Magnesium in PDB 4klo: Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min

All present enzymatic activity of Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min, PDB code: 4klo 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)	22.62 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.814, 79.966, 55.380, 90.00, 107.75, 90.00
R / Rfree (%)	18.2 / 23

The structure of Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Magnesium atom in the Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min (pdb code 4klo). 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 Nick Complex with MG2+ and Ppi, 30 Min, PDB code: 4klo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 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 Nick Complex with MG2+ and Ppi, 30 Min within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:33.8 occ:0.60 O A:HOH835 2.0 28.8 1.0 O A:HOH834 2.0 37.0 1.0 O P:HOH223 2.1 45.9 1.0 O P:HOH208 2.1 30.1 1.0 OP2 P:DC11 2.3 22.4 1.0 O12 A:PPV405 2.3 29.6 1.0 P P:DC11 3.4 19.8 1.0 O P:HOH215 3.5 33.3 1.0 P2 A:PPV405 3.8 21.2 1.0 O5' P:DC11 4.0 18.5 1.0 O21 A:PPV405 4.0 31.4 1.0 OP1 P:DC11 4.0 15.8 1.0 O A:HOH521 4.1 20.7 1.0 O A:HOH533 4.1 25.2 1.0 O A:HOH720 4.4 39.0 1.0 OPP A:PPV405 4.5 21.8 1.0 O22 A:PPV405 4.6 17.9 1.0 O32 A:PPV405 4.7 20.4 1.0 O3' P:DC10 4.8 20.0 1.0 P1 A:PPV405 4.9 29.8 1.0 OD2 A:ASP276 4.9 35.4 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 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 Nick Complex with MG2+ and Ppi, 30 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:17.4 occ:1.00 O32 A:PPV405 2.0 20.4 1.0 OD2 A:ASP192 2.0 14.3 1.0 OP1 P:DC11 2.0 15.8 1.0 O A:HOH506 2.1 19.4 1.0 O A:HOH533 2.1 25.2 1.0 OD1 A:ASP190 2.1 18.7 1.0 CG A:ASP192 3.0 13.8 1.0 CG A:ASP190 3.2 22.1 1.0 P2 A:PPV405 3.2 21.2 1.0 OD1 A:ASP192 3.4 16.4 1.0 P P:DC11 3.5 19.8 1.0 NA A:NA401 3.5 17.9 1.0 O12 A:PPV405 3.5 29.6 1.0 OD2 A:ASP190 3.6 23.2 1.0 O11 A:PPV405 3.7 24.2 1.0 C5' P:DC11 4.0 17.5 1.0 O5' P:DC11 4.0 18.5 1.0 O A:ASP190 4.1 19.2 1.0 OPP A:PPV405 4.1 21.8 1.0 O A:HOH502 4.3 18.6 1.0 P1 A:PPV405 4.3 29.8 1.0 N A:ASP190 4.3 16.6 1.0 C A:ASP190 4.3 17.4 1.0 O P:HOH208 4.4 30.1 1.0 O22 A:PPV405 4.4 17.9 1.0 CB A:ASP192 4.4 14.2 1.0 OP2 P:DC11 4.4 22.4 1.0 CA A:GLY179 4.4 17.0 1.0 O3' P:DC10 4.5 20.0 1.0 CB A:ASP190 4.5 18.8 1.0 O21 A:PPV405 4.5 31.4 1.0 CA A:ASP190 4.6 15.8 1.0 N A:SER180 4.6 17.8 1.0 N A:ASP192 4.8 18.0 1.0 N A:MET191 5.0 14.1 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