Magnesium in PDB 4klf: Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S

All present enzymatic activity of Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S, PDB code: 4klf 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)	24.20 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.750, 79.956, 55.320, 90.00, 107.52, 90.00
R / Rfree (%)	17.9 / 23.1

The structure of Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 S (pdb code 4klf). 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 Reactant Complex with MG2+, 20 S, PDB code: 4klf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 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 Reactant Complex with MG2+, 20 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:13.5 occ:1.00 O2A A:DCP403 2.0 19.6 0.5 O A:HOH512 2.1 25.5 1.0 OD2 A:ASP192 2.2 18.1 1.0 OD1 A:ASP190 2.2 20.2 1.0 O2G A:DCP403 2.2 23.1 0.5 O2B A:DCP403 2.2 19.5 0.5 O32 A:PPV404 2.5 17.4 0.5 OP1 P:DC11 2.5 18.0 0.5 O11 A:PPV404 2.6 25.1 0.5 O12 A:PPV404 3.1 21.6 0.5 CG A:ASP192 3.1 14.0 1.0 PB A:DCP403 3.3 19.6 0.5 P2 A:PPV404 3.3 20.4 0.5 CG A:ASP190 3.3 23.0 1.0 PA A:DCP403 3.4 17.2 0.5 OD1 A:ASP192 3.5 16.7 1.0 PG A:DCP403 3.5 29.7 0.5 MG A:MG402 3.6 13.1 1.0 O3A A:DCP403 3.7 27.4 0.5 O A:ASP190 3.7 22.2 1.0 P1 A:PPV404 3.8 26.6 0.5 O3B A:DCP403 3.9 22.1 0.5 P P:DC11 3.9 16.7 0.5 OPP A:PPV404 4.0 22.7 0.5 N A:ASP190 4.0 17.3 1.0 C A:ASP190 4.0 17.6 1.0 OD2 A:ASP190 4.0 28.8 1.0 C5' A:DCP403 4.1 19.2 0.5 O1G A:DCP403 4.2 20.7 0.5 O A:HOH505 4.2 19.8 1.0 O5' A:DCP403 4.3 17.6 0.5 CA A:ASP190 4.3 14.8 1.0 O5' P:DC11 4.4 17.5 0.5 O1A A:DCP403 4.4 18.8 0.5 C5' P:DC11 4.4 18.2 0.5 CB A:ASP190 4.4 18.2 1.0 O A:HOH532 4.4 29.2 1.0 CB A:ASP192 4.5 17.4 1.0 O31 A:PPV404 4.6 22.0 0.5 O22 A:PPV404 4.6 19.8 0.5 CA A:GLY179 4.6 16.0 1.0 O3G A:DCP403 4.6 27.4 0.5 N A:SER180 4.6 17.8 1.0 O1B A:DCP403 4.6 20.1 0.5 N A:MET191 4.7 15.2 1.0 OG A:SER180 4.7 25.3 1.0 OP2 P:DC11 4.8 20.6 0.5 N A:ASP192 4.8 17.7 1.0 O3' P:DC10 4.9 29.3 0.5 O21 A:PPV404 4.9 29.5 0.5

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Matched Reactant Complex with MG2+, 20 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 Reactant Complex with MG2+, 20 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:13.1 occ:1.00 O A:HOH532 2.1 29.2 1.0 OP1 P:DC11 2.2 18.0 0.5 OD2 A:ASP256 2.2 22.6 1.0 OD2 A:ASP190 2.2 28.8 1.0 OD1 A:ASP192 2.2 16.7 1.0 O3' P:DC10 2.4 29.3 0.5 O3' P:DC10 2.5 29.3 0.5 O2A A:DCP403 2.6 19.6 0.5 OD1 A:ASP190 2.7 20.2 1.0 CG A:ASP190 2.8 23.0 1.0 P P:DC11 2.8 16.7 0.5 CG A:ASP192 3.3 14.0 1.0 CG A:ASP256 3.4 21.0 1.0 C3' P:DC10 3.5 21.7 0.5 MG A:MG401 3.6 13.5 1.0 OD2 A:ASP192 3.6 18.1 1.0 C3' P:DC10 3.7 21.7 0.5 PA A:DCP403 3.8 17.2 0.5 OP2 P:DC11 3.8 20.6 0.5 O1A A:DCP403 4.0 18.8 0.5 C4' P:DC10 4.0 18.7 0.5 CB A:ASP256 4.1 17.8 1.0 O5' P:DC11 4.1 17.5 0.5 C4' P:DC10 4.1 18.7 0.5 C5' P:DC10 4.1 22.2 0.5 C5' P:DC10 4.1 22.2 0.5 O5' A:DCP403 4.2 17.6 0.5 C5' P:DC11 4.3 18.2 0.5 CB A:ASP190 4.3 18.2 1.0 OD1 A:ASP256 4.4 18.4 1.0 C5' A:DCP403 4.4 19.2 0.5 CB A:ASP192 4.6 17.4 1.0 O A:MET191 4.7 19.9 1.0 NH2 A:ARG254 4.7 18.3 1.0 O5' P:DC10 4.7 20.6 0.5 O5' P:DC10 4.7 20.6 0.5 C2' P:DC10 4.8 19.2 0.5 O2G A:DCP403 4.8 23.1 0.5 OP1 P:DC10 4.8 21.8 0.5 OP1 P:DC10 4.8 21.8 0.5 C2' P:DC10 4.8 19.2 0.5 C A:MET191 5.0 17.4 1.0 N A:ASP256 5.0 16.8 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