Magnesium in PDB 5v1p: Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog, PDB code: 5v1p was solved by B.D.Freudenthal, M.R.Smith, A.M.Whitaker, M.A.Schaich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.68 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.676, 79.990, 55.706, 90.00, 107.50, 90.00
R / Rfree (%)	17.5 / 23.1

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog (pdb code 5v1p). 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 Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog, PDB code: 5v1p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog


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 Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg402 b:17.7 occ:1.00 OD1 A:ASP192 2.0 14.6 1.0 OD2 A:ASP190 2.1 19.0 1.0 OD2 A:ASP256 2.2 16.7 0.5 O3' P:8OG10 2.2 18.4 0.5 O P:HOH501 2.2 20.0 1.0 O3' P:8OG10 2.3 15.8 0.5 O1A A:XC5401 2.4 13.5 1.0 OD2 A:ASP256 2.4 14.8 0.5 CG A:ASP190 3.1 15.9 1.0 CG A:ASP192 3.1 16.4 1.0 CG A:ASP256 3.1 19.1 0.5 C3' P:8OG10 3.3 17.5 0.5 OD1 A:ASP190 3.4 14.3 1.0 OD1 A:ASP256 3.4 15.8 0.5 CG A:ASP256 3.4 17.7 0.5 C3' P:8OG10 3.4 17.7 0.5 PA A:XC5401 3.5 15.0 1.0 OD2 A:ASP192 3.5 13.7 1.0 MG A:MG406 3.7 13.0 1.0 O2A A:XC5401 3.7 16.2 1.0 O5' A:XC5401 3.9 17.3 1.0 CB A:ASP256 4.0 19.1 0.5 O5' P:8OG10 4.0 21.6 0.5 C5' A:XC5401 4.1 13.0 1.0 C4' P:8OG10 4.2 21.9 0.5 C4' P:8OG10 4.2 21.9 0.5 C5' P:8OG10 4.4 17.1 0.5 OD1 A:ASP256 4.4 17.5 0.5 CB A:ASP192 4.4 13.8 1.0 O A:HOH527 4.4 32.0 1.0 CB A:ASP190 4.4 14.0 1.0 C2' P:8OG10 4.4 19.5 0.5 O A:HOH613 4.5 20.9 1.0 CB A:ASP256 4.5 16.7 0.5 C2' P:8OG10 4.5 19.5 0.5 NH1 A:ARG254 4.5 23.9 1.0 OP2 P:8OG10 4.6 21.3 0.5 O5' P:8OG10 4.6 21.1 0.5 C5' P:8OG10 4.7 21.3 0.5 O A:MET191 4.8 14.2 1.0 CA A:ASP192 4.9 12.4 1.0 O1G A:XC5401 5.0 14.4 1.0 P P:8OG10 5.0 18.7 0.5

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog


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 Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:13.0 occ:1.00 OD1 A:ASP190 2.0 14.3 1.0 O2B A:XC5401 2.1 11.8 1.0 O1A A:XC5401 2.1 13.5 1.0 O1G A:XC5401 2.1 14.4 1.0 OD2 A:ASP192 2.1 13.7 1.0 O A:HOH617 2.2 13.9 1.0 CG A:ASP190 3.1 15.9 1.0 PB A:XC5401 3.1 13.4 1.0 CG A:ASP192 3.1 16.4 1.0 PA A:XC5401 3.3 15.0 1.0 PG A:XC5401 3.4 17.3 1.0 OD1 A:ASP192 3.5 14.6 1.0 OD2 A:ASP190 3.6 19.0 1.0 O3B A:XC5401 3.6 16.0 1.0 C3A A:XC5401 3.6 12.9 1.0 MG P:MG402 3.7 17.7 1.0 O A:HOH613 3.9 20.9 1.0 O A:ASP190 4.1 15.1 1.0 C5' A:XC5401 4.1 13.0 1.0 O2G A:XC5401 4.1 17.0 1.0 O5' A:XC5401 4.2 17.3 1.0 C A:ASP190 4.3 15.2 1.0 O A:HOH584 4.3 15.6 1.0 CB A:ASP190 4.3 14.0 1.0 N A:ASP190 4.4 11.8 1.0 O2A A:XC5401 4.4 16.2 1.0 O1B A:XC5401 4.5 15.3 1.0 CB A:ASP192 4.5 13.8 1.0 N A:SER180 4.5 15.5 1.0 OG A:SER180 4.5 22.2 1.0 CA A:GLY179 4.5 13.4 1.0 CA A:ASP190 4.6 13.2 1.0 O3G A:XC5401 4.6 22.5 1.0 O P:HOH501 4.7 20.0 1.0 N A:ASP192 4.9 13.4 1.0 N A:MET191 4.9 12.5 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