Magnesium in PDB 3gdx: Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp

All present enzymatic activity of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp:
2.7.7.7;

The structure of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp, PDB code: 3gdx was solved by S.H.Wilson, V.K.Batra, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.58 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.500, 79.700, 55.300, 90.00, 107.90, 90.00
R / Rfree (%)	20.8 / 26.6

The structure of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp (pdb code 3gdx). 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 with A Gapped Dnd Substrate and Dtmp(CF2)Pp, PDB code: 3gdx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp


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 with A Gapped Dnd Substrate and Dtmp(CF2)Pp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg347 b:15.0 occ:1.00 OD1 A:ASP190 1.8 20.1 1.0 O1A A:4BD346 2.0 12.3 1.0 O3G A:4BD346 2.1 16.9 1.0 OD2 A:ASP192 2.1 17.5 1.0 O2B A:4BD346 2.2 15.0 1.0 O A:HOH1 2.2 11.9 1.0 CG A:ASP190 2.8 19.0 1.0 CG A:ASP192 3.1 19.1 1.0 PG A:4BD346 3.2 21.8 1.0 OD2 A:ASP190 3.2 18.6 1.0 PB A:4BD346 3.2 15.0 1.0 PA A:4BD346 3.2 18.6 1.0 OD1 A:ASP192 3.4 21.3 1.0 MG A:MG348 3.4 19.6 1.0 O2G A:4BD346 3.4 18.0 1.0 O3B A:4BD346 3.5 17.9 1.0 C3A A:4BD346 3.5 19.3 1.0 O A:HOH427 3.7 12.6 1.0 F2A A:4BD346 3.8 18.4 1.0 C5' A:4BD346 4.0 15.6 1.0 O5' A:4BD346 4.1 17.2 1.0 O A:ASP190 4.1 22.0 1.0 CB A:ASP190 4.1 19.1 1.0 N A:ASP190 4.2 18.7 1.0 O A:HOH2 4.2 19.0 1.0 C A:ASP190 4.2 21.3 1.0 O A:HOH432 4.3 18.2 1.0 O2A A:4BD346 4.4 20.6 1.0 O1G A:4BD346 4.4 23.0 1.0 CB A:ASP192 4.4 17.6 1.0 CA A:ASP190 4.4 19.9 1.0 O1B A:4BD346 4.6 15.8 1.0 CA A:GLY179 4.7 16.6 1.0 N A:MET191 4.8 22.2 1.0 F1A A:4BD346 4.8 18.9 1.0 N A:ASP192 4.8 21.5 1.0 O3' P:DC10 4.9 27.2 1.0 N A:SER180 4.9 19.2 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp


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 with A Gapped Dnd Substrate and Dtmp(CF2)Pp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg348 b:19.6 occ:1.00 OD1 A:ASP192 2.0 21.3 1.0 OD2 A:ASP256 2.0 19.9 1.0 O3' P:DC10 2.1 27.2 1.0 O A:HOH2 2.2 19.0 1.0 OD2 A:ASP190 2.3 18.6 1.0 O1A A:4BD346 2.3 12.3 1.0 CG A:ASP192 3.0 19.1 1.0 CG A:ASP256 3.2 20.4 1.0 PA A:4BD346 3.3 18.6 1.0 CG A:ASP190 3.3 19.0 1.0 OD2 A:ASP192 3.4 17.5 1.0 C3' P:DC10 3.4 25.0 1.0 MG A:MG347 3.4 15.0 1.0 O2A A:4BD346 3.6 20.6 1.0 OD1 A:ASP190 3.6 20.1 1.0 O5' A:4BD346 3.6 17.2 1.0 CB A:ASP256 3.8 18.5 1.0 C4' P:DC10 4.0 25.5 1.0 C5' P:DC10 4.0 24.3 1.0 C5' A:4BD346 4.2 15.6 1.0 OD1 A:ASP256 4.2 16.1 1.0 O A:HOH427 4.3 12.6 1.0 CB A:ASP192 4.4 17.6 1.0 O5' P:DC10 4.6 25.0 1.0 OP1 P:DC10 4.6 25.8 1.0 C2' P:DC10 4.6 24.5 1.0 CB A:ASP190 4.6 19.1 1.0 O3G A:4BD346 4.7 16.9 1.0 O2B A:4BD346 4.9 15.0 1.0 C3A A:4BD346 4.9 19.3 1.0 O A:MET191 4.9 18.8 1.0 NH2 A:ARG254 4.9 19.2 1.0 CA A:ASP192 5.0 19.4 1.0 O A:HOH538 5.0 12.1 1.0

T.G.Upton, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, G.K.Prakash, R.Kultyshev, V.K.Batra, D.D.Shock, L.C.Pedersen, W.A.Beard, S.H.Wilson. Alpha,Beta-Difluoromethylene Deoxynucleoside 5'-Triphosphates: A Convenient Synthesis of Useful Probes For Dna Polymerase Beta Structure and Function Org.Lett. V. 11 1883 2009.
ISSN: ISSN 1523-7060
PubMed: 19351147
DOI: 10.1021/OL701755K