Magnesium in PDB 4ub3: Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S

All present enzymatic activity of Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S:
2.7.7.7;

The structure of Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S, PDB code: 4ub3 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)	21.34 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.698, 80.094, 55.358, 90.00, 107.80, 90.00
R / Rfree (%)	21.4 / 27.4

The structure of Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S (pdb code 4ub3). 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 Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S, PDB code: 4ub3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 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 Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:31.0 occ:0.61 O P:HOH203 2.0 29.0 1.0 O12 A:PPV402 2.0 29.2 0.6 O P:HOH207 2.0 30.6 1.0 OP1 P:8OG11 2.0 27.7 1.0 O A:HOH612 2.0 30.1 1.0 O P:HOH215 2.1 30.5 1.0 O12 A:PPV402 2.6 27.1 0.4 P P:8OG11 3.1 34.5 1.0 P2 A:PPV402 3.4 26.7 0.6 O5' P:8OG11 3.4 27.6 1.0 O P:HOH214 3.5 36.1 1.0 OP2 P:8OG11 3.6 23.5 1.0 O11 A:PPV402 3.8 31.4 0.6 OPP A:PPV402 3.8 31.2 0.6 P2 A:PPV402 3.9 31.0 0.4 O A:HOH538 4.0 19.8 1.0 O8 P:8OG11 4.0 27.9 1.0 O22 A:PPV402 4.1 29.7 0.6 O21 A:PPV402 4.1 27.2 0.6 P1 A:PPV402 4.1 32.7 0.6 O11 A:PPV402 4.2 28.3 0.4 O31 A:PPV402 4.3 29.8 0.4 OPP A:PPV402 4.3 29.7 0.4 MG A:MG401 4.4 16.2 1.0 O3' P:DC10 4.4 34.1 1.0 O32 A:PPV402 4.4 19.2 0.6 P1 A:PPV402 4.5 33.6 0.4 O22 A:PPV402 4.6 25.8 0.4 C5' P:8OG11 4.8 24.6 1.0 C3' P:DC10 4.8 30.4 1.0 O32 A:PPV402 5.0 23.1 0.4

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 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 Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:16.2 occ:1.00 O32 A:PPV402 1.9 19.2 0.6 OD1 A:ASP190 2.0 26.4 1.0 O A:HOH544 2.1 24.9 1.0 OP2 P:8OG11 2.2 23.5 1.0 OD2 A:ASP192 2.2 18.3 1.0 O21 A:PPV402 2.3 27.2 0.6 O32 A:PPV402 2.7 23.1 0.4 P2 A:PPV402 2.9 26.7 0.6 O12 A:PPV402 2.9 27.1 0.4 O12 A:PPV402 2.9 29.2 0.6 O11 A:PPV402 2.9 28.3 0.4 CG A:ASP190 3.2 27.3 1.0 CG A:ASP192 3.3 23.7 1.0 P2 A:PPV402 3.3 31.0 0.4 P1 A:PPV402 3.5 32.7 0.6 OPP A:PPV402 3.5 31.2 0.6 P P:8OG11 3.5 34.5 1.0 O P:HOH215 3.6 30.5 1.0 OD1 A:ASP192 3.6 31.5 1.0 NA A:NA403 3.7 26.5 1.0 OD2 A:ASP190 3.8 35.3 1.0 O5' P:8OG11 4.0 27.6 1.0 OPP A:PPV402 4.0 29.7 0.4 P1 A:PPV402 4.1 33.6 0.4 N A:ASP190 4.1 22.6 1.0 OP1 P:8OG11 4.2 27.7 1.0 O22 A:PPV402 4.2 29.7 0.6 O A:ASP190 4.3 21.7 1.0 C5' P:8OG11 4.3 24.6 1.0 C A:ASP190 4.4 17.7 1.0 O31 A:PPV402 4.4 24.7 0.6 CB A:ASP190 4.4 22.9 1.0 MG P:MG101 4.4 31.0 0.6 O A:HOH541 4.5 22.2 1.0 CA A:ASP190 4.5 16.0 1.0 O11 A:PPV402 4.5 31.4 0.6 CB A:ASP192 4.6 22.2 1.0 CA A:GLY179 4.6 18.2 1.0 N A:SER180 4.6 16.0 1.0 OG A:SER180 4.6 23.0 1.0 O3' P:DC10 4.7 34.1 1.0 O22 A:PPV402 4.7 25.8 0.4 C A:GLY189 4.9 30.8 1.0 O21 A:PPV402 5.0 24.6 0.4 N A:MET191 5.0 21.2 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