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Platinum in PDB 6u6b: Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site, PDB code: 6u6b was solved by H.Ouzon-Shubeita, C.K.Vilas, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.14 / 3.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.430, 78.216, 53.965, 90.00, 110.57, 90.00
R / Rfree (%) 22.2 / 26.8

Other elements in 6u6b:

The structure of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Sodium (Na) 2 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site (pdb code 6u6b). 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 Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site, PDB code: 6u6b:

Platinum binding site 1 out of 1 in 6u6b

Go back to Platinum Binding Sites List in 6u6b
Platinum binding site 1 out of 1 in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt101

b:0.9
occ:1.00
 PT1 T:CPT101 0.0 0.9 1.0
N2 T:CPT101 2.0 0.7 1.0
N1 T:CPT101 2.0 91.4 1.0
H23 T:CPT101 2.4 0.2 1.0
H22 T:CPT101 2.4 0.2 1.0
H21 T:CPT101 2.4 0.2 1.0
H11 T:CPT101 2.4 0.7 1.0
H12 T:CPT101 2.4 0.7 1.0
H13 T:CPT101 2.4 0.7 1.0
N7 T:DG7 2.5 78.6 1.0
N7 T:DG6 2.5 0.2 1.0
C8 T:DG6 2.7 97.6 1.0
H8 T:DG7 2.9 95.5 1.0
H8 T:DG6 2.9 0.1 1.0
C5 T:DG6 3.0 91.3 1.0
C8 T:DG7 3.1 79.5 1.0
N9 T:DG6 3.3 88.5 1.0
C4 T:DG6 3.5 82.0 1.0
H2' T:DG6 3.6 96.6 1.0
C5 T:DG7 3.7 77.1 1.0
C6 T:DG6 3.9 97.6 1.0
C1' T:DG6 4.3 87.1 1.0
O6 T:DG6 4.3 0.1 1.0
C2' T:DG6 4.3 80.5 1.0
O6 T:DG7 4.4 69.4 1.0
N9 T:DG7 4.4 75.3 1.0
C6 T:DG7 4.5 75.7 1.0
N3 T:DG6 4.5 84.2 1.0
H1' T:DG6 4.6 0.6 1.0
H2'' T:DG6 4.6 96.6 1.0
O T:HOH206 4.6 50.0 1.0
H41 T:DC8 4.7 65.5 1.0
C4 T:DG7 4.7 79.3 1.0
N1 T:DG6 4.8 86.1 1.0

Reference:

H.Ouzon-Shubeita, C.K.Vilas, S.Lee. Structures of the Mutagenic Bypass of the Major Cisplatin-Dna Lesion By Human Dna Polymerase Beta Reveal Insights Into Cisplatin-Induced Mutagenesis To Be Published.
Page generated: Tue Aug 19 00:00:42 2025

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