Magnesium in PDB 4m9j: Dna Polymerase Beta E295K Soaked with Dumpnpp

All present enzymatic activity of Dna Polymerase Beta E295K Soaked with Dumpnpp:
2.7.7.7;

The structure of Dna Polymerase Beta E295K Soaked with Dumpnpp, PDB code: 4m9j was solved by B.E.Eckenroth, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.98 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.580, 79.129, 54.979, 90.00, 105.95, 90.00
R / Rfree (%)	18.6 / 23

The structure of Dna Polymerase Beta E295K Soaked with Dumpnpp also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Dna Polymerase Beta E295K Soaked with Dumpnpp (pdb code 4m9j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dna Polymerase Beta E295K Soaked with Dumpnpp, PDB code: 4m9j:

Magnesium binding site 1 out of 1 in the Dna Polymerase Beta E295K Soaked with Dumpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta E295K Soaked with Dumpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:25.8 occ:0.83 O2B A:DUP406 2.0 29.4 0.8 O1A A:DUP406 2.0 23.2 0.8 OD1 A:ASP190 2.1 26.4 1.0 O3G A:DUP406 2.2 32.2 0.8 OD2 A:ASP192 2.2 38.9 1.0 O A:HOH522 2.2 28.8 1.0 CG A:ASP192 3.1 39.4 1.0 PA A:DUP406 3.2 33.2 0.8 CG A:ASP190 3.2 27.5 1.0 O A:HOH651 3.3 30.2 1.0 OD1 A:ASP192 3.4 35.2 1.0 PG A:DUP406 3.4 31.7 0.8 PB A:DUP406 3.5 34.5 0.8 OD2 A:ASP190 3.7 31.8 1.0 N3A A:DUP406 3.8 41.5 0.8 O A:ASP190 3.9 27.2 1.0 O2G A:DUP406 4.0 37.4 0.8 O3B A:DUP406 4.0 36.5 0.8 C A:ASP190 4.2 23.1 1.0 O5' A:DUP406 4.3 36.1 0.8 O A:HOH542 4.3 28.1 1.0 N A:ASP190 4.3 22.1 1.0 O2A A:DUP406 4.4 54.7 0.8 C5' A:DUP406 4.4 34.5 0.8 CB A:ASP190 4.4 19.5 1.0 CB A:ASP192 4.5 30.2 1.0 O1B A:DUP406 4.5 40.1 0.8 CA A:GLY179 4.5 31.7 1.0 CA A:ASP190 4.5 19.4 1.0 O1G A:DUP406 4.6 32.4 0.8 N A:SER180 4.6 36.9 1.0 OG A:SER180 4.7 30.0 1.0 N A:ASP192 4.8 19.0 1.0 N A:MET191 4.9 21.1 1.0 O A:HOH561 5.0 48.4 1.0

B.E.Eckenroth, J.B.Towle-Weicksel, J.B.Sweasy, S.Doublie. The E295K Cancer Variant of Human Polymerase Beta Favors the Mismatch Conformational Pathway During Nucleotide Selection. J.Biol.Chem. V. 288 34850 2013.
ISSN: ISSN 0021-9258
PubMed: 24133209
DOI: 10.1074/JBC.M113.510891