Magnesium in PDB 4klj: Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min

All present enzymatic activity of Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min, PDB code: 4klj was solved by B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.99 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.000, 80.600, 55.500, 90.00, 107.90, 90.00
R / Rfree (%)	17.9 / 22.7

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	3 atoms

The binding sites of Magnesium atom in the Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min (pdb code 4klj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min, PDB code: 4klj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:24.9 occ:0.40 O A:HOH707 2.0 24.0 1.0 O A:HOH801 2.0 32.9 1.0 O P:HOH221 2.1 44.9 1.0 O P:HOH201 2.1 32.7 1.0 OP2 P:DC11 2.2 17.9 1.0 O12 A:PPV402 2.3 29.8 0.9 P P:DC11 3.3 20.6 1.0 O P:HOH210 3.6 32.1 1.0 O21 A:PPV402 3.7 31.9 0.9 OP1 P:DC11 3.8 16.0 1.0 P2 A:PPV402 3.8 21.5 0.9 O5' P:DC11 3.9 18.1 1.0 O A:HOH502 4.0 23.8 1.0 O A:HOH505 4.1 19.4 1.0 O A:HOH728 4.3 42.0 1.0 OPP A:PPV402 4.3 24.7 0.9 O22 A:PPV402 4.6 17.0 0.9 O32 A:PPV402 4.7 20.5 0.9 O3' P:DC10 4.7 20.1 1.0 P1 A:PPV402 4.7 31.4 0.9 O A:HOH800 4.9 43.5 1.0 MG A:MG401 4.9 16.3 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:16.3 occ:1.00 O A:HOH502 2.1 23.8 1.0 O32 A:PPV402 2.1 20.5 0.9 OP1 P:DC11 2.1 16.0 1.0 OD2 A:ASP192 2.1 15.1 1.0 O A:HOH501 2.1 18.6 1.0 OD1 A:ASP190 2.1 21.6 1.0 CG A:ASP192 3.0 14.4 1.0 CG A:ASP190 3.2 22.1 1.0 P2 A:PPV402 3.2 21.5 0.9 OD1 A:ASP192 3.4 18.5 1.0 NA A:NA404 3.5 20.8 1.0 P P:DC11 3.5 20.6 1.0 O12 A:PPV402 3.5 29.8 0.9 OD2 A:ASP190 3.7 23.0 1.0 O11 A:PPV402 3.8 21.0 0.9 O A:ASP190 3.9 18.2 1.0 C5' P:DC11 4.0 16.6 1.0 OPP A:PPV402 4.1 24.7 0.9 O5' P:DC11 4.1 18.1 1.0 O P:HOH201 4.2 32.7 1.0 C A:ASP190 4.3 15.6 1.0 P1 A:PPV402 4.3 31.4 0.9 N A:ASP190 4.3 16.1 1.0 O A:HOH504 4.3 20.4 1.0 CB A:ASP192 4.4 15.1 1.0 O22 A:PPV402 4.4 17.0 0.9 OP2 P:DC11 4.4 17.9 1.0 CB A:ASP190 4.4 21.6 1.0 O3' P:DC10 4.4 20.1 1.0 O21 A:PPV402 4.5 31.9 0.9 CA A:GLY179 4.5 13.5 1.0 CA A:ASP190 4.5 17.3 1.0 N A:SER180 4.6 15.9 1.0 OG A:SER180 4.8 21.3 1.0 N A:ASP192 4.8 15.5 1.0 MG P:MG101 4.9 24.9 0.4 N A:MET191 5.0 15.7 1.0

B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson. Observing A Dna Polymerase Choose Right From Wrong. Cell(Cambridge,Mass.) V. 154 157 2013.
ISSN: ISSN 0092-8674
PubMed: 23827680
DOI: 10.1016/J.CELL.2013.05.048