Fluorine in PDB 5wny: Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp, PDB code: 5wny was solved by M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.65 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.480, 79.747, 55.570, 90.00, 107.23, 90.00
R / Rfree (%)	18.1 / 23.7

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Fluorine atom in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp (pdb code 5wny). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp, PDB code: 5wny:

Fluorine binding site 1 out of 1 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp


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 Substrate Complex with Incoming 5-Fdutp within 5.0Å range: probe atom residue distance (Å) B Occ A:F409 b:20.6 occ:1.00 F24 A:B7P409 0.0 20.6 1.0 C23 A:B7P409 1.3 31.4 1.0 C22 A:B7P409 2.3 23.7 1.0 C25 A:B7P409 2.3 21.6 1.0 O26 A:B7P409 2.7 26.6 1.0 C6 P:DC10 3.2 29.8 1.0 C5 P:DC10 3.4 28.2 1.0 N1 P:DC10 3.5 27.9 1.0 C2' P:DC10 3.6 40.5 1.0 O A:HOH651 3.6 38.5 1.0 N27 A:B7P409 3.6 24.8 1.0 N21 A:B7P409 3.6 20.4 1.0 C4 P:DC10 3.9 27.2 1.0 O10 A:B7P409 3.9 28.4 1.0 C2 P:DC10 3.9 29.7 1.0 CB A:ASP276 4.1 21.2 1.0 N3 P:DC10 4.1 24.5 1.0 C28 A:B7P409 4.1 20.8 1.0 C1' P:DC10 4.2 31.8 1.0 O08 A:B7P409 4.3 22.8 1.0 OD2 A:ASP276 4.5 43.4 1.0 C3' P:DC10 4.6 28.1 1.0 N4 P:DC10 4.6 23.6 1.0 CG A:ASP276 4.6 35.1 1.0 O2 P:DC10 4.7 28.2 1.0 P09 A:B7P409 4.7 30.2 1.0 C04 A:B7P409 4.8 21.3 1.0 O05 A:B7P409 4.9 19.0 1.0

M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal. Structures of A Dna Polymerase Inserting Therapeutic Nucleotide Analogues. Chem. Res. Toxicol. V. 30 1993 2017.
ISSN: ISSN 1520-5010
PubMed: 28862449
DOI: 10.1021/ACS.CHEMRESTOX.7B00173