Fluorine in PDB 7f35: Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin

The structure of Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin, PDB code: 7f35 was solved by L.T.Wang, W.Y.Jiao, X.Shen, H.T.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 2.60
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	184.071, 184.071, 100.66, 90, 90, 90
R / Rfree (%)	20 / 23.5

The structure of Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin also contains other interesting chemical elements:

Sodium	(Na)	8 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin (pdb code 7f35). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin, PDB code: 7f35:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:48.2 occ:1.00 F27 A:GFN301 0.0 48.2 1.0 C09 A:GFN301 1.4 52.2 1.0 C10 A:GFN301 2.3 48.6 1.0 C08 A:GFN301 2.4 50.5 1.0 N04 A:GFN301 2.7 51.5 1.0 C03 A:GFN301 2.9 46.5 1.0 CD2 A:PHE34 3.1 52.3 1.0 CG A:PHE34 3.4 49.0 1.0 CZ3 B:TRP99 3.4 51.2 1.0 C02 A:GFN301 3.5 45.5 1.0 C11 A:GFN301 3.6 46.9 1.0 C13 A:GFN301 3.7 46.6 1.0 CB A:PHE34 3.7 47.4 1.0 CE2 A:PHE34 3.7 52.6 1.0 CH2 B:TRP99 3.8 54.5 1.0 CE3 B:TRP99 3.9 47.9 1.0 NE2 A:HIS36 4.0 44.4 1.0 C05 A:GFN301 4.1 46.2 1.0 CG2 A:THR93 4.1 44.1 1.0 C12 A:GFN301 4.1 46.9 1.0 CD1 A:PHE34 4.2 49.6 1.0 CD2 A:HIS36 4.2 44.5 1.0 CB A:THR93 4.4 47.0 1.0 C01 A:GFN301 4.4 40.1 1.0 CZ A:PHE34 4.4 54.3 1.0 OG1 A:THR93 4.5 55.6 1.0 CZ2 B:TRP99 4.5 53.4 1.0 C06 A:GFN301 4.6 43.0 1.0 CE1 A:PHE34 4.6 55.0 1.0 CD2 B:TRP99 4.6 52.0 1.0 N07 A:GFN301 4.6 47.4 1.0 O14 A:GFN301 4.8 48.0 1.0 C19 A:GFN301 4.8 52.7 1.0 CE2 B:TRP99 4.9 51.5 1.0 O20 A:GFN301 5.0 49.7 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:47.8 occ:1.00 F27 C:GFN301 0.0 47.8 1.0 C09 C:GFN301 1.3 48.9 1.0 C08 C:GFN301 2.4 46.8 1.0 C10 C:GFN301 2.4 44.1 1.0 N04 C:GFN301 2.7 51.7 1.0 C03 C:GFN301 2.9 48.9 1.0 CD2 C:PHE34 3.3 46.3 1.0 C02 C:GFN301 3.4 47.5 1.0 CG C:PHE34 3.6 46.4 1.0 C11 C:GFN301 3.6 48.2 1.0 C13 C:GFN301 3.6 43.9 1.0 CZ3 D:TRP99 3.6 52.5 1.0 CE1 C:HIS36 3.7 39.4 1.0 CE2 C:PHE34 3.8 48.3 1.0 CH2 D:TRP99 3.9 54.4 1.0 CB C:PHE34 3.9 42.9 1.0 CG2 C:THR93 4.0 48.1 1.0 C05 C:GFN301 4.0 43.4 1.0 CE3 D:TRP99 4.1 51.7 1.0 C12 C:GFN301 4.1 46.9 1.0 CB C:THR93 4.2 46.5 1.0 ND1 C:HIS36 4.2 48.1 1.0 CD1 C:PHE34 4.3 44.1 1.0 OG1 C:THR93 4.4 54.2 1.0 C01 C:GFN301 4.4 41.0 1.0 C06 C:GFN301 4.4 45.2 1.0 CZ C:PHE34 4.5 48.9 1.0 CZ2 D:TRP99 4.5 50.2 1.0 N07 C:GFN301 4.5 43.6 1.0 NE2 C:HIS36 4.6 41.6 1.0 CE1 C:PHE34 4.7 52.5 1.0 CD2 D:TRP99 4.7 50.4 1.0 O14 C:GFN301 4.7 46.0 1.0 C19 C:GFN301 4.9 50.9 1.0 CE2 D:TRP99 4.9 49.5 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range: probe atom residue distance (Å) B Occ E:F301 b:66.6 occ:1.00 F27 E:GFN301 0.0 66.6 1.0 C09 E:GFN301 1.3 68.4 1.0 C10 E:GFN301 2.3 69.2 1.0 C08 E:GFN301 2.3 69.1 1.0 N04 E:GFN301 2.7 66.0 1.0 CD2 E:PHE34 3.0 75.2 1.0 C03 E:GFN301 3.1 65.6 1.0 CG E:PHE34 3.3 82.7 1.0 C11 E:GFN301 3.6 68.9 1.0 CE2 E:PHE34 3.6 75.4 1.0 OG1 E:THR93 3.6 76.1 1.0 C13 E:GFN301 3.6 68.8 1.0 CB E:PHE34 3.7 80.4 1.0 CH2 F:TRP99 3.9 64.7 1.0 C02 E:GFN301 3.9 66.6 1.0 CZ3 F:TRP99 3.9 63.6 1.0 C05 E:GFN301 4.0 65.8 1.0 C12 E:GFN301 4.1 69.7 1.0 CD1 E:PHE34 4.1 74.2 1.0 CE1 E:HIS36 4.2 76.9 1.0 CZ E:PHE34 4.3 79.5 1.0 CZ2 F:TRP99 4.5 60.5 1.0 ND1 E:HIS36 4.6 74.3 1.0 CE1 E:PHE34 4.6 76.6 1.0 CE3 F:TRP99 4.6 61.2 1.0 C06 E:GFN301 4.7 69.9 1.0 O14 E:GFN301 4.7 69.1 1.0 C19 E:GFN301 4.7 73.6 1.0 O20 E:GFN301 4.9 71.5 1.0 CB E:THR93 4.9 74.2 1.0 C01 E:GFN301 4.9 62.1 1.0 N07 E:GFN301 4.9 64.7 1.0

L.T.Wang, W.Xie, W.Y.Jiao, C.Zhang, X.Li, Z.Xu, X.Huang, H.T.Lei, X.Shen. Conformational Adaptability Determining Antibody Recognition to Distomer: Structure Analysis of Enantioselective Antibody Against Chiral Drug Gatifloxacin Rsc Adv V. 11 39534 2021.
ISSN: ESSN 2046-2069
DOI: 10.1039/D1RA07143B