Magnesium in PDB 5j2d: Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C Mismatch at the Primer Terminus

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

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C Mismatch at the Primer Terminus, PDB code: 5j2d 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 (°)	50.740, 79.940, 55.480, 90.00, 107.63, 90.00
R / Rfree (%)	20.1 / 25.6

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

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

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C Mismatch at the Primer Terminus (pdb code 5j2d). 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 C:C Mismatch at the Primer Terminus, PDB code: 5j2d:
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 C: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 C:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:8.8 occ:1.00 O2B A:DUP401 1.9 6.8 1.0 OD2 A:ASP192 2.0 11.6 1.0 OD1 A:ASP190 2.0 13.0 1.0 O A:HOH563 2.0 13.6 1.0 O1G A:DUP401 2.1 10.3 1.0 O2A A:DUP401 2.2 12.8 1.0 PB A:DUP401 3.0 12.4 1.0 CG A:ASP192 3.0 11.6 1.0 CG A:ASP190 3.1 12.8 1.0 PG A:DUP401 3.2 15.0 1.0 PA A:DUP401 3.3 15.1 1.0 N3A A:DUP401 3.4 12.6 1.0 O3B A:DUP401 3.5 12.3 1.0 OD1 A:ASP192 3.5 9.3 1.0 OD2 A:ASP190 3.5 13.8 1.0 MG A:MG403 3.6 15.8 1.0 O2G A:DUP401 3.9 8.3 1.0 O A:ASP190 3.9 12.4 1.0 C5' A:DUP401 4.1 11.0 1.0 O A:HOH637 4.1 22.4 1.0 O A:HOH605 4.2 13.0 1.0 O5' A:DUP401 4.2 12.7 1.0 C A:ASP190 4.2 12.7 1.0 CB A:ASP192 4.3 12.4 1.0 OG A:SER180 4.3 20.4 1.0 N A:ASP190 4.4 11.7 1.0 CB A:ASP190 4.4 13.0 1.0 O1B A:DUP401 4.4 11.2 1.0 N A:SER180 4.4 15.5 1.0 O3G A:DUP401 4.4 15.1 1.0 CA A:GLY179 4.4 14.1 1.0 O1A A:DUP401 4.5 16.3 1.0 CA A:ASP190 4.6 11.0 1.0 N A:ASP192 4.8 11.7 1.0 O P:HOH107 4.8 9.2 1.0 O P:HOH109 4.8 11.7 1.0 N A:MET191 4.9 11.4 1.0 C A:GLY179 5.0 15.2 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:15.8 occ:1.00 OD2 A:ASP256 2.0 16.7 1.0 OD1 A:ASP192 2.0 9.3 1.0 OD2 A:ASP190 2.0 13.8 1.0 O P:HOH109 2.1 11.7 1.0 O P:HOH107 2.2 9.2 1.0 O2A A:DUP401 2.3 12.8 1.0 CG A:ASP190 3.0 12.8 1.0 CG A:ASP192 3.0 11.6 1.0 CG A:ASP256 3.2 16.5 1.0 OD1 A:ASP190 3.3 13.0 1.0 OD2 A:ASP192 3.3 11.6 1.0 PA A:DUP401 3.4 15.1 1.0 MG A:MG402 3.6 8.8 1.0 O1A A:DUP401 3.7 16.3 1.0 O5' A:DUP401 3.8 12.7 1.0 CB A:ASP256 3.9 14.8 1.0 O P:HOH105 4.1 27.1 1.0 C5' A:DUP401 4.1 11.0 1.0 OD1 A:ASP256 4.2 16.0 1.0 O5' P:DC10 4.2 51.7 1.0 OP1 P:DC10 4.2 50.3 1.0 O A:HOH637 4.3 22.4 1.0 CB A:ASP190 4.3 13.0 1.0 CB A:ASP192 4.3 12.4 1.0 O P:HOH101 4.5 28.3 1.0 C3' P:DC10 4.5 49.4 0.5 O1G A:DUP401 4.5 10.3 1.0 O3' P:DC10 4.7 50.0 0.5 N3A A:DUP401 4.8 12.6 1.0 NH2 A:ARG254 4.8 17.0 1.0 P P:DC10 4.8 50.4 1.0 O A:MET191 4.8 13.2 1.0 O2B A:DUP401 5.0 6.8 1.0 CA A:ASP192 5.0 11.9 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