Magnesium in PDB 5ugn: Dna Polymerase Beta Imidodiphosphate Reactant Complex

All present enzymatic activity of Dna Polymerase Beta Imidodiphosphate Reactant Complex:
2.7.7.7;

The structure of Dna Polymerase Beta Imidodiphosphate Reactant Complex, PDB code: 5ugn was solved by B.D.Freudenthal, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.15 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.778, 79.922, 55.321, 90.00, 107.67, 90.00
R / Rfree (%)	18.1 / 24.3

The binding sites of Magnesium atom in the Dna Polymerase Beta Imidodiphosphate Reactant Complex (pdb code 5ugn). 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 Imidodiphosphate Reactant Complex, PDB code: 5ugn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Imidodiphosphate Reactant Complex


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 Imidodiphosphate Reactant Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:30.6 occ:1.00 O1B A:8CP404 1.9 26.3 0.4 O2A A:8CP404 2.0 24.0 0.4 OD1 A:ASP190 2.0 29.9 1.0 OD2 A:ASP192 2.1 24.7 1.0 O3G A:8CP404 2.1 29.8 0.4 O6 A:2PN401 2.2 26.8 0.4 OP1 P:DC11 2.2 21.7 0.6 O2 A:2PN401 2.3 29.7 0.4 O A:HOH544 2.4 30.4 1.0 CG A:ASP192 3.1 23.1 1.0 PB A:8CP404 3.1 27.8 0.4 CG A:ASP190 3.1 27.6 1.0 P2 A:2PN401 3.2 26.3 0.4 PA A:8CP404 3.3 25.1 0.4 O5 A:2PN401 3.3 33.5 0.4 PG A:8CP404 3.3 41.5 0.4 OD1 A:ASP192 3.4 24.1 1.0 MG A:MG403 3.5 31.1 1.0 O3A A:8CP404 3.5 32.0 0.4 P P:DC11 3.6 30.2 0.6 OD2 A:ASP190 3.6 32.7 1.0 P1 A:2PN401 3.6 42.0 0.4 N3B A:8CP404 3.7 33.4 0.4 N1 A:2PN401 3.8 34.4 0.4 O1G A:8CP404 3.9 28.3 0.4 O A:ASP190 4.0 26.7 1.0 C5' P:DC11 4.0 25.0 0.6 C5' A:8CP404 4.0 25.1 0.4 O5' P:DC11 4.0 27.1 0.6 O5' A:8CP404 4.2 26.7 0.4 C A:ASP190 4.3 25.1 1.0 O A:HOH593 4.3 26.8 1.0 O2B A:8CP404 4.4 22.9 0.4 O1A A:8CP404 4.4 26.4 0.4 N A:ASP190 4.4 20.0 1.0 CB A:ASP190 4.4 26.9 1.0 CB A:ASP192 4.4 21.7 1.0 OP2 P:DC11 4.5 28.9 0.6 O4 A:2PN401 4.5 24.6 0.4 CA A:GLY179 4.5 20.7 1.0 CA A:ASP190 4.6 21.4 1.0 N A:SER180 4.6 24.1 1.0 O2G A:8CP404 4.6 39.5 0.4 O3 A:2PN401 4.6 40.4 0.4 O3' P:DC10 4.6 31.7 0.6 O1 A:2PN401 4.6 28.4 0.4 OG A:SER180 4.8 31.6 1.0 N A:ASP192 4.8 24.2 1.0 N A:MET191 4.9 19.2 1.0 O3' P:DC10 4.9 30.6 0.4

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Imidodiphosphate Reactant Complex


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 Imidodiphosphate Reactant Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:31.1 occ:1.00 OD2 A:ASP190 2.0 32.7 1.0 OD1 A:ASP192 2.1 24.1 1.0 OD2 A:ASP256 2.2 35.4 1.0 OP1 P:DC11 2.2 21.7 0.6 O3' P:DC10 2.4 31.7 0.6 O3' P:DC10 2.4 30.6 0.4 O2A A:8CP404 2.7 24.0 0.4 P P:DC11 2.8 30.2 0.6 CG A:ASP190 2.8 27.6 1.0 OD1 A:ASP190 3.0 29.9 1.0 CG A:ASP192 3.1 23.1 1.0 CG A:ASP256 3.3 32.1 1.0 OD2 A:ASP192 3.5 24.7 1.0 MG A:MG402 3.5 30.6 1.0 C3' P:DC10 3.6 27.0 0.4 C3' P:DC10 3.7 25.9 0.6 PA A:8CP404 3.8 25.1 0.4 OP2 P:DC11 3.9 28.9 0.6 CB A:ASP256 3.9 28.3 1.0 O5' P:DC11 4.0 27.1 0.6 C4' P:DC10 4.0 28.4 0.6 O5' A:8CP404 4.1 26.7 0.4 C4' P:DC10 4.1 28.1 0.4 C5' A:8CP404 4.2 25.1 0.4 O1A A:8CP404 4.2 26.4 0.4 CB A:ASP190 4.2 26.9 1.0 C5' P:DC10 4.2 30.1 0.4 C5' P:DC11 4.2 25.0 0.6 C5' P:DC10 4.2 30.3 0.6 OD1 A:ASP256 4.3 27.8 1.0 CB A:ASP192 4.4 21.7 1.0 O A:MET191 4.5 21.8 1.0 O3G A:8CP404 4.7 29.8 0.4 C2' P:DC10 4.7 25.9 0.6 NH2 A:ARG254 4.8 28.5 1.0 O5' P:DC10 4.8 25.1 0.4 C2' P:DC10 4.8 25.5 0.4 OP1 P:DC10 4.8 28.6 0.6 C A:MET191 4.8 21.0 1.0 CA A:ASP192 4.8 21.5 1.0 N A:ASP256 4.9 22.7 1.0 O5' P:DC10 4.9 24.6 0.6 O1B A:8CP404 5.0 26.3 0.4 N A:ASP192 5.0 24.2 1.0

D.D.Shock, B.D.Freudenthal, W.A.Beard, S.H.Wilson. Modulating the Dna Polymerase Beta Reaction Equilibrium to Dissect the Reverse Reaction. Nat. Chem. Biol. V. 13 1074 2017.
ISSN: ESSN 1552-4469
PubMed: 28759020
DOI: 10.1038/NCHEMBIO.2450