Fluorine in PDB 5sde: Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z1619978933

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z1619978933, PDB code: 5sde was solved by C.T.Tham, J.A.Coker, T.Krojer, W.R.Foster, L.Koekemoer, A.Douangamath, R.Talon, D.Fearon, F.Von Delft, W.W.Yue, C.Bountra, G.A.Bezerra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.63 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.472, 117.837, 147.651, 90, 90, 90
R / Rfree (%)	23.9 / 26.5

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z1619978933 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z1619978933 (pdb code 5sde). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z1619978933, PDB code: 5sde:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z1619978933


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z1619978933 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:20.0 occ:0.42 F12 A:U0M801 0.0 20.0 0.4 C11 A:U0M801 1.3 19.9 0.4 C10 A:U0M801 2.3 20.0 0.4 C13 A:U0M801 2.4 20.7 0.4 CB A:TRP675 3.2 24.0 1.0 CB A:LYS336 3.4 27.3 1.0 CB A:TRP219 3.5 26.8 1.0 CG A:TRP675 3.5 24.9 1.0 N07 A:U0M801 3.6 21.7 0.4 CD1 A:TRP219 3.7 27.9 1.0 C09 A:U0M801 3.7 20.8 0.4 CD1 A:TRP675 3.7 26.2 1.0 CG A:LYS336 3.8 27.6 1.0 CG A:TRP219 3.9 26.9 1.0 CD A:LYS336 3.9 29.3 1.0 O A:ASN218 4.0 28.6 1.0 C08 A:U0M801 4.1 21.5 0.4 O A:HOH949 4.3 25.6 1.0 O A:LYS336 4.4 27.3 1.0 CA A:LYS336 4.4 26.8 1.0 CD1 A:ILE220 4.4 27.1 1.0 C A:LYS336 4.5 26.9 1.0 CD2 A:TRP675 4.5 25.8 1.0 O A:TRP219 4.6 24.9 1.0 CA A:TRP675 4.6 24.6 1.0 NE1 A:TRP675 4.7 26.9 1.0 CA A:TRP219 4.7 26.8 1.0 C A:TRP219 4.8 24.9 1.0 NE1 A:TRP219 4.8 28.2 1.0 C06 A:U0M801 4.8 22.7 0.4 CE A:LYS336 4.8 30.6 1.0 O A:HOH1028 5.0 36.2 1.0 C A:ASN218 5.0 28.7 1.0

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z1619978933


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z1619978933 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:22.2 occ:0.38 F12 B:U0M801 0.0 22.2 0.4 C11 B:U0M801 1.3 22.2 0.4 C10 B:U0M801 2.3 22.1 0.4 C13 B:U0M801 2.4 22.9 0.4 CB B:LYS336 3.3 26.4 1.0 CB B:TRP675 3.4 25.1 1.0 CG B:LYS336 3.6 28.4 1.0 N07 B:U0M801 3.6 23.9 0.4 CB B:TRP219 3.7 25.4 1.0 C09 B:U0M801 3.7 22.5 0.4 CD1 B:TRP219 3.7 26.4 1.0 CG B:TRP675 3.7 25.9 1.0 CD B:LYS336 3.8 32.2 1.0 CD1 B:TRP675 3.9 26.8 1.0 CG B:TRP219 4.0 26.1 1.0 O B:ASN218 4.1 26.2 1.0 C08 B:U0M801 4.1 23.1 0.4 CA B:LYS336 4.2 25.5 1.0 O B:HOH933 4.2 22.1 1.0 O B:LYS336 4.2 26.7 1.0 C B:LYS336 4.4 26.3 1.0 CD1 B:ILE220 4.5 25.1 1.0 CD2 B:TRP675 4.6 27.1 1.0 CE B:LYS336 4.7 34.6 1.0 CA B:TRP675 4.8 25.5 1.0 O B:TRP219 4.8 23.1 1.0 C06 B:U0M801 4.8 25.5 0.4 NE1 B:TRP219 4.8 27.0 1.0 NE1 B:TRP675 4.9 27.5 1.0 CA B:TRP219 4.9 25.5 1.0 C B:TRP219 5.0 23.3 1.0

C.T.Tham, J.A.Coker, T.Krojer, W.R.Foster, L.Koekemoer, A.Douangamath, R.Talon, D.Fearon, F.Von Delft, W.W.Yue, C.Bountra, G.A.Bezerra. Pandda Analysis Group Deposition To Be Published.