Magnesium in PDB 5j2b: 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: 5j2b 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 (°)	50.710, 79.880, 55.470, 90.00, 107.58, 90.00
R / Rfree (%)	21 / 28.8

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 5j2b). 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: 5j2b:
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:10.6 occ:1.00 O2B A:DUP401 1.9 11.7 1.0 OD1 A:ASP190 2.0 11.1 1.0 OD2 A:ASP192 2.0 18.7 1.0 O3G A:DUP401 2.1 16.9 1.0 O2A A:DUP401 2.2 10.9 1.0 O A:HOH503 2.4 14.2 1.0 PB A:DUP401 3.0 16.8 1.0 CG A:ASP192 3.0 19.5 1.0 CG A:ASP190 3.1 12.1 1.0 PG A:DUP401 3.2 16.5 1.0 PA A:DUP401 3.3 14.1 1.0 N3A A:DUP401 3.3 14.1 1.0 OD1 A:ASP192 3.4 21.6 1.0 O3B A:DUP401 3.4 17.2 1.0 OD2 A:ASP190 3.6 11.0 1.0 O A:ASP190 3.7 15.3 1.0 MG A:MG403 3.7 7.6 1.0 O2G A:DUP401 3.8 16.7 1.0 C5' A:DUP401 4.1 13.4 1.0 O5' A:DUP401 4.1 14.0 1.0 C A:ASP190 4.2 15.5 1.0 O A:HOH511 4.2 8.0 1.0 O1B A:DUP401 4.3 14.9 1.0 CB A:ASP190 4.3 12.9 1.0 CB A:ASP192 4.3 18.4 1.0 O1G A:DUP401 4.4 17.5 1.0 N A:ASP190 4.4 13.2 1.0 O P:HOH101 4.4 23.1 1.0 CA A:GLY179 4.5 20.2 1.0 N A:SER180 4.5 21.2 1.0 O1A A:DUP401 4.5 17.5 1.0 OG A:SER180 4.5 18.4 1.0 CA A:ASP190 4.6 13.6 1.0 O A:HOH634 4.7 27.0 1.0 O A:HOH544 4.8 4.8 1.0 N A:ASP192 4.8 17.4 1.0 N A:MET191 4.9 16.9 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:7.6 occ:1.00 OD2 A:ASP256 2.0 15.9 1.0 O P:HOH101 2.0 23.1 1.0 OD2 A:ASP190 2.1 11.0 1.0 O A:HOH544 2.1 4.8 1.0 OD1 A:ASP192 2.2 21.6 1.0 O2A A:DUP401 2.4 10.9 1.0 CG A:ASP190 3.1 12.1 1.0 CG A:ASP256 3.1 16.6 1.0 CG A:ASP192 3.2 19.5 1.0 OD1 A:ASP190 3.4 11.1 1.0 PA A:DUP401 3.5 14.1 1.0 OD2 A:ASP192 3.6 18.7 1.0 MG A:MG402 3.7 10.6 1.0 CB A:ASP256 3.7 13.8 1.0 O5' A:DUP401 3.8 14.0 1.0 O1A A:DUP401 3.9 17.5 1.0 OP1 P:DG10 3.9 37.6 1.0 OD1 A:ASP256 4.2 16.8 1.0 C5' A:DUP401 4.3 13.4 1.0 CB A:ASP190 4.4 12.9 1.0 CB A:ASP192 4.6 18.4 1.0 NH2 A:ARG254 4.7 14.5 1.0 O P:HOH109 4.7 31.4 1.0 O A:MET191 4.8 18.8 1.0 O3G A:DUP401 4.9 16.9 1.0 N3A A:DUP401 4.9 14.1 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