Magnesium in PDB 5j2g: Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus, PDB code: 5j2g was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.670, 80.480, 55.420, 90.00, 108.04, 90.00
R / Rfree (%)	20.6 / 26.5

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus (pdb code 5j2g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus, PDB code: 5j2g:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.2 occ:1.00 O3G A:DUP401 2.0 11.5 1.0 OD1 A:ASP190 2.0 15.2 1.0 O2B A:DUP401 2.0 11.4 1.0 O A:HOH588 2.1 16.9 1.0 OD2 A:ASP192 2.1 11.2 1.0 O2A A:DUP401 2.2 11.0 1.0 CG A:ASP190 3.0 13.4 1.0 PB A:DUP401 3.1 15.3 1.0 CG A:ASP192 3.1 14.4 1.0 PG A:DUP401 3.2 17.3 1.0 PA A:DUP401 3.3 15.3 1.0 N3A A:DUP401 3.4 14.6 1.0 OD1 A:ASP192 3.4 11.1 1.0 OD2 A:ASP190 3.5 15.4 1.0 MG A:MG403 3.5 12.9 1.0 O3B A:DUP401 3.5 17.9 1.0 O2G A:DUP401 3.9 17.4 1.0 C5' A:DUP401 4.0 12.9 1.0 O A:ASP190 4.1 14.1 1.0 O A:HOH653 4.1 23.5 1.0 O5' A:DUP401 4.1 12.8 1.0 C A:ASP190 4.3 15.2 1.0 O1G A:DUP401 4.3 16.5 1.0 CB A:ASP190 4.3 15.0 1.0 O A:HOH572 4.4 9.9 1.0 N A:ASP190 4.4 15.5 1.0 OG A:SER180 4.4 18.7 1.0 CB A:ASP192 4.5 13.7 1.0 O1B A:DUP401 4.5 14.7 1.0 O1A A:DUP401 4.5 15.2 1.0 N A:SER180 4.5 16.7 1.0 CA A:ASP190 4.6 13.9 1.0 CA A:GLY179 4.6 13.3 1.0 O A:HOH548 4.7 19.3 1.0 N A:ASP192 4.8 14.0 1.0 N A:MET191 4.8 14.1 1.0 O A:HOH644 5.0 12.6 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:12.9 occ:1.00 OD1 A:ASP192 2.0 11.1 1.0 OD2 A:ASP256 2.2 14.7 1.0 OD2 A:ASP190 2.2 15.4 1.0 O A:HOH644 2.2 12.6 1.0 O2A A:DUP401 2.2 11.0 1.0 O A:HOH548 2.3 19.3 1.0 CG A:ASP192 3.1 14.4 1.0 CG A:ASP190 3.1 13.4 1.0 PA A:DUP401 3.3 15.3 1.0 CG A:ASP256 3.3 15.4 1.0 OD1 A:ASP190 3.4 15.2 1.0 OD2 A:ASP192 3.4 11.2 1.0 MG A:MG402 3.5 15.2 1.0 O5' A:DUP401 3.6 12.8 1.0 O1A A:DUP401 3.8 15.2 1.0 CB A:ASP256 3.9 15.1 1.0 C5' A:DUP401 4.0 12.9 1.0 O A:HOH664 4.0 20.4 1.0 O P:HOH102 4.3 27.3 1.0 OD1 A:ASP256 4.3 15.7 1.0 CB A:ASP192 4.4 13.7 1.0 CB A:ASP190 4.5 15.0 1.0 O P:HOH117 4.6 18.3 1.0 O A:HOH731 4.6 19.4 1.0 O A:HOH653 4.6 23.5 1.0 O3G A:DUP401 4.7 11.5 1.0 N3A A:DUP401 4.7 14.6 1.0 OP1 P:DG10 4.8 43.0 1.0 O A:MET191 4.9 13.3 1.0 O2B A:DUP401 4.9 11.4 1.0 NH2 A:ARG254 4.9 15.9 1.0

V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Mispaired Dna Termini Transitioning to Pre-Catalytic Complexes Support An Induced-Fit Fidelity Mechanism. Structure V. 24 1863 2016.
ISSN: ISSN 0969-2126
PubMed: 27642161
DOI: 10.1016/J.STR.2016.08.006