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Platinum in PDB 3o62: Nucleosome Core Particle Modified with A Cisplatin 1,3-Cis-{Pt(NH3) 2}2+-D(Gptpg) Intrastrand Cross-Link

Protein crystallography data

The structure of Nucleosome Core Particle Modified with A Cisplatin 1,3-Cis-{Pt(NH3) 2}2+-D(Gptpg) Intrastrand Cross-Link, PDB code: 3o62 was solved by S.J.Lippard, R.C.Todd, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.03 / 3.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.095, 109.551, 177.176, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 30.6

Platinum Binding Sites:

The binding sites of Platinum atom in the Nucleosome Core Particle Modified with A Cisplatin 1,3-Cis-{Pt(NH3) 2}2+-D(Gptpg) Intrastrand Cross-Link (pdb code 3o62). 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 Nucleosome Core Particle Modified with A Cisplatin 1,3-Cis-{Pt(NH3) 2}2+-D(Gptpg) Intrastrand Cross-Link, PDB code: 3o62:

Platinum binding site 1 out of 1 in 3o62

Go back to Platinum Binding Sites List in 3o62
Platinum binding site 1 out of 1 in the Nucleosome Core Particle Modified with A Cisplatin 1,3-Cis-{Pt(NH3) 2}2+-D(Gptpg) Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Nucleosome Core Particle Modified with A Cisplatin 1,3-Cis-{Pt(NH3) 2}2+-D(Gptpg) Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pt147

b:0.3
occ:1.00
PT1 I:CPT147 0.0 0.3 1.0
N1 I:CPT147 2.0 0.4 1.0
N7 I:DG70 2.0 0.2 1.0
N2 I:CPT147 2.1 0.7 1.0
N7 I:DG72 2.1 0.6 1.0
C8 I:DG70 3.0 0.8 1.0
C8 I:DG72 3.0 0.3 1.0
C5 I:DG70 3.1 1.0 1.0
C5 I:DG72 3.2 0.2 1.0
O6 I:DG70 3.5 0.7 1.0
C6 I:DG70 3.7 0.9 1.0
O6 I:DG72 3.8 0.7 1.0
C6 I:DG72 3.9 0.5 1.0
N9 I:DG70 4.2 0.9 1.0
N9 I:DG72 4.2 0.4 1.0
C4 I:DG70 4.3 0.6 1.0
OP2 I:DG72 4.3 0.9 1.0
C4 I:DG72 4.4 1.0 1.0
N7 I:DA73 4.4 0.5 1.0
N6 I:DA73 4.4 0.4 1.0
C5 I:DA73 4.4 0.7 1.0
C6 I:DA73 4.5 0.3 1.0
OP1 I:DG72 4.5 0.7 1.0
P I:DG72 4.7 0.9 1.0
O5' I:DG72 4.9 0.3 1.0
C8 I:DA73 5.0 0.5 1.0

Reference:

R.C.Todd, S.J.Lippard. Consequences of Cisplatin Binding on Nucleosome Structure and Dynamics. Chem.Biol. V. 17 1334 2010.
ISSN: ISSN 1074-5521
PubMed: 21168769
DOI: 10.1016/J.CHEMBIOL.2010.10.018
Page generated: Wed Dec 16 02:04:22 2020

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