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Platinum in PDB 4tur: Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2)

Enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2)

All present enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2):
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2), PDB code: 4tur was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.785, 79.335, 54.786, 90.00, 107.81, 90.00
R / Rfree (%) 20.2 / 25.6

Other elements in 4tur:

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) (pdb code 4tur). 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 Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2), PDB code: 4tur:

Platinum binding site 1 out of 1 in 4tur

Go back to Platinum Binding Sites List in 4tur
Platinum binding site 1 out of 1 in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Pt101

b:35.1
occ:1.00
 PT1 T:CPT101 0.0 35.1 1.0
N2 T:CPT101 2.0 24.3 1.0
N1 T:CPT101 2.0 23.0 1.0
N7 T:DG6 2.5 48.6 1.0
N7 T:DG7 2.5 41.0 1.0
O6 T:DG7 3.3 30.9 1.0
C5 T:DG7 3.3 37.4 1.0
C5 T:DG6 3.4 44.0 1.0
C8 T:DG6 3.4 45.9 1.0
C8 T:DG7 3.5 42.6 1.0
O6 T:DG6 3.5 38.0 1.0
C6 T:DG7 3.6 36.5 1.0
O T:HOH204 3.7 40.3 1.0
O T:HOH213 3.8 38.2 1.0
C6 T:DG6 3.8 45.0 1.0
OP1 T:DG6 4.0 47.1 1.0
O T:HOH216 4.3 36.5 1.0
O T:HOH202 4.4 41.2 1.0
N9 T:DG6 4.5 50.9 1.0
C4 T:DG6 4.5 46.8 1.0
C4 T:DG7 4.5 40.9 1.0
N9 T:DG7 4.6 42.9 1.0
P T:DG6 4.9 42.8 1.0
N1 T:DG7 4.9 34.9 1.0

Reference:

M.C.Koag, L.Lai, S.Lee. Structural Basis For the Inefficient Nucleotide Incorporation Opposite Cisplatin-Dna Lesion By Human Dna Polymerase Beta J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25237188
DOI: 10.1074/JBC.M114.605451
Page generated: Thu Oct 10 11:10:43 2024

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