Magnesium in PDB 5j2f: Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus

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

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus, PDB code: 5j2f 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 (°)	50.700, 79.900, 55.500, 90.00, 107.70, 90.00
R / Rfree (%)	19.8 / 26.1

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A 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:A Mismatch at the Primer Terminus (pdb code 5j2f). 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:A Mismatch at the Primer Terminus, PDB code: 5j2f:
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:A 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:A Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:19.5 occ:1.00 OD1 A:ASP190 1.9 19.9 1.0 O3G A:DUP401 2.0 16.6 1.0 O2B A:DUP401 2.0 13.5 1.0 O2A A:DUP401 2.1 16.4 1.0 OD2 A:ASP192 2.1 19.0 1.0 O A:HOH539 2.2 16.1 1.0 CG A:ASP190 3.0 18.5 1.0 CG A:ASP192 3.1 18.0 1.0 PB A:DUP401 3.1 17.6 1.0 PG A:DUP401 3.2 21.0 1.0 PA A:DUP401 3.2 19.2 1.0 OD1 A:ASP192 3.3 18.2 1.0 N3A A:DUP401 3.4 19.8 1.0 OD2 A:ASP190 3.4 19.1 1.0 O3B A:DUP401 3.5 20.0 1.0 MG A:MG403 3.5 18.9 1.0 O2G A:DUP401 3.8 17.8 1.0 O A:ASP190 3.9 19.6 1.0 O A:HOH673 4.1 28.9 1.0 C5' A:DUP401 4.1 18.3 1.0 O5' A:DUP401 4.2 17.6 1.0 C A:ASP190 4.2 19.2 1.0 CB A:ASP190 4.3 17.4 1.0 O A:HOH587 4.3 19.1 1.0 N A:ASP190 4.3 16.5 1.0 O1G A:DUP401 4.3 21.8 1.0 O1A A:DUP401 4.4 21.4 1.0 O1B A:DUP401 4.4 18.0 1.0 CB A:ASP192 4.5 17.8 1.0 OG A:SER180 4.5 24.1 1.0 O A:HOH556 4.5 16.0 1.0 CA A:ASP190 4.5 17.3 1.0 N A:SER180 4.6 21.0 1.0 CA A:GLY179 4.6 17.6 1.0 N A:ASP192 4.8 17.2 1.0 N A:MET191 4.9 17.1 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A 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:A Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:18.9 occ:1.00 OD2 A:ASP190 2.0 19.1 1.0 OD1 A:ASP192 2.0 18.2 1.0 OD2 A:ASP256 2.0 15.8 1.0 O3' P:DA10 2.3 32.7 1.0 O A:HOH556 2.3 16.0 1.0 O2A A:DUP401 2.4 16.4 1.0 CG A:ASP190 3.0 18.5 1.0 CG A:ASP192 3.1 18.0 1.0 CG A:ASP256 3.1 18.0 1.0 OD1 A:ASP190 3.3 19.9 1.0 C3' P:DA10 3.4 37.7 1.0 PA A:DUP401 3.4 19.2 1.0 MG A:MG402 3.5 19.5 1.0 OD2 A:ASP192 3.6 19.0 1.0 CB A:ASP256 3.7 18.3 1.0 O5' A:DUP401 3.8 17.6 1.0 O1A A:DUP401 3.9 21.4 1.0 O P:HOH106 4.1 37.0 1.0 C4' P:DA10 4.1 37.4 1.0 C5' P:DA10 4.1 36.4 1.0 OD1 A:ASP256 4.2 20.3 1.0 C5' A:DUP401 4.2 18.3 1.0 CB A:ASP190 4.3 17.4 1.0 O P:HOH110 4.3 25.5 1.0 CB A:ASP192 4.4 17.8 1.0 O A:HOH673 4.6 28.9 1.0 O5' P:DA10 4.6 35.8 1.0 O3G A:DUP401 4.7 16.6 1.0 C2' P:DA10 4.7 36.5 1.0 O A:MET191 4.8 15.5 1.0 N3A A:DUP401 4.9 19.8 1.0 O2B A:DUP401 4.9 13.5 1.0 CA A:ASP192 4.9 17.1 1.0 CA A:ASP256 5.0 19.5 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