Magnesium in PDB 4kle: Dna Polymerase Beta Matched Reactant Complex with MG2+, 10 S

All present enzymatic activity of Dna Polymerase Beta Matched Reactant Complex with MG2+, 10 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Reactant Complex with MG2+, 10 S, PDB code: 4kle 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)	22.14 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.525, 79.329, 55.146, 90.00, 107.33, 90.00
R / Rfree (%)	18.5 / 24.9

The binding sites of Magnesium atom in the Dna Polymerase Beta Matched Reactant Complex with MG2+, 10 S (pdb code 4kle). 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+, 10 S, PDB code: 4kle:
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+, 10 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+, 10 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.4 occ:1.00 O P:HOH102 2.1 29.2 1.0 OD2 A:ASP256 2.1 23.9 1.0 OD2 A:ASP190 2.1 32.3 1.0 OD1 A:ASP192 2.1 20.6 1.0 O3' P:DC10 2.3 34.4 0.7 O2A A:DCP401 2.3 20.4 0.7 O3' P:DC10 2.4 34.4 0.3 OP1 P:DC11 2.4 20.5 0.3 CG A:ASP190 2.9 24.4 1.0 P P:DC11 2.9 21.0 0.3 OD1 A:ASP190 3.0 27.9 1.0 CG A:ASP192 3.2 17.9 1.0 CG A:ASP256 3.3 27.1 1.0 PA A:DCP401 3.5 22.6 0.7 C3' P:DC10 3.6 23.5 0.7 OD2 A:ASP192 3.6 21.8 1.0 C3' P:DC10 3.6 23.5 0.3 MG A:MG403 3.7 15.3 1.0 O1A A:DCP401 3.8 25.2 0.7 CB A:ASP256 3.9 22.9 1.0 C4' P:DC10 3.9 23.5 0.3 OP2 P:DC11 4.0 25.7 0.3 O5' P:DC11 4.1 19.7 0.3 C4' P:DC10 4.1 23.5 0.7 C5' P:DC10 4.1 23.2 0.7 C5' P:DC10 4.1 23.2 0.3 O5' A:DCP401 4.2 22.1 0.7 C5' P:DC11 4.2 18.8 0.3 C5' A:DCP401 4.3 18.6 0.7 OD1 A:ASP256 4.3 21.2 1.0 CB A:ASP190 4.4 24.1 1.0 CB A:ASP192 4.5 17.7 1.0 O A:MET191 4.6 22.7 1.0 O A:HOH630 4.6 35.2 1.0 C2' P:DC10 4.6 20.8 0.3 O5' P:DC10 4.8 22.9 0.7 O5' P:DC10 4.8 22.9 0.3 C2' P:DC10 4.8 20.8 0.7 NH2 A:ARG254 4.9 24.0 1.0 OP1 P:DC10 4.9 25.0 0.3 C A:MET191 4.9 21.9 1.0 O3A A:DCP401 4.9 30.7 0.7 OP1 P:DC10 4.9 25.0 0.7 CA A:ASP192 4.9 17.3 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Matched Reactant Complex with MG2+, 10 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+, 10 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:15.3 occ:1.00 OD1 A:ASP190 2.0 27.9 1.0 O A:HOH502 2.1 24.6 1.0 O2B A:DCP401 2.1 19.9 0.7 OD2 A:ASP192 2.2 21.8 1.0 O21 A:PPV404 2.2 29.1 0.3 O2G A:DCP401 2.2 29.2 0.7 O2A A:DCP401 2.3 20.4 0.7 O32 A:PPV404 2.4 19.3 0.3 OP1 P:DC11 2.4 20.5 0.3 PB A:DCP401 3.1 24.7 0.7 CG A:ASP192 3.2 17.9 1.0 CG A:ASP190 3.2 24.4 1.0 P2 A:PPV404 3.2 24.3 0.3 O12 A:PPV404 3.3 25.3 0.3 PA A:DCP401 3.4 22.6 0.7 P1 A:PPV404 3.4 30.6 0.3 O3A A:DCP401 3.5 30.7 0.7 OD1 A:ASP192 3.5 20.6 1.0 PG A:DCP401 3.5 31.0 0.7 O A:ASP190 3.7 26.9 1.0 MG A:MG402 3.7 15.4 1.0 O3B A:DCP401 3.8 29.5 0.7 OPP A:PPV404 3.8 29.0 0.3 OD2 A:ASP190 3.8 32.3 1.0 P P:DC11 3.9 21.0 0.3 C A:ASP190 4.0 20.8 1.0 O31 A:PPV404 4.1 22.6 0.3 N A:ASP190 4.1 19.6 1.0 O1G A:DCP401 4.2 22.6 0.7 O A:HOH513 4.2 22.6 1.0 C5' A:DCP401 4.2 18.6 0.7 O A:HOH630 4.3 35.2 1.0 C5' P:DC11 4.3 18.8 0.3 CB A:ASP190 4.3 24.1 1.0 CA A:ASP190 4.4 15.5 1.0 O1B A:DCP401 4.4 24.0 0.7 O5' P:DC11 4.4 19.7 0.3 O1A A:DCP401 4.5 25.2 0.7 O5' A:DCP401 4.5 22.1 0.7 O P:HOH102 4.5 29.2 1.0 CB A:ASP192 4.5 17.7 1.0 O22 A:PPV404 4.6 21.6 0.3 O3G A:DCP401 4.6 30.7 0.7 O11 A:PPV404 4.6 29.6 0.3 CA A:GLY179 4.6 20.2 1.0 N A:SER180 4.6 24.8 1.0 O3' P:DC10 4.7 34.4 0.3 OG A:SER180 4.7 29.0 1.0 N A:MET191 4.8 16.5 1.0 OP2 P:DC11 4.8 25.7 0.3 N A:ASP192 4.9 22.2 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