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Platinum in PDB 3co3: X-Ray Crystal Structure of A Monofunctional Platinum-Dna Adduct, Cis- {Pt(NH3)2(Pyridine)}2+ Bound to Deoxyguanosine in A Dodecamer Duplex

Protein crystallography data

The structure of X-Ray Crystal Structure of A Monofunctional Platinum-Dna Adduct, Cis- {Pt(NH3)2(Pyridine)}2+ Bound to Deoxyguanosine in A Dodecamer Duplex, PDB code: 3co3 was solved by K.S.Lovejoy, R.C.Todd, S.Zhang, M.S.Mccormick, J.A.D'aquino, J.T.Reardon, A.Sancar, K.M.Giacomini, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.44 / 2.16
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 46.440, 66.010, 56.050, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 25.4

Platinum Binding Sites:

The binding sites of Platinum atom in the X-Ray Crystal Structure of A Monofunctional Platinum-Dna Adduct, Cis- {Pt(NH3)2(Pyridine)}2+ Bound to Deoxyguanosine in A Dodecamer Duplex (pdb code 3co3). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total only one binding site of Platinum was determined in the X-Ray Crystal Structure of A Monofunctional Platinum-Dna Adduct, Cis- {Pt(NH3)2(Pyridine)}2+ Bound to Deoxyguanosine in A Dodecamer Duplex, PDB code: 3co3:

Platinum binding site 1 out of 1 in 3co3

Go back to Platinum Binding Sites List in 3co3
Platinum binding site 1 out of 1 in the X-Ray Crystal Structure of A Monofunctional Platinum-Dna Adduct, Cis- {Pt(NH3)2(Pyridine)}2+ Bound to Deoxyguanosine in A Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of X-Ray Crystal Structure of A Monofunctional Platinum-Dna Adduct, Cis- {Pt(NH3)2(Pyridine)}2+ Bound to Deoxyguanosine in A Dodecamer Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt25

b:45.4
occ:1.00
PT1 A:C7P25 0.0 45.4 1.0
N1 A:C7P25 1.9 31.9 1.0
N2 A:C7P25 1.9 39.1 1.0
N3 A:C7P25 1.9 39.2 1.0
N7 A:DG7 1.9 24.1 1.0
C1 A:C7P25 2.8 55.4 1.0
C5 A:C7P25 2.8 53.7 1.0
C8 A:DG7 2.9 31.4 1.0
C5 A:DG7 3.0 30.3 1.0
O6 A:DG7 3.3 36.8 1.0
O A:HOH30 3.5 42.2 1.0
C6 A:DG7 3.5 25.6 1.0
C2 A:C7P25 4.1 46.4 1.0
N9 A:DG7 4.1 34.1 1.0
C4 A:C7P25 4.1 39.7 1.0
C4 A:DG7 4.2 26.5 1.0
O A:HOH31 4.2 31.3 1.0
O4 A:DT8 4.5 37.9 1.0
C5 A:DC6 4.6 30.3 1.0
C6 A:DC6 4.6 36.5 1.0
C3 A:C7P25 4.7 49.1 1.0
N1 A:DG7 4.9 28.4 1.0

Reference:

K.S.Lovejoy, R.C.Todd, S.Zhang, M.S.Mccormick, J.A.D'aquino, J.T.Reardon, A.Sancar, K.M.Giacomini, S.J.Lippard. Cis-Diammine(Pyridine)Chloroplatinum(II), A Monofunctional Platinum(II) Antitumor Agent: Uptake, Structure, Function, and Prospects. Proc.Natl.Acad.Sci.Usa V. 105 8902 2008.
ISSN: ISSN 0027-8424
PubMed: 18579768
DOI: 10.1073/PNAS.0803441105
Page generated: Wed Dec 16 02:04:13 2020

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