Chemical elements
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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 The Primary Mode Of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G (pdb 5bna)






The binding sites of Platinum atom in the structure of The Primary Mode Of Binding of Cisplatin to A B-Dna Dodecamer: C-G-C-G-A-A-T-T-C-G-C-G (pdb code 5bna). This binding sites where shown with 5.0 Angstroms radius around Platinum atom.
The 5bna structure was solved by R.M.WING, P.PJURA, H.R.DREW, R.E.DICKERSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)8.0-2.6
Space groupP212121
a (A)24.160
b (A)39.930
c (A)66.120
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)10.2
Rfree (%)n/a


Platinum Binding Sites:

Platinum binding site 1 out of 3 in 5bna


Platinum binding site 1 out of 3 in 5bna
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stereopicture of Platinum binding site 1 out of 3 in 5bna
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 5bna. 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: Dt8, B: Dc15, B: Dg16, B: Da17, A: Ptn25, A: Hoh33, A: Hoh71, A: Hoh137, A: Hoh152, B: Hoh57,

conact list:


AtomAtomDistance (A)
PtO4 A:Dt84.85
PtC6 B:Dc154.72
PtC5 B:Dc154.82
PtN9 B:Dg164.35
PtC8 B:Dg163.15
PtC6 B:Dg163.73
PtC5 B:Dg163.19
PtN7 B:Dg162.16
PtC4 B:Dg164.37
PtOP2 B:Dg164.45
PtO6 B:Dg163.52
PtN6 B:Da174.45
PtN1 A:Ptn252.02
PtN3 A:Ptn252.00
PtPT A:Ptn250.00
PtN2 A:Ptn251.81
PtO A:Hoh333.56
PtO A:Hoh714.96
PtO A:Hoh1374.02
PtO A:Hoh1524.93
PtO B:Hoh574.56

interactive model:


Platinum binding site 2 out of 3 in 5bna


Platinum binding site 2 out of 3 in 5bna
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stereopicture of Platinum binding site 2 out of 3 in 5bna
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 5bna. 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: Dc3, A: Dg4, A: Da5, A: Ptn26, A: Hoh109,

conact list:


AtomAtomDistance (A)
PtC6 A:Dc34.24
PtN1 A:Dc34.72
PtC5 A:Dc34.38
PtC4 A:Dc34.98
PtC2' A:Dc34.25
PtN9 A:Dg44.47
PtC8 A:Dg43.23
PtC6 A:Dg43.95
PtC5 A:Dg43.38
PtN7 A:Dg42.31
PtC4 A:Dg44.52
PtOP2 A:Dg44.73
PtO6 A:Dg43.74
PtN6 A:Da54.73
PtN1 A:Ptn261.75
PtN3 A:Ptn262.23
PtPT A:Ptn260.00
PtN2 A:Ptn262.25
PtO A:Hoh1094.45

interactive model:


Platinum binding site 3 out of 3 in 5bna


Platinum binding site 3 out of 3 in 5bna
Click to enlarge
stereopicture of Platinum binding site 3 out of 3 in 5bna
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Platinum in the PDB 5bna. 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: Dg10, B: Ptn27, A: Hoh139, B: Hoh99,

conact list:


AtomAtomDistance (A)
PtN9 A:Dg104.17
PtC8 A:Dg102.96
PtC6 A:Dg104.02
PtC5 A:Dg103.33
PtN7 A:Dg102.23
PtC4 A:Dg104.35
PtO6 A:Dg103.93
PtN1 B:Ptn271.83
PtN3 B:Ptn272.14
PtPT B:Ptn270.00
PtN2 B:Ptn272.10
PtO A:Hoh1393.89
PtO B:Hoh994.61

interactive model:




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