Fluorine 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:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

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

Fluorine 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 Fluorine with other atoms in the F 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:F346 b:18.9 occ:1.00 F1A A:4BD346 0.0 18.9 1.0 C3A A:4BD346 1.3 19.3 1.0 F2A A:4BD346 2.1 18.4 1.0 PB A:4BD346 2.5 15.0 1.0 PA A:4BD346 2.6 18.6 1.0 O1B A:4BD346 2.7 15.8 1.0 O A:HOH362 2.8 28.4 1.0 O5' A:4BD346 3.0 17.2 1.0 O2A A:4BD346 3.1 20.6 1.0 O3B A:4BD346 3.4 17.9 1.0 C3' A:4BD346 3.4 15.2 1.0 O2B A:4BD346 3.7 15.0 1.0 C5' A:4BD346 3.7 15.6 1.0 O1A A:4BD346 3.8 12.3 1.0 C6 A:4BD346 3.8 18.9 1.0 C5M A:4BD346 3.8 14.3 1.0 O3' A:4BD346 4.0 12.3 1.0 C4' A:4BD346 4.1 15.0 1.0 C5 A:4BD346 4.2 17.0 1.0 O3G A:4BD346 4.4 16.9 1.0 O A:HOH459 4.4 29.6 1.0 PG A:4BD346 4.5 21.8 1.0 CB A:ASP276 4.5 22.4 1.0 C2' A:4BD346 4.5 16.9 1.0 O4' A:4BD346 4.6 14.1 1.0 CG A:ASP276 4.6 25.8 1.0 N1 A:4BD346 4.7 15.9 1.0 MG A:MG347 4.8 15.0 1.0 N A:ASP276 4.8 21.3 1.0 O1G A:4BD346 4.8 23.0 1.0 OD2 A:ASP276 4.9 26.3 1.0 C1' A:4BD346 4.9 14.2 1.0 O A:HOH536 4.9 25.4 1.0 OD1 A:ASP276 5.0 26.1 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F346 b:18.4 occ:1.00 F2A A:4BD346 0.0 18.4 1.0 C3A A:4BD346 1.3 19.3 1.0 F1A A:4BD346 2.1 18.9 1.0 PB A:4BD346 2.5 15.0 1.0 PA A:4BD346 2.5 18.6 1.0 O3B A:4BD346 2.6 17.9 1.0 O3G A:4BD346 2.7 16.9 1.0 O2A A:4BD346 2.9 20.6 1.0 PG A:4BD346 3.0 21.8 1.0 O1G A:4BD346 3.1 23.0 1.0 O A:HOH536 3.2 25.4 1.0 O1A A:4BD346 3.2 12.3 1.0 O2B A:4BD346 3.5 15.0 1.0 O1B A:4BD346 3.5 15.8 1.0 O A:HOH427 3.6 12.6 1.0 O A:HOH459 3.7 29.6 1.0 MG A:MG347 3.8 15.0 1.0 O5' A:4BD346 3.9 17.2 1.0 O A:HOH362 4.1 28.4 1.0 O2G A:4BD346 4.4 18.0 1.0 O A:HOH2 4.5 19.0 1.0 C5' A:4BD346 4.6 15.6 1.0 OD1 A:ASP190 4.9 20.1 1.0 C5M A:4BD346 4.9 14.3 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