Magnesium in PDB 5v1o: Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp

All present enzymatic activity of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp:
2.7.7.7;

The structure of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp, PDB code: 5v1o was solved by B.D.Freudenthal, M.A.Schaich, A.M.Whitaker, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.80 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.574, 79.685, 55.416, 90.00, 107.76, 90.00
R / Rfree (%)	17.9 / 21.5

The structure of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp (pdb code 5v1o). 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 8-Oxog:A and Inserted Dctp, PDB code: 5v1o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp


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 8-Oxog:A and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:35.6 occ:1.00 O A:HOH559 1.9 22.3 1.0 O A:HOH571 2.1 31.1 1.0 OP2 P:DC11 2.1 28.2 1.0 O P:HOH208 2.2 23.2 1.0 O12 A:PPV408 2.2 24.3 1.0 O P:HOH204 2.2 28.7 1.0 P P:DC11 3.2 14.8 1.0 P2 A:PPV408 3.7 17.7 1.0 OP1 P:DC11 3.7 12.7 1.0 O5' P:DC11 3.7 11.3 1.0 O21 A:PPV408 3.9 20.9 1.0 O11 A:PPV408 3.9 28.8 1.0 O A:HOH565 4.1 19.0 1.0 OPP A:PPV408 4.1 21.4 1.0 P1 A:PPV408 4.3 28.4 1.0 O P:HOH224 4.3 38.1 1.0 O32 A:PPV408 4.5 15.9 1.0 O3' P:8OG10 4.6 12.1 1.0 O22 A:PPV408 4.6 15.2 1.0 O A:HOH501 4.7 27.6 1.0 O A:HOH507 4.7 40.3 1.0 MG A:MG401 4.7 11.8 1.0 O A:HOH521 4.9 43.3 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp


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 8-Oxog:A and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:11.8 occ:1.00 OD2 A:ASP192 2.0 13.3 1.0 OP1 P:DC11 2.0 12.7 1.0 O32 A:PPV408 2.0 15.9 1.0 OD1 A:ASP190 2.1 13.8 1.0 O A:HOH545 2.2 20.7 1.0 O21 A:PPV408 2.4 20.9 1.0 CG A:ASP192 3.0 9.2 1.0 P2 A:PPV408 3.2 17.7 1.0 CG A:ASP190 3.2 16.8 1.0 OD1 A:ASP192 3.4 13.7 1.0 P P:DC11 3.4 14.8 1.0 O12 A:PPV408 3.5 24.3 1.0 NA A:NA407 3.5 24.9 1.0 P1 A:PPV408 3.6 28.4 1.0 OD2 A:ASP190 3.7 28.0 1.0 OPP A:PPV408 3.8 21.4 1.0 C5' P:DC11 3.9 10.4 1.0 O5' P:DC11 4.0 11.3 1.0 O P:HOH208 4.0 23.2 1.0 O A:ASP190 4.1 15.5 1.0 O31 A:PPV408 4.3 20.4 1.0 O A:HOH599 4.3 20.7 1.0 OP2 P:DC11 4.3 28.2 1.0 CB A:ASP192 4.4 8.9 1.0 C A:ASP190 4.4 14.4 1.0 O22 A:PPV408 4.4 15.2 1.0 N A:ASP190 4.4 12.2 1.0 O A:HOH501 4.4 27.6 1.0 O3' P:8OG10 4.5 12.1 1.0 CB A:ASP190 4.5 13.5 1.0 CA A:GLY179 4.5 10.5 1.0 N A:SER180 4.6 12.0 1.0 CA A:ASP190 4.6 13.7 1.0 MG P:MG101 4.7 35.6 1.0 O11 A:PPV408 4.8 28.8 1.0 OG A:SER180 4.8 21.3 1.0 N A:ASP192 4.9 13.5 1.0

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293