Magnesium in PDB 5eoz: Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta

All present enzymatic activity of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta:
2.7.7.7;

The structure of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta, PDB code: 5eoz 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)	19.82 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.754, 80.015, 55.589, 90.00, 107.76, 90.00
R / Rfree (%)	18.4 / 23.8

The structure of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta (pdb code 5eoz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta, PDB code: 5eoz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:11.6 occ:1.00 OD1 A:ASP190 2.0 15.4 1.0 O2A A:0KX404 2.0 13.8 1.0 OD2 A:ASP192 2.0 12.6 1.0 O1G A:0KX404 2.1 13.3 1.0 O A:HOH537 2.1 12.0 1.0 O1B A:0KX404 2.1 11.6 1.0 CG A:ASP192 3.0 12.5 1.0 CG A:ASP190 3.0 15.9 1.0 PB A:0KX404 3.1 11.6 1.0 PA A:0KX404 3.2 13.5 1.0 OD1 A:ASP192 3.3 15.6 1.0 PG A:0KX404 3.4 14.8 1.0 OD2 A:ASP190 3.4 19.1 1.0 MG A:MG401 3.5 21.5 1.0 O3B A:0KX404 3.6 11.6 1.0 N3A A:0KX404 3.7 12.5 1.0 O A:ASP190 4.0 15.3 1.0 O A:HOH615 4.1 21.6 1.0 O2G A:0KX404 4.2 11.9 1.0 O A:HOH558 4.2 15.3 1.0 C5' A:0KX404 4.2 13.8 1.0 O5' A:0KX404 4.3 14.7 1.0 C A:ASP190 4.3 14.6 1.0 CB A:ASP190 4.4 15.1 1.0 CB A:ASP192 4.4 16.0 1.0 O1A A:0KX404 4.4 15.7 1.0 N A:ASP190 4.4 13.1 1.0 OG A:SER180 4.4 17.8 1.0 N A:SER180 4.5 15.9 1.0 O3G A:0KX404 4.5 16.0 1.0 CA A:GLY179 4.5 13.0 1.0 O2B A:0KX404 4.6 11.5 1.0 CA A:ASP190 4.6 12.3 1.0 N A:ASP192 4.7 15.3 1.0 N A:MET191 4.8 12.5 1.0 O P:HOH104 4.8 23.5 1.0 C A:MET191 4.9 14.9 1.0

Magnesium binding site 2 out of 2 in the Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:21.5 occ:1.00 OD2 A:ASP190 2.1 19.1 1.0 OD1 A:ASP192 2.2 15.6 1.0 O P:HOH104 2.3 23.5 1.0 O2A A:0KX404 2.3 13.8 1.0 OD2 A:ASP256 2.5 22.8 1.0 CG A:ASP190 3.0 15.9 1.0 CG A:ASP192 3.2 12.5 1.0 OD1 A:ASP190 3.3 15.4 1.0 PA A:0KX404 3.4 13.5 1.0 O3' P:DA10 3.4 28.2 1.0 MG A:MG400 3.5 11.6 1.0 CG A:ASP256 3.5 18.4 1.0 C3' P:DA10 3.5 19.7 1.0 OD2 A:ASP192 3.6 12.6 1.0 O1A A:0KX404 3.8 15.7 1.0 O5' A:0KX404 3.8 14.7 1.0 C5' A:0KX404 4.0 13.8 1.0 CB A:ASP256 4.1 20.7 1.0 O A:HOH615 4.3 21.6 1.0 CB A:ASP190 4.4 15.1 1.0 OD1 A:ASP256 4.5 19.8 1.0 C2' P:DA10 4.6 20.4 1.0 CB A:ASP192 4.6 16.0 1.0 C4' P:DA10 4.6 22.8 1.0 OP1 P:DA10 4.6 17.9 1.0 NH2 A:ARG254 4.6 19.8 1.0 O1G A:0KX404 4.7 13.3 1.0 O A:MET191 4.7 15.4 1.0 C5' P:DA10 4.8 22.4 1.0 O5' P:DA10 4.9 21.6 1.0 N3A A:0KX404 5.0 12.5 1.0

Y.Kou, M.C.Koag, S.Lee. Structural and Kinetic Studies of the Effect of Guanine-N7 Alkylation and Metal Cofactors on Dna Replication. Biochemistry 2018.
ISSN: ISSN 1520-4995
PubMed: 29957995
DOI: 10.1021/ACS.BIOCHEM.8B00331