Fluorine in PDB 4n94: E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide

All present enzymatic activity of E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide:
2.7.7.7;

The structure of E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide, PDB code: 4n94 was solved by Z.Yin, A.J.Oakley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.91 / 1.73
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.740, 64.510, 71.720, 74.01, 83.21, 84.54
R / Rfree (%)	24.9 / 29.3

The structure of E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Fluorine atom in the E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide (pdb code 4n94). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide, PDB code: 4n94:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:49.6 occ:1.00 F10 A:2HO401 0.0 49.6 1.0 C9 A:2HO401 1.3 43.6 1.0 C11 A:2HO401 2.4 42.1 1.0 C7 A:2HO401 2.4 42.6 1.0 F8 A:2HO401 2.8 42.2 1.0 O A:HOH616 3.1 24.8 1.0 OG A:SER346 3.5 19.5 0.7 C4 A:2HO401 3.6 41.8 1.0 C6 A:2HO401 3.6 40.2 1.0 O A:HOH617 3.9 36.4 1.0 CG A:MET362 4.0 23.7 1.0 C5 A:2HO401 4.1 40.2 1.0 CE A:MET362 4.3 30.1 1.0 CG1 A:VAL247 4.3 19.5 1.0 CB A:SER346 4.5 17.8 0.7 CB A:SER346 4.5 16.2 0.3 O A:GLY174 4.9 17.3 1.0 C2 A:2HO401 4.9 39.2 1.0 OG A:SER346 4.9 15.7 0.3 CG1 A:VAL360 5.0 14.9 1.0

Fluorine binding site 2 out of 2 in the E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of E. Coli Sliding Clamp in Complex with 3,4-Difluorobenzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:42.2 occ:1.00 F8 A:2HO401 0.0 42.2 1.0 C7 A:2HO401 1.3 42.6 1.0 C6 A:2HO401 2.4 40.2 1.0 C9 A:2HO401 2.4 43.6 1.0 F10 A:2HO401 2.8 49.6 1.0 O A:HIS175 3.3 14.9 1.0 C5 A:2HO401 3.6 40.2 1.0 C A:HIS175 3.7 14.7 1.0 C11 A:2HO401 3.7 42.1 1.0 CG A:MET362 3.9 23.7 1.0 O A:VAL360 3.9 14.0 1.0 CG1 A:VAL360 3.9 14.9 1.0 N A:MET362 4.0 15.9 1.0 CA A:ARG176 4.0 13.8 1.0 N A:ARG176 4.0 14.1 1.0 OG A:SER346 4.1 19.5 0.7 CG1 A:VAL247 4.1 19.5 1.0 C4 A:2HO401 4.1 41.8 1.0 C A:VAL360 4.2 14.0 1.0 C A:ARG176 4.4 13.4 1.0 N A:VAL361 4.4 14.0 1.0 N A:LEU177 4.4 12.6 1.0 CA A:VAL361 4.4 14.5 1.0 C A:VAL361 4.4 15.5 1.0 CA A:HIS175 4.5 16.2 1.0 CB A:VAL360 4.5 14.5 1.0 O A:HOH616 4.5 24.8 1.0 O A:GLY174 4.6 17.3 1.0 CB A:SER346 4.6 17.8 0.7 CA A:MET362 4.7 18.3 1.0 CB A:LEU177 4.7 12.3 1.0 CB A:SER346 4.8 16.2 0.3 N A:HIS175 4.8 16.5 1.0 CB A:MET362 4.8 20.9 1.0 C A:GLY174 4.9 16.4 1.0

Z.Yin, L.R.Whittell, Y.Wang, S.Jergic, M.Liu, E.J.Harry, N.E.Dixon, J.L.Beck, M.J.Kelso, A.J.Oakley. Discovery of Lead Compounds Targeting the Bacterial Sliding Clamp Using A Fragment-Based Approach. J.Med.Chem. V. 57 2799 2014.
ISSN: ISSN 0022-2623
PubMed: 24592885
DOI: 10.1021/JM500122R