Magnesium in PDB 4tur: 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;

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

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:

Platinum	(Pt)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2), PDB code: 4tur:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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 A:Mg401 b:34.6 occ:1.00 O A:HOH599 1.9 44.1 1.0 OD1 A:ASP190 2.0 29.5 1.0 O2B A:0KX405 2.0 29.4 1.0 O1G A:0KX405 2.0 31.0 1.0 O1A A:0KX405 2.1 29.6 1.0 O A:HOH600 2.3 29.1 1.0 PB A:0KX405 3.0 30.7 1.0 OD2 A:ASP192 3.0 42.9 1.0 CG A:ASP190 3.0 29.5 1.0 PA A:0KX405 3.2 34.7 1.0 PG A:0KX405 3.3 31.1 1.0 MG A:MG402 3.4 36.9 1.0 OD2 A:ASP190 3.5 37.1 1.0 O3B A:0KX405 3.5 31.3 1.0 N3A A:0KX405 3.5 30.3 1.0 CG A:ASP192 3.7 30.0 1.0 O A:HOH550 3.7 39.3 1.0 OD1 A:ASP192 3.8 33.6 1.0 O3G A:0KX405 4.0 33.8 1.0 O A:ASP190 4.2 28.1 1.0 O2A A:0KX405 4.2 37.1 1.0 N A:ASP190 4.2 29.2 1.0 CB A:ASP190 4.3 25.2 1.0 C A:ASP190 4.3 27.2 1.0 O5' A:0KX405 4.4 34.9 1.0 C5' A:0KX405 4.4 33.2 1.0 O2G A:0KX405 4.5 37.6 1.0 O1B A:0KX405 4.5 29.0 1.0 CA A:ASP190 4.5 27.7 1.0 OG A:SER180 4.6 32.8 1.0 O A:HOH598 4.6 30.3 1.0 N A:SER180 4.6 30.5 1.0 CA A:GLY179 4.7 32.2 1.0 CB A:ASP192 4.9 26.5 1.0 N A:MET191 5.0 25.9 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg binding site number 2 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 A:Mg402 b:36.9 occ:1.00 O1A A:0KX405 2.2 29.6 1.0 OD2 A:ASP190 2.3 37.1 1.0 O3' P:DC10 2.4 41.8 1.0 OD1 A:ASP192 2.5 33.6 1.0 CG A:ASP190 3.1 29.5 1.0 CG A:ASP192 3.2 30.0 1.0 OD2 A:ASP192 3.2 42.9 1.0 OD1 A:ASP190 3.2 29.5 1.0 MG A:MG401 3.4 34.6 1.0 C3' P:DC10 3.4 37.4 1.0 PA A:0KX405 3.4 34.7 1.0 OD2 A:ASP256 3.5 37.1 1.0 O2A A:0KX405 3.6 37.1 1.0 O A:HOH550 4.0 39.3 1.0 O5' A:0KX405 4.0 34.9 1.0 C4' P:DC10 4.1 38.5 1.0 O A:HOH599 4.3 44.1 1.0 CB A:ASP190 4.5 25.2 1.0 CG A:ASP256 4.5 31.3 1.0 O1G A:0KX405 4.6 31.0 1.0 CB A:ASP192 4.6 26.5 1.0 C5' A:0KX405 4.6 33.2 1.0 C2' P:DC10 4.7 42.2 1.0 C5' P:DC10 4.7 34.5 1.0 O2B A:0KX405 4.8 29.4 1.0 O P:HOH114 4.9 30.4 1.0 N3A A:0KX405 4.9 30.3 1.0

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