Fluorine in PDB 5sdo: Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z19735067

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z19735067, PDB code: 5sdo 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)	83.86 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.802, 117.06, 147.933, 90, 90, 90
R / Rfree (%)	22.1 / 24.2

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z19735067 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 Z19735067 (pdb code 5sdo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z19735067, PDB code: 5sdo:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z19735067


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 Z19735067 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:38.8 occ:0.71 F1 A:I8G801 0.0 38.8 0.7 C1 A:I8G801 1.4 38.5 0.7 C2 A:I8G801 2.3 38.3 0.7 C12 A:I8G801 2.3 38.1 0.7 CB A:LYS336 3.2 34.2 1.0 CD1 A:TRP219 3.3 38.4 1.0 CG A:LYS336 3.5 34.9 1.0 CB A:TRP219 3.5 35.3 1.0 C11 A:I8G801 3.6 38.1 0.7 C3 A:I8G801 3.6 38.1 0.7 CG A:TRP219 3.7 37.1 1.0 CD A:LYS336 3.7 37.1 1.0 O A:ASN218 3.8 36.3 1.0 CB A:TRP675 3.8 29.4 1.0 O A:HOH967 4.0 36.0 1.0 C4 A:I8G801 4.1 38.5 0.7 CG A:TRP675 4.2 29.8 1.0 CA A:LYS336 4.2 33.1 1.0 O A:LYS336 4.3 34.5 1.0 CD1 A:TRP675 4.4 31.0 1.0 NE1 A:TRP219 4.4 38.9 1.0 C A:LYS336 4.4 33.6 1.0 CE A:LYS336 4.4 39.0 1.0 CA A:TRP219 4.7 34.8 1.0 C A:ASN218 4.7 36.5 1.0 O A:TRP219 4.8 33.0 1.0 CD2 A:TRP219 4.9 37.8 1.0 CD1 A:ILE220 4.9 32.5 1.0 C A:TRP219 5.0 32.9 1.0

Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z19735067


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 Z19735067 within 5.0Å range: probe atom residue distance (Å) B Occ A:F804 b:34.9 occ:0.38 F1 A:I8G804 0.0 34.9 0.4 C1 A:I8G804 1.4 34.9 0.4 C12 A:I8G804 2.3 35.0 0.4 C2 A:I8G804 2.3 34.6 0.4 CG A:GLN29 2.8 45.5 1.0 CB A:GLN29 2.9 41.3 1.0 C11 A:I8G804 3.6 35.0 0.4 C3 A:I8G804 3.6 34.8 0.4 CD A:GLN29 3.8 48.1 1.0 OD2 A:ASP130 3.8 54.1 1.0 CD2 A:LEU189 3.9 36.5 1.0 CD1 A:LEU187 4.0 42.5 1.0 OE1 A:GLN29 4.0 46.9 1.0 C4 A:I8G804 4.1 35.2 0.4 CD1 A:LEU27 4.1 36.0 1.0 CA A:GLN29 4.4 39.7 1.0 CD2 A:LEU187 4.4 42.0 1.0 CG A:ASP130 4.5 49.9 1.0 CB A:ASP130 4.6 45.9 1.0 CG A:LEU187 4.7 41.2 1.0 CD1 A:LEU189 4.9 35.3 1.0 CG A:LEU189 4.9 35.6 1.0 NE2 A:GLN29 4.9 48.9 1.0 C A:GLN29 4.9 40.2 1.0

Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z19735067


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z19735067 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:22.5 occ:0.38 F1 B:I8G801 0.0 22.5 0.4 C1 B:I8G801 1.4 21.8 0.4 C12 B:I8G801 2.3 21.7 0.4 C2 B:I8G801 2.3 22.0 0.4 CB B:LYS336 3.0 33.8 1.0 CD1 B:TRP219 3.2 35.7 1.0 CG B:LYS336 3.3 36.5 1.0 CB B:TRP219 3.5 33.0 1.0 CD B:LYS336 3.5 39.6 1.0 O B:ASN218 3.6 32.9 1.0 C11 B:I8G801 3.6 22.1 0.4 C3 B:I8G801 3.6 22.2 0.4 CG B:TRP219 3.6 34.5 1.0 O B:HOH955 3.8 30.1 1.0 CB B:TRP675 4.1 31.8 1.0 C4 B:I8G801 4.1 22.4 0.4 CA B:LYS336 4.2 31.9 1.0 NE1 B:TRP219 4.2 36.3 1.0 CE B:LYS336 4.2 41.5 1.0 O B:LYS336 4.3 32.5 1.0 C B:LYS336 4.4 32.2 1.0 C B:ASN218 4.5 33.4 1.0 CG B:TRP675 4.6 32.3 1.0 CA B:TRP219 4.6 32.4 1.0 CD1 B:TRP675 4.8 33.3 1.0 NZ B:LYS336 4.8 40.6 1.0 CD2 B:TRP219 4.8 35.5 1.0 O B:TRP219 4.9 30.1 1.0 C B:TRP219 5.0 30.2 1.0 N B:TRP219 5.0 32.4 1.0 CD1 B:ILE220 5.0 33.3 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.