Magnesium in PDB 4uaz: Dna Polymerase Beta Reactant Complex with A Templating Adenine and Incoming 8-Oxodgtp, 20 S

All present enzymatic activity of Dna Polymerase Beta Reactant Complex with A Templating Adenine and Incoming 8-Oxodgtp, 20 S:
2.7.7.7;

The structure of Dna Polymerase Beta Reactant Complex with A Templating Adenine and Incoming 8-Oxodgtp, 20 S, PDB code: 4uaz was solved by B.D.Freudenthal, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.87 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.835, 79.921, 55.420, 90.00, 107.64, 90.00
R / Rfree (%)	17.9 / 22

The binding sites of Magnesium atom in the Dna Polymerase Beta Reactant Complex with A Templating Adenine and Incoming 8-Oxodgtp, 20 S (pdb code 4uaz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Beta Reactant Complex with A Templating Adenine and Incoming 8-Oxodgtp, 20 S, PDB code: 4uaz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Reactant Complex with A Templating Adenine and Incoming 8-Oxodgtp, 20 S


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 Reactant Complex with A Templating Adenine and Incoming 8-Oxodgtp, 20 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:16.5 occ:1.00 O A:HOH621 2.1 49.7 1.0 OD2 A:ASP190 2.1 34.6 1.0 OD1 A:ASP192 2.1 20.7 1.0 OD2 A:ASP256 2.1 25.6 1.0 OP2 P:8OG11 2.5 21.8 0.6 O3' P:DC10 2.5 24.8 0.6 O2A A:8DG403 2.5 13.7 0.4 O3' P:DC10 2.7 22.9 0.4 OD1 A:ASP190 2.7 29.4 1.0 CG A:ASP190 2.7 27.4 1.0 P P:8OG11 3.1 27.3 0.6 CG A:ASP192 3.2 18.2 1.0 CG A:ASP256 3.3 23.9 1.0 OD2 A:ASP192 3.5 21.8 1.0 PA A:8DG403 3.6 15.5 0.4 MG A:MG402 3.6 15.2 1.0 C3' P:DC10 3.7 23.1 0.6 O5' A:8DG403 3.8 20.9 0.4 C3' P:DC10 3.9 21.3 0.4 O1A A:8DG403 4.0 21.8 0.4 CB A:ASP256 4.0 20.0 1.0 C4' P:DC10 4.1 23.6 0.4 OP1 P:8OG11 4.1 25.1 0.6 C4' P:DC10 4.2 23.8 0.6 C5' P:DC10 4.2 22.4 0.6 CB A:ASP190 4.2 22.5 1.0 C5' P:DC10 4.2 22.5 0.4 O5' P:8OG11 4.3 25.7 0.6 OD1 A:ASP256 4.3 20.2 1.0 C5' P:8OG11 4.3 23.1 0.6 C5' A:8DG403 4.4 18.2 0.4 CB A:ASP192 4.5 18.2 1.0 O A:MET191 4.5 19.2 1.0 O A:HOH728 4.6 50.2 1.0 O3G A:8DG403 4.7 22.2 0.4 OP1 P:DC10 4.9 21.4 0.6 NH2 A:ARG254 4.9 21.3 1.0 C A:MET191 4.9 18.3 1.0 C2' P:DC10 4.9 21.6 0.6 C2' P:DC10 4.9 22.4 0.4 N A:ASP256 4.9 16.1 1.0 O5' P:DC10 5.0 21.4 0.6 CA A:ASP192 5.0 15.8 1.0 O5' P:DC10 5.0 22.7 0.4

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Reactant Complex with A Templating Adenine and Incoming 8-Oxodgtp, 20 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Beta Reactant Complex with A Templating Adenine and Incoming 8-Oxodgtp, 20 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.2 occ:1.00 O3G A:8DG403 2.0 22.2 0.4 O2A A:8DG403 2.0 13.7 0.4 O2B A:8DG403 2.1 14.9 0.4 O A:HOH571 2.1 21.5 1.0 OD2 A:ASP192 2.1 21.8 1.0 OD1 A:ASP190 2.1 29.4 1.0 O32 A:PPV404 2.3 18.9 0.6 OP2 P:8OG11 2.4 21.8 0.6 O11 A:PPV404 2.7 27.8 0.6 O12 A:PPV404 3.2 25.0 0.6 CG A:ASP192 3.2 18.2 1.0 PB A:8DG403 3.2 18.6 0.4 P2 A:PPV404 3.3 24.2 0.6 PG A:8DG403 3.3 23.7 0.4 PA A:8DG403 3.3 15.5 0.4 CG A:ASP190 3.3 27.4 1.0 OD1 A:ASP192 3.5 20.7 1.0 O3B A:8DG403 3.5 17.2 0.4 O3A A:8DG403 3.6 22.1 0.4 O A:ASP190 3.6 20.2 1.0 MG A:MG401 3.6 16.5 1.0 P P:8OG11 3.8 27.3 0.6 P1 A:PPV404 3.9 27.9 0.6 OPP A:PPV404 4.0 23.5 0.6 N A:ASP190 4.0 16.3 1.0 C A:ASP190 4.0 18.4 1.0 O1G A:8DG403 4.0 21.4 0.4 OD2 A:ASP190 4.1 34.6 1.0 O5' A:8DG403 4.3 20.9 0.4 O1A A:8DG403 4.3 21.8 0.4 CA A:ASP190 4.3 14.8 1.0 O A:HOH579 4.3 17.7 1.0 C5' A:8DG403 4.4 18.2 0.4 CB A:ASP190 4.4 22.5 1.0 O A:HOH728 4.4 50.2 1.0 O A:HOH621 4.4 49.7 1.0 O5' P:8OG11 4.5 25.7 0.6 O2G A:8DG403 4.5 23.1 0.4 CB A:ASP192 4.5 18.2 1.0 O1B A:8DG403 4.5 18.8 0.4 O22 A:PPV404 4.5 22.4 0.6 CA A:GLY179 4.5 14.3 1.0 N A:SER180 4.6 13.3 1.0 OP1 P:8OG11 4.6 25.1 0.6 C5' P:8OG11 4.6 23.1 0.6 OG A:SER180 4.6 22.8 1.0 O31 A:PPV404 4.6 26.6 0.6 N A:MET191 4.8 19.4 1.0 N A:ASP192 4.8 16.9 1.0 O3' P:DC10 4.8 22.9 0.4

B.D.Freudenthal, W.A.Beard, L.Perera, D.D.Shock, T.Kim, T.Schlick, S.H.Wilson. Uncovering the Polymerase-Induced Cytotoxicty of An Oxidized Nucleotide Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13886