Fluorine in PDB 5sdp: Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z2277255954

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z2277255954, PDB code: 5sdp 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)	84.03 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	102.111, 117.236, 147.926, 90, 90, 90
R / Rfree (%)	21.6 / 24.8

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z2277255954 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 Z2277255954 (pdb code 5sdp). 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 Z2277255954, PDB code: 5sdp:
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 Z2277255954


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 Z2277255954 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:43.0 occ:0.58 F1 A:I8J801 0.0 43.0 0.6 C8 A:I8J801 1.4 43.6 0.6 O A:LYS336 2.2 37.3 0.4 C7 A:I8J801 2.3 43.8 0.6 C9 A:I8J801 2.4 43.8 0.6 O A:LYS336 2.8 37.5 0.6 C A:LYS336 2.9 36.6 0.4 C A:LYS336 3.0 36.5 0.6 CA A:ARG337 3.2 36.4 1.0 N A:ARG337 3.2 36.3 1.0 CB A:TRP675 3.4 30.2 1.0 C6 A:I8J801 3.7 43.9 0.6 N1 A:I8J801 3.7 43.7 0.6 CG1 A:VAL678 3.9 41.0 1.0 N A:GLY340 4.0 35.5 1.0 C A:ARG337 4.0 35.9 1.0 CB A:LYS336 4.0 35.8 0.6 CA A:GLY340 4.0 35.4 1.0 CA A:LYS336 4.0 36.2 0.4 CB A:LYS336 4.0 37.5 0.4 CA A:LYS336 4.1 35.6 0.6 O A:ARG337 4.1 35.4 1.0 C5 A:I8J801 4.1 43.8 0.6 CA A:TRP675 4.2 30.6 1.0 CB A:ARG337 4.3 38.0 1.0 CG A:TRP675 4.5 29.9 1.0 CG A:TRP219 4.5 39.2 1.0 CD1 A:TRP219 4.6 40.1 1.0 O A:TRP675 4.7 31.7 1.0 CB A:TRP219 4.7 38.0 1.0 CD2 A:TRP219 4.7 39.2 1.0 O2 A:I8J801 4.7 44.1 0.6 CG2 A:VAL678 4.8 40.8 1.0 NE1 A:TRP219 4.8 40.7 1.0 CG A:ARG337 4.9 44.3 1.0 C A:TRP675 4.9 31.3 1.0 CE2 A:TRP219 4.9 40.1 1.0 S1 A:I8J801 4.9 44.1 0.6 CB A:VAL678 5.0 39.7 1.0

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Porphyromonas Gingivalis in Complex with Z2277255954


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 Z2277255954 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:42.4 occ:0.53 F1 B:I8J801 0.0 42.4 0.5 C8 B:I8J801 1.3 42.2 0.5 C7 B:I8J801 2.3 41.9 0.5 C9 B:I8J801 2.4 42.1 0.5 O B:LYS336 2.8 42.4 1.0 CB B:TRP675 3.2 34.0 1.0 C B:LYS336 3.3 41.2 1.0 CA B:ARG337 3.4 39.2 0.5 CA B:GLY340 3.5 38.1 1.0 CA B:ARG337 3.5 39.9 0.5 N B:ARG337 3.6 40.1 0.5 N B:ARG337 3.6 40.5 0.5 N B:GLY340 3.6 38.0 1.0 N1 B:I8J801 3.6 42.2 0.5 C6 B:I8J801 3.7 41.9 0.5 CG1 B:VAL678 3.9 43.6 1.0 CA B:TRP675 4.0 34.1 1.0 O B:ARG337 4.0 39.1 0.5 O B:ARG337 4.0 38.9 0.5 C B:ARG337 4.1 38.9 0.5 C B:ARG337 4.1 39.2 0.5 C5 B:I8J801 4.1 41.8 0.5 CG B:TRP675 4.2 34.0 1.0 O B:TRP675 4.3 35.3 1.0 CA B:LYS336 4.4 41.4 1.0 CB B:LYS336 4.4 43.5 1.0 C B:TRP675 4.6 34.6 1.0 CB B:ARG337 4.6 39.0 0.5 C B:GLY340 4.6 38.0 1.0 CE3 B:TRP675 4.7 34.6 1.0 CG2 B:VAL678 4.7 42.5 1.0 CD2 B:TRP675 4.7 34.5 1.0 CG B:TRP219 4.8 38.2 1.0 C B:ILE339 4.8 38.3 1.0 CB B:ARG337 4.9 40.8 0.5 CB B:TRP219 4.9 35.7 1.0 CB B:VAL678 4.9 41.9 1.0 CD1 B:TRP219 4.9 39.6 1.0 CD2 B:TRP219 5.0 39.5 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.