Fluorine in PDB 2w5u: Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor

The structure of Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor, PDB code: 2w5u was solved by N.Cremades, I.Perez-Dorado, J.A.Hermoso, M.Martinez-Julvez, J.Sancho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.00 / 2.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.533, 50.967, 72.806, 90.00, 98.64, 90.00
R / Rfree (%)	22.7 / 26.4

The binding sites of Fluorine atom in the Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor (pdb code 2w5u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor, PDB code: 2w5u:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F166 b:46.8 occ:0.50 F3 A:IC3166 0.0 46.8 0.5 O2 A:FMN165 1.1 37.7 0.5 C7 A:IC3166 1.3 46.8 0.5 C2 A:FMN165 1.5 37.3 0.5 F1 A:IC3166 2.1 47.5 0.5 F2 A:IC3166 2.2 47.2 0.5 N3 A:FMN165 2.2 36.9 0.5 C4 A:IC3166 2.4 46.5 0.5 N1 A:FMN165 2.5 37.5 0.5 O A:ASP88 2.7 29.0 1.0 O A:THR95 3.0 29.5 1.0 N A:ASP88 3.0 28.5 1.0 C5 A:IC3166 3.1 46.3 0.5 C A:ASP88 3.2 28.6 1.0 C3 A:IC3166 3.3 46.7 0.5 C4 A:FMN165 3.3 37.0 0.5 CA A:PHE96 3.4 25.6 1.0 CB A:TYR92 3.4 22.1 1.0 CD1 A:PHE96 3.5 23.1 1.0 CA A:ASP88 3.6 28.4 1.0 C10 A:FMN165 3.6 37.6 0.5 CD2 A:TYR92 3.7 19.5 1.0 N A:ALA97 3.7 25.8 1.0 O A:TYR92 3.8 22.5 1.0 C4A A:FMN165 3.9 37.6 0.5 CG A:TYR92 3.9 21.4 1.0 C A:THR95 4.0 27.4 1.0 CB A:ASP88 4.0 28.5 1.0 CB A:PHE96 4.0 25.1 1.0 C A:GLY87 4.1 28.6 1.0 C A:PHE96 4.1 25.7 1.0 N A:GLN89 4.2 28.2 1.0 N A:PHE96 4.2 26.6 1.0 CG A:PHE96 4.2 23.5 1.0 CA A:GLY87 4.2 27.6 1.0 O4 A:FMN165 4.3 36.9 0.5 C6 A:IC3166 4.4 45.9 0.5 CE1 A:PHE96 4.4 20.7 1.0 CA A:TYR92 4.4 22.2 1.0 C2 A:IC3166 4.5 47.5 0.5 C A:TYR92 4.5 22.9 1.0 CA A:GLN89 4.7 28.0 1.0 N A:TYR92 4.7 22.1 1.0 CE2 A:TYR92 4.8 21.1 1.0 N10 A:FMN165 4.8 36.5 0.5 CA A:ALA97 4.9 25.8 1.0

Fluorine binding site 2 out of 3 in the Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F166 b:47.2 occ:0.50 F2 A:IC3166 0.0 47.2 0.5 C7 A:IC3166 1.3 46.8 0.5 N3 A:FMN165 1.3 36.9 0.5 C2 A:FMN165 1.8 37.3 0.5 O2 A:FMN165 1.9 37.7 0.5 F1 A:IC3166 2.1 47.5 0.5 F3 A:IC3166 2.2 46.8 0.5 C4 A:IC3166 2.3 46.5 0.5 O A:THR95 2.3 29.5 1.0 C4 A:FMN165 2.6 37.0 0.5 C3 A:IC3166 2.7 46.7 0.5 N A:ALA97 2.8 25.8 1.0 CA A:PHE96 3.0 25.6 1.0 C A:THR95 3.0 27.4 1.0 N1 A:FMN165 3.1 37.5 0.5 O4 A:FMN165 3.1 36.9 0.5 C A:PHE96 3.2 25.7 1.0 N A:PHE96 3.3 26.6 1.0 C5 A:IC3166 3.5 46.3 0.5 CG2 A:THR54 3.5 19.5 1.0 C4A A:FMN165 3.6 37.6 0.5 CB A:THR54 3.8 20.8 1.0 CA A:ALA97 3.8 25.8 1.0 C10 A:FMN165 3.9 37.6 0.5 N A:GLU98 4.0 26.9 1.0 OG1 A:THR54 4.0 21.1 1.0 C2 A:IC3166 4.0 47.5 0.5 OG1 A:THR95 4.2 28.0 1.0 CB A:PHE96 4.3 25.1 1.0 CA A:THR95 4.3 27.4 1.0 CB A:TYR92 4.3 22.1 1.0 O A:PHE96 4.4 26.0 1.0 CB A:THR95 4.4 27.6 1.0 CD1 A:PHE96 4.5 23.1 1.0 C A:ALA97 4.5 26.5 1.0 O1 A:IC3166 4.5 50.6 0.5 C6 A:IC3166 4.6 45.9 0.5 O A:TYR92 4.6 22.5 1.0 N A:ASP88 4.7 28.5 1.0 O A:ASP88 4.8 29.0 1.0 N3 A:IC3166 4.8 49.1 0.5 CG A:PHE96 4.8 23.5 1.0 CG A:TYR92 4.9 21.4 1.0 N5 A:FMN165 4.9 37.7 0.5 CA A:GLY87 4.9 27.6 1.0 C1 A:IC3166 4.9 46.3 0.5

Fluorine binding site 3 out of 3 in the Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Flavodoxin From Helicobacter Pylori in Complex with the C3 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F166 b:47.5 occ:0.50 F1 A:IC3166 0.0 47.5 0.5 O2 A:FMN165 1.1 37.7 0.5 C7 A:IC3166 1.3 46.8 0.5 C2 A:FMN165 1.4 37.3 0.5 N1 A:FMN165 2.1 37.5 0.5 F3 A:IC3166 2.1 46.8 0.5 F2 A:IC3166 2.1 47.2 0.5 C4 A:IC3166 2.3 46.5 0.5 N3 A:FMN165 2.4 36.9 0.5 C5 A:IC3166 2.7 46.3 0.5 CA A:GLY87 2.8 27.6 1.0 N A:ALA97 2.8 25.8 1.0 N A:ASP88 3.0 28.5 1.0 C10 A:FMN165 3.3 37.6 0.5 C A:GLY87 3.4 28.6 1.0 CB A:THR54 3.5 20.8 1.0 C3 A:IC3166 3.5 46.7 0.5 CA A:ALA97 3.5 25.8 1.0 C4 A:FMN165 3.5 37.0 0.5 OG1 A:THR54 3.6 21.1 1.0 C4A A:FMN165 3.8 37.6 0.5 C A:PHE96 3.9 25.7 1.0 CD1 A:PHE96 3.9 23.1 1.0 O A:LEU86 3.9 28.2 1.0 CA A:PHE96 4.0 25.6 1.0 C6 A:IC3166 4.0 45.9 0.5 N A:GLY87 4.1 27.8 1.0 CG2 A:THR54 4.1 19.5 1.0 O A:THR95 4.2 29.5 1.0 CA A:ASP88 4.2 28.4 1.0 N10 A:FMN165 4.4 36.5 0.5 CB A:ALA97 4.4 24.8 1.0 O A:ASP88 4.4 29.0 1.0 C A:LEU86 4.4 28.1 1.0 O2' A:FMN165 4.5 41.4 1.0 CE1 A:PHE96 4.5 20.7 1.0 C A:ASP88 4.5 28.6 1.0 O4 A:FMN165 4.5 36.9 0.5 C2 A:IC3166 4.6 47.5 0.5 C1' A:FMN165 4.6 44.6 1.0 O A:GLY87 4.6 28.8 1.0 C A:ALA97 4.7 26.5 1.0 N A:GLU98 4.7 26.9 1.0 CA A:THR54 4.8 20.8 1.0 CG A:PHE96 4.8 23.5 1.0 CB A:ASP88 4.8 28.5 1.0 C1 A:IC3166 4.9 46.3 0.5 CB A:PHE96 4.9 25.1 1.0 N A:PHE96 4.9 26.6 1.0 C A:THR95 5.0 27.4 1.0 N A:THR54 5.0 20.5 1.0

N.Cremades, A.Velazquez-Campoy, M.Martinez-Julvez, J.L.Neira, I.Perez-Dorado, J.Hermoso, P.Jimenez, A.Lanas, P.S.Hoffman, J.Sancho. Discovery of Specific Flavodoxin Inhibitors As Potential Therapeutic Agents Against Helicobacter Pylori Infection. Acs Chem.Biol. V. 4 928 2009.
ISSN: ISSN 1554-8929
PubMed: 19725577
DOI: 10.1021/CB900166Q