.74
PtC4 T:Dg64.23
PtC4 T:Dg63.18
PtO6 T:Dg63.43
PtO6 T:Dg63.51
PtN4 T:Dc74.75
PtN4 T:Dc74.72
PtN1 T:Cpt1012.06
PtN1 T:Cpt1013.89
PtN2 T:Cpt1012.01
PtN2 T:Cpt1012.42
PtPT1 T:Cpt1010.00
PtPT1 T:Cpt1011.92
PtO T:Hoh2024.26

interactive model:


Platinum binding site 2 out of 2 in 4dl6


Platinum binding site 2 out of 2 in 4dl6
Click to enlarge
stereopicture of Platinum binding site 2 out of 2 in 4dl6
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 4dl6. 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: Dc4, T: Dg5, T: Dg6, T: Cpt101, T: Hoh203,

conact list:


AtomAtomDistance (A)
PtC6 T:Dc44.46
PtC5 T:Dc44.13
PtC4 T:Dc44.47
PtN4 T:Dc44.78
PtN9 T:Dg53.94
PtN9 T:Dg54.10
PtN3 T:Dg54.92
PtC8 T:Dg52.89
PtC8 T:Dg53.02
PtC6 T:Dg52.87
PtC6 T:Dg53.45
PtN1 T:Dg54.25
PtN1 T:Dg54.78
PtC5 T:Dg52.50
PtC5 T:Dg52.97
PtN7 T:Dg51.72
PtN7 T:Dg52.07
PtC4 T:Dg53.75
PtC4 T:Dg54.07
PtO6 T:Dg52.60
PtO6 T:Dg53.26
PtN9 T:Dg64.10
PtC8 T:Dg64.38
PtC8 T:Dg62.96
PtC6 T:Dg64.30
PtC6 T:Dg63.72
PtC5 T:Dg64.13
PtC5 T:Dg63.12
PtN7 T:Dg63.48
PtN7 T:Dg62.12
PtC4 T:Dg64.15
PtO6 T:Dg63.90
PtO6 T:Dg63.67
PtN1 T:Cpt1011.86
PtN1 T:Cpt1012.06
PtN2 T:Cpt1013.58
PtN2 T:Cpt1012.01
PtPT1 T:Cpt1011.92
PtPT1 T:Cpt1010.00
PtO T:Hoh2034.44

interactive model:




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