Magnesium in PDB 4klg: Dna Polymerase Beta Matched Product Complex with MG2+, 40 S

All present enzymatic activity of Dna Polymerase Beta Matched Product Complex with MG2+, 40 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 40 S, PDB code: 4klg 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)	32.02 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.109, 80.478, 55.529, 90.00, 107.78, 90.00
R / Rfree (%)	18.8 / 22.9

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 40 S also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Dna Polymerase Beta Matched Product Complex with MG2+, 40 S (pdb code 4klg). 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+, 40 S, PDB code: 4klg:
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+, 40 S


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+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:17.1 occ:0.60 O A:HOH506 2.1 20.8 1.0 O A:HOH505 2.1 28.9 1.0 O A:HOH504 2.1 26.7 1.0 O P:HOH201 2.1 32.3 1.0 OP2 P:DC11 2.1 17.1 1.0 O12 A:PPV402 2.1 20.2 0.6 O12 A:PPV402 2.4 19.1 0.4 P P:DC11 3.2 16.5 1.0 OP1 P:DC11 3.6 16.1 1.0 P2 A:PPV402 3.6 16.1 0.6 O11 A:PPV402 3.6 21.1 0.6 O P:HOH204 3.7 27.4 1.0 P2 A:PPV402 3.8 16.7 0.4 O5' P:DC11 3.8 14.4 1.0 O11 A:PPV402 3.9 22.1 0.4 O A:HOH503 4.0 17.1 0.6 O A:HOH697 4.1 33.1 1.0 O31 A:PPV402 4.1 24.8 0.4 O A:HOH508 4.2 16.3 1.0 OPP A:PPV402 4.2 17.7 0.4 P1 A:PPV402 4.3 23.7 0.4 OPP A:PPV402 4.3 17.8 0.6 O22 A:PPV402 4.4 15.6 0.6 O32 A:PPV402 4.5 16.2 0.6 O3' P:DC10 4.5 17.3 1.0 O22 A:PPV402 4.6 14.7 0.4 P1 A:PPV402 4.6 23.3 0.6 MG A:MG401 4.6 9.2 1.0 O A:HOH560 4.7 37.8 1.0 O32 A:PPV402 4.7 15.9 0.4

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Matched Product Complex with MG2+, 40 S


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+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:9.2 occ:1.00 O32 A:PPV402 2.0 16.2 0.6 O A:HOH503 2.0 17.1 0.6 OP1 P:DC11 2.1 16.1 1.0 O A:HOH501 2.1 18.0 1.0 OD2 A:ASP192 2.1 15.1 1.0 OD1 A:ASP190 2.2 18.2 1.0 O32 A:PPV402 2.3 15.9 0.4 O11 A:PPV402 2.6 22.1 0.4 CG A:ASP192 3.1 16.7 1.0 P2 A:PPV402 3.2 16.1 0.6 O12 A:PPV402 3.2 19.1 0.4 P2 A:PPV402 3.2 16.7 0.4 CG A:ASP190 3.3 22.7 1.0 O12 A:PPV402 3.4 20.2 0.6 OD1 A:ASP192 3.4 17.1 1.0 P P:DC11 3.5 16.5 1.0 NA A:NA407 3.6 14.7 1.0 O21 A:PPV402 3.8 17.3 0.6 P1 A:PPV402 3.8 23.7 0.4 OPP A:PPV402 3.9 17.7 0.4 OD2 A:ASP190 3.9 29.6 1.0 O A:HOH504 4.0 26.7 1.0 O A:ASP190 4.0 16.1 1.0 OPP A:PPV402 4.1 17.8 0.6 C5' P:DC11 4.1 15.3 1.0 O5' P:DC11 4.1 14.4 1.0 P1 A:PPV402 4.3 23.3 0.6 N A:ASP190 4.3 13.6 1.0 O22 A:PPV402 4.3 15.6 0.6 O A:HOH502 4.3 17.8 1.0 C A:ASP190 4.3 13.3 1.0 O11 A:PPV402 4.3 21.1 0.6 OP2 P:DC11 4.4 17.1 1.0 O21 A:PPV402 4.4 16.4 0.4 CB A:ASP192 4.5 12.0 1.0 CB A:ASP190 4.5 15.2 1.0 O22 A:PPV402 4.5 14.7 0.4 O3' P:DC10 4.6 17.3 1.0 CA A:ASP190 4.6 13.5 1.0 CA A:GLY179 4.6 12.6 1.0 N A:SER180 4.6 13.1 1.0 OG A:SER180 4.6 17.9 1.0 MG P:MG101 4.6 17.1 0.6 N A:ASP192 4.9 12.1 1.0 O31 A:PPV402 5.0 24.8 0.4

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