Magnesium in PDB 3lk9: Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P

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

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P, PDB code: 3lk9 was solved by M.Zibinsky, G.K.Surya Prakash, T.G.Upton, B.A.Kashemirov, C.E.Mckenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.28 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.960, 79.800, 55.050, 90.00, 108.46, 90.00
R / Rfree (%)	19.8 / 28.1

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

Fluorine	(F)	4 atoms
Chlorine	(Cl)	3 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P (pdb code 3lk9). 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 Dna Substrate and Dtmp(CF2)P(CF2)P, PDB code: 3lk9:
Jump to Magnesium binding site number: 1; 2;

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


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 Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg339 b:29.4 occ:1.00 OD2 A:ASP192 1.9 38.2 1.0 O2B A:TFF338 1.9 29.2 1.0 OD1 A:ASP190 2.0 27.8 1.0 O1A A:TFF338 2.0 27.3 1.0 O A:HOH349 2.3 28.4 1.0 O3G A:TFF338 2.6 32.6 1.0 CG A:ASP192 2.9 38.9 1.0 CG A:ASP190 2.9 30.4 1.0 PB A:TFF338 3.0 32.2 1.0 PA A:TFF338 3.1 30.1 1.0 OD2 A:ASP190 3.2 29.3 1.0 OD1 A:ASP192 3.3 40.9 1.0 C3A A:TFF338 3.3 32.1 1.0 MG A:MG340 3.3 21.4 1.0 F2A A:TFF338 3.5 31.8 1.0 PG A:TFF338 3.5 33.8 1.0 C5' A:TFF338 3.7 30.1 1.0 O2G A:TFF338 3.7 32.0 1.0 C3B A:TFF338 3.8 32.4 1.0 O5' A:TFF338 3.8 30.6 1.0 O A:HOH437 4.1 26.5 1.0 O A:ASP190 4.1 34.5 1.0 CB A:ASP192 4.2 36.2 1.0 O1B A:TFF338 4.3 30.5 1.0 CB A:ASP190 4.3 28.9 1.0 O2A A:TFF338 4.4 32.7 1.0 C A:ASP190 4.4 33.9 1.0 CA A:GLY179 4.5 34.5 1.0 N A:ASP190 4.5 32.9 1.0 O3' P:DC10 4.6 34.7 1.0 O A:HOH372 4.6 39.8 1.0 O A:HOH413 4.6 32.2 1.0 F1A A:TFF338 4.6 33.0 1.0 CA A:ASP190 4.7 31.9 1.0 F1B A:TFF338 4.7 33.7 1.0 O1G A:TFF338 4.8 35.8 1.0 N A:ASP192 4.9 34.8 1.0 F2B A:TFF338 4.9 31.0 1.0 N A:SER180 5.0 35.4 1.0

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


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 Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg340 b:21.4 occ:1.00 OD1 A:ASP192 1.8 40.9 1.0 OD2 A:ASP190 2.1 29.3 1.0 OD2 A:ASP256 2.2 38.6 1.0 O3' P:DC10 2.3 34.7 1.0 O A:HOH437 2.3 26.5 1.0 O1A A:TFF338 2.4 27.3 1.0 CG A:ASP192 2.8 38.9 1.0 CG A:ASP190 3.0 30.4 1.0 CG A:ASP256 3.2 35.9 1.0 OD2 A:ASP192 3.2 38.2 1.0 MG A:MG339 3.3 29.4 1.0 OD1 A:ASP190 3.4 27.8 1.0 C3' P:DC10 3.6 33.3 1.0 PA A:TFF338 3.6 30.1 1.0 CB A:ASP256 3.7 33.7 1.0 O5' A:TFF338 4.1 30.6 1.0 O2A A:TFF338 4.1 32.7 1.0 CB A:ASP192 4.1 36.2 1.0 C4' P:DC10 4.2 32.9 1.0 OD1 A:ASP256 4.3 34.9 1.0 CB A:ASP190 4.4 28.9 1.0 C5' P:DC10 4.4 33.7 1.0 C5' A:TFF338 4.4 30.1 1.0 CA A:ASP192 4.6 35.6 1.0 O A:MET191 4.6 32.7 1.0 C2' P:DC10 4.8 32.2 1.0 N A:ASP256 4.8 31.2 1.0 N A:ASP192 4.9 34.8 1.0 CA A:ASP256 4.9 30.5 1.0 C A:MET191 4.9 33.6 1.0 O2B A:TFF338 4.9 29.2 1.0 OP1 P:DC10 4.9 36.8 1.0

G.K.Surya Prakash, M.Zibinsky, T.G.Upton, B.A.Kashemirov, C.E.Mckenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, D.D.Shock, S.H.Wilson, G.A.Olah. Synthesis and Biological Evaluation of Fluorinated Deoxynucleotide Analogs Based on Bis-(Difluoromethylene)Triphosphoric Acid. Proc.Natl.Acad.Sci.Usa V. 107 15693 2010.
ISSN: ISSN 0027-8424
PubMed: 20724659
DOI: 10.1073/PNAS.1007430107