Magnesium in PDB 5j2a: Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus

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

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus, PDB code: 5j2a 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 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.420, 79.220, 55.340, 90.00, 107.07, 90.00
R / Rfree (%)	22.5 / 29.6

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

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

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus (pdb code 5j2a). 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 A:C Mismatch at the Primer Terminus, PDB code: 5j2a:
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 A:C 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 A:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:20.6 occ:1.00 OD1 A:ASP190 1.8 12.9 1.0 O2A A:DUP401 1.8 16.4 1.0 O3G A:DUP401 2.0 14.0 1.0 OD2 A:ASP192 2.1 16.3 1.0 O A:HOH537 2.2 33.2 1.0 O2B A:DUP401 2.2 13.6 1.0 CG A:ASP190 2.8 13.7 1.0 CG A:ASP192 3.0 14.5 1.0 PA A:DUP401 3.1 17.2 1.0 OD2 A:ASP190 3.1 12.2 1.0 OD1 A:ASP192 3.2 14.6 1.0 PB A:DUP401 3.3 15.1 1.0 MG A:MG403 3.3 6.1 1.0 PG A:DUP401 3.3 16.7 1.0 N3A A:DUP401 3.5 15.1 1.0 O3B A:DUP401 3.7 17.3 1.0 O A:HOH502 3.8 25.1 1.0 O2G A:DUP401 3.9 15.6 1.0 O A:ASP190 3.9 16.4 1.0 O1A A:DUP401 4.1 16.2 1.0 CB A:ASP190 4.1 13.8 1.0 O5' A:DUP401 4.2 15.0 1.0 O A:HOH509 4.2 22.7 1.0 C A:ASP190 4.2 15.7 1.0 C5' A:DUP401 4.2 12.9 1.0 O1G A:DUP401 4.3 16.1 1.0 CB A:ASP192 4.3 14.5 1.0 N A:ASP190 4.4 15.9 1.0 CA A:ASP190 4.5 14.3 1.0 O1B A:DUP401 4.6 16.1 1.0 CA A:GLY179 4.7 15.2 1.0 N A:ASP192 4.7 15.2 1.0 OG A:SER180 4.8 18.9 1.0 N A:MET191 4.8 15.7 1.0 N A:SER180 4.8 17.5 1.0 C A:MET191 4.9 16.6 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C 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 A:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:6.1 occ:1.00 O A:HOH502 1.5 25.1 1.0 OD2 A:ASP256 2.0 10.1 1.0 OD2 A:ASP190 2.1 12.2 1.0 OD1 A:ASP192 2.1 14.6 1.0 O2A A:DUP401 2.4 16.4 1.0 CG A:ASP192 3.1 14.5 1.0 CG A:ASP190 3.1 13.7 1.0 CG A:ASP256 3.2 12.5 1.0 PA A:DUP401 3.3 17.2 1.0 MG A:MG402 3.3 20.6 1.0 OD2 A:ASP192 3.4 16.3 1.0 C5' P:DC10 3.5 55.6 1.0 O1A A:DUP401 3.5 16.2 1.0 OD1 A:ASP190 3.5 12.9 1.0 O5' A:DUP401 3.6 15.0 1.0 OP1 P:DC10 3.9 44.7 1.0 C5' A:DUP401 3.9 12.9 1.0 C4' P:DC10 4.0 59.9 1.0 C3' P:DC10 4.0 61.4 1.0 CB A:ASP256 4.0 13.3 1.0 OD1 A:ASP256 4.1 13.9 1.0 CB A:ASP192 4.4 14.5 1.0 CB A:ASP190 4.5 13.8 1.0 O3G A:DUP401 4.6 14.0 1.0 O5' P:DC10 4.6 51.5 1.0 O3' P:DC10 4.7 62.1 1.0 N3A A:DUP401 4.8 15.1 1.0 O A:MET191 4.8 18.0 1.0 O2B A:DUP401 4.9 13.6 1.0 P P:DC10 4.9 45.2 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