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Platinum in PDB 3lpv: X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link

Protein crystallography data

The structure of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link, PDB code: 3lpv was solved by R.C.Todd, S.J.Lippard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.31 / 1.77
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 31.303, 35.425, 45.128, 80.06, 84.09, 81.77
R / Rfree (%) 17.2 / 19.8

Other elements in 3lpv:

The structure of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link (pdb code 3lpv). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link, PDB code: 3lpv:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 3lpv

Go back to Platinum Binding Sites List in 3lpv
Platinum binding site 1 out of 2 in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) 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 X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt49

b:28.6
occ:1.00
PT1 A:CPT49 0.0 28.6 1.0
N2 A:CPT49 2.0 28.2 1.0
N1 A:CPT49 2.1 31.5 1.0
N7 A:DG6 2.1 24.9 1.0
N7 A:DG7 2.1 28.7 1.0
C8 A:DG7 3.0 27.8 1.0
C8 A:DG6 3.0 23.5 1.0
C5 A:DG6 3.0 24.7 1.0
C5 A:DG7 3.2 27.8 1.0
O6 A:DG6 3.3 24.3 1.0
O A:HOH1078 3.4 30.9 1.0
C6 A:DG6 3.5 27.4 1.0
O6 A:DG7 3.6 30.4 1.0
O A:HOH1005 3.7 27.9 1.0
C6 A:DG7 3.7 30.2 1.0
OP2 A:DG6 4.0 29.4 1.0
C4 A:DG6 4.1 26.6 1.0
N9 A:DG6 4.1 27.6 1.0
O A:HOH1075 4.1 50.8 1.0
N9 A:DG7 4.2 29.0 1.0
O A:HOH1053 4.2 42.7 1.0
O A:HOH1076 4.2 47.4 1.0
O A:HOH1077 4.2 47.7 1.0
C4 A:DG7 4.2 27.8 1.0
O A:HOH1074 4.7 50.4 1.0
N1 A:DG6 4.8 25.4 1.0
C4 A:DT5 4.9 27.9 1.0
N3 A:DT5 5.0 25.1 1.0

Platinum binding site 2 out of 2 in 3lpv

Go back to Platinum Binding Sites List in 3lpv
Platinum binding site 2 out of 2 in the X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of X-Ray Crystal Structure of Duplex Dna Containing A Cisplatin 1,2- D(Gpg) Intrastrand Cross-Link within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt50

b:28.7
occ:1.00
PT1 C:CPT50 0.0 28.7 1.0
N2 C:CPT50 1.9 26.0 1.0
N7 C:DG30 2.0 24.7 1.0
N1 C:CPT50 2.1 33.5 1.0
N7 C:DG31 2.1 29.1 1.0
C8 C:DG30 3.0 26.5 1.0
C8 C:DG31 3.0 26.6 1.0
C5 C:DG30 3.0 24.8 1.0
C5 C:DG31 3.2 27.2 1.0
O6 C:DG30 3.4 25.7 1.0
C6 C:DG30 3.5 27.7 1.0
O6 C:DG31 3.6 30.7 1.0
O C:HOH1003 3.6 35.7 1.0
C6 C:DG31 3.7 30.9 1.0
O C:HOH1002 3.8 32.3 1.0
O C:HOH1073 3.8 52.9 1.0
OP2 C:DG30 3.9 32.3 1.0
N9 C:DG30 4.1 28.2 1.0
O C:HOH1020 4.1 43.2 1.0
C4 C:DG30 4.1 27.5 1.0
N9 C:DG31 4.2 27.8 1.0
C4 C:DG31 4.2 28.0 1.0
O C:HOH1121 4.7 53.3 1.0
O C:HOH1116 4.9 58.6 1.0
C4 C:DT29 4.9 31.5 1.0
N1 C:DG30 4.9 26.1 1.0
O5' C:DG30 4.9 28.2 1.0

Reference:

R.C.Todd, S.J.Lippard. Structure of Duplex Dna Containing the Cisplatin 1,2-{Pt(Nh(3))(2)}(2+)-D(Gpg) Cross-Link at 1.77A Resolution. J.Inorg.Biochem. V. 104 902 2010.
ISSN: ISSN 0162-0134
PubMed: 20541266
DOI: 10.1016/J.JINORGBIO.2010.04.005
Page generated: Wed Dec 16 02:04:13 2020

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