Fluorine in PDB 5fve: Crystal Structure of Helicobacter Pylori Beta Clamp in Complex with 3, 4-Difluorobenzamide

All present enzymatic activity of Crystal Structure of Helicobacter Pylori Beta Clamp in Complex with 3, 4-Difluorobenzamide:
2.7.7.7;

The structure of Crystal Structure of Helicobacter Pylori Beta Clamp in Complex with 3, 4-Difluorobenzamide, PDB code: 5fve was solved by P.Pandey, S.Gourinath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.76 / 2.07
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.071, 66.383, 82.778, 90.00, 115.43, 90.00
R / Rfree (%)	21.3 / 24.7

The binding sites of Fluorine atom in the Crystal Structure of Helicobacter Pylori Beta Clamp in Complex with 3, 4-Difluorobenzamide (pdb code 5fve). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Helicobacter Pylori Beta Clamp in Complex with 3, 4-Difluorobenzamide, PDB code: 5fve:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Helicobacter Pylori Beta 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 Crystal Structure of Helicobacter Pylori Beta Clamp in Complex with 3, 4-Difluorobenzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F1375 b:70.6 occ:1.00 F10 A:2HO1375 0.0 70.6 1.0 C9 A:2HO1375 1.3 70.5 1.0 C7 A:2HO1375 2.3 70.2 1.0 C11 A:2HO1375 2.4 70.3 1.0 F8 A:2HO1375 2.6 69.9 1.0 CA A:ARG177 2.9 47.0 1.0 N A:ARG177 3.1 48.8 1.0 C A:ARG177 3.2 45.5 1.0 O A:LYS176 3.2 49.3 1.0 N A:LEU178 3.2 44.6 1.0 C A:LYS176 3.3 51.4 1.0 O A:LEU368 3.4 42.3 1.0 C6 A:2HO1375 3.6 70.9 1.0 C4 A:2HO1375 3.6 71.2 1.0 C A:LEU368 3.9 41.9 1.0 CB A:LEU178 3.9 46.9 1.0 O A:ARG177 4.0 45.1 1.0 C5 A:2HO1375 4.1 70.4 1.0 N A:MET369 4.2 42.5 1.0 CA A:LEU178 4.2 45.0 1.0 CA A:MET369 4.2 44.7 1.0 CD2 A:LEU368 4.2 46.7 1.0 CB A:ARG177 4.3 46.1 1.0 N A:MET370 4.4 46.3 1.0 CA A:LYS176 4.4 53.5 1.0 O A:THR175 4.4 52.9 1.0 CB A:LEU368 4.5 44.4 1.0 CG A:LEU368 4.5 45.6 1.0 C A:MET369 4.6 45.4 1.0 C A:THR175 4.7 52.8 1.0 N A:LYS176 4.7 53.4 1.0 CG A:MET370 4.8 51.2 1.0 CA A:LEU368 4.9 42.2 1.0 C2 A:2HO1375 4.9 72.0 1.0 OG1 A:THR173 5.0 48.3 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Helicobacter Pylori Beta 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 Crystal Structure of Helicobacter Pylori Beta Clamp in Complex with 3, 4-Difluorobenzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F1375 b:69.9 occ:1.00 F8 A:2HO1375 0.0 69.9 1.0 C7 A:2HO1375 1.3 70.2 1.0 C9 A:2HO1375 2.3 70.5 1.0 C6 A:2HO1375 2.4 70.9 1.0 F10 A:2HO1375 2.6 70.6 1.0 CB A:PRO347 3.3 52.6 1.0 CG A:PRO347 3.4 53.5 1.0 CD2 A:LEU368 3.4 46.7 1.0 N A:MET370 3.4 46.3 1.0 C A:MET369 3.5 45.4 1.0 CG A:MET370 3.6 51.2 1.0 C11 A:2HO1375 3.6 70.3 1.0 C5 A:2HO1375 3.7 70.4 1.0 CG A:LEU368 3.7 45.6 1.0 N A:MET369 3.8 42.5 1.0 CA A:MET369 3.9 44.7 1.0 O A:MET369 4.0 44.4 1.0 CA A:MET370 4.0 48.4 1.0 O A:LYS176 4.1 49.3 1.0 C4 A:2HO1375 4.1 71.2 1.0 C A:LEU368 4.2 41.9 1.0 CA A:PRO347 4.3 51.1 1.0 CB A:MET370 4.3 49.3 1.0 O A:LEU368 4.5 42.3 1.0 CB A:LEU368 4.5 44.4 1.0 CE A:MET370 4.7 53.8 1.0 CD A:PRO347 4.8 53.7 1.0 C A:LYS176 4.8 51.4 1.0 CD1 A:LEU368 4.8 45.5 1.0 O A:HOH2058 4.9 55.3 1.0 CA A:LEU368 5.0 42.2 1.0

P.Pandey, V.Verma, S.K.Dhar, S.Gourinath. Screening of E. Coli Beta-Clamp Inhibitors Revealed That Few Inhibit Helicobacter Pylori More Effectively: Structural and Functional Characterization. Antibiotics (Basel) V. 7 2018.
ISSN: ESSN 2079-6382
PubMed: 29324718
DOI: 10.3390/ANTIBIOTICS7010005