Magnesium in PDB 4uay: Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S

All present enzymatic activity of Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S:
2.7.7.7;

The structure of Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S, PDB code: 4uay 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)	31.27 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.867, 80.445, 55.391, 90.00, 107.69, 90.00
R / Rfree (%)	18.4 / 24.7

The structure of Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Magnesium atom in the Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S (pdb code 4uay). 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 Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S, PDB code: 4uay:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 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 Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:40.9 occ:0.70 O P:HOH215 2.0 34.0 0.7 O A:HOH717 2.1 44.5 1.0 O A:HOH716 2.1 38.8 1.0 O P:HOH209 2.1 33.6 1.0 O12 A:PPV401 2.3 27.8 1.0 OP1 P:8OG11 2.3 25.1 0.9 O21 A:PPV401 3.4 32.7 1.0 P P:8OG11 3.5 26.7 0.9 O A:HOH715 3.5 17.9 1.0 P2 A:PPV401 3.7 24.6 1.0 OP2 P:8OG11 3.7 17.2 0.9 N2 P:8OG11 3.8 24.1 0.9 O A:HOH614 3.9 36.0 1.0 OPP A:PPV401 4.0 31.8 1.0 O5' P:8OG11 4.1 18.4 0.9 O A:HOH560 4.3 15.8 1.0 P1 A:PPV401 4.3 32.1 1.0 O22 A:PPV401 4.6 21.8 1.0 O32 A:PPV401 4.6 19.2 1.0 MG A:MG402 4.8 15.3 1.0 O3' P:DC10 4.8 29.4 1.0 C2 P:8OG11 4.9 25.8 0.9

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 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 Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.3 occ:1.00 OD2 A:ASP192 2.1 15.1 1.0 O A:HOH715 2.1 17.9 1.0 OD1 A:ASP190 2.1 20.9 1.0 O32 A:PPV401 2.1 19.2 1.0 O A:HOH567 2.1 18.9 1.0 OP2 P:8OG11 2.2 17.2 0.9 CG A:ASP192 3.1 16.7 1.0 P2 A:PPV401 3.3 24.6 1.0 CG A:ASP190 3.3 24.4 1.0 O12 A:PPV401 3.4 27.8 1.0 O11 A:PPV401 3.5 27.8 1.0 OD1 A:ASP192 3.5 26.3 1.0 NA A:NA403 3.6 23.1 1.0 P P:8OG11 3.6 26.7 0.9 OD2 A:ASP190 3.9 32.1 1.0 O A:ASP190 3.9 17.2 1.0 OPP A:PPV401 4.1 31.8 1.0 O5' P:8OG11 4.2 18.4 0.9 C A:ASP190 4.2 20.3 1.0 P1 A:PPV401 4.2 32.1 1.0 C5' P:8OG11 4.3 16.4 0.9 N A:ASP190 4.3 12.0 1.0 O P:HOH209 4.4 33.6 1.0 CB A:ASP192 4.4 16.4 1.0 CA A:GLY179 4.4 12.6 1.0 O22 A:PPV401 4.4 21.8 1.0 O A:HOH571 4.5 15.3 1.0 OP1 P:8OG11 4.5 25.1 0.9 CB A:ASP190 4.5 13.8 1.0 O21 A:PPV401 4.5 32.7 1.0 CA A:ASP190 4.5 14.2 1.0 O3' P:DC10 4.6 29.4 1.0 N A:SER180 4.7 18.7 1.0 N A:ASP192 4.8 15.7 1.0 MG P:MG101 4.8 40.9 0.7 N A:MET191 4.9 13.0 1.0

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