Zinc in PDB 7poq: Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P41212.

The structure of Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P41212., PDB code: 7poq was solved by U.Eckhard, T.Guevara, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.96 / 1.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.83, 83.83, 266.32, 90, 90, 90
R / Rfree (%)	19.1 / 20.4

The structure of Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P41212. also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P41212. (pdb code 7poq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P41212., PDB code: 7poq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P41212.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P41212. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:30.7 occ:0.82 OD1 A:ASP194 1.9 53.2 1.0 NE2 A:HIS358 2.0 38.8 1.0 NE2 A:HIS352 2.0 32.3 1.0 NE2 A:HIS348 2.0 30.0 1.0 CG A:ASP194 2.5 55.0 1.0 OD2 A:ASP194 2.6 56.7 1.0 CD2 A:HIS358 2.9 37.5 1.0 CD2 A:HIS352 3.0 31.2 1.0 CD2 A:HIS348 3.0 28.9 1.0 CE1 A:HIS358 3.0 39.6 1.0 CE1 A:HIS352 3.0 32.5 1.0 CE1 A:HIS348 3.1 29.8 1.0 CB A:TYR191 3.7 68.7 1.0 O A:TYR191 3.8 70.8 1.0 CB A:ASP194 4.0 55.2 1.0 CG A:HIS358 4.1 36.8 1.0 CG A:HIS352 4.1 30.4 1.0 ND1 A:HIS358 4.1 38.8 1.0 CG A:HIS348 4.1 28.3 1.0 ND1 A:HIS352 4.1 32.1 1.0 ND1 A:HIS348 4.2 29.4 1.0 CG A:TYR191 4.2 67.3 1.0 CD2 A:TYR195 4.4 60.5 1.0 CE A:MET366 4.5 29.3 1.0 CD1 A:TYR191 4.5 67.1 1.0 O A:ASP194 4.6 55.1 1.0 C A:TYR191 4.7 70.5 1.0 CA A:TYR191 4.7 70.5 1.0 C A:ASP194 4.7 55.6 1.0 CA A:ASP194 4.8 56.1 1.0 OE1 A:GLU349 4.8 32.0 1.0 N A:ASP194 4.9 58.1 1.0 CD2 A:TYR191 4.9 67.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P41212.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P41212. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:31.6 occ:0.89 NE2 B:HIS358 1.9 36.5 1.0 NE2 B:HIS348 2.0 30.7 1.0 NE2 B:HIS352 2.0 31.6 1.0 OD1 B:ASP194 2.0 48.6 1.0 OD2 B:ASP194 2.6 49.1 1.0 CG B:ASP194 2.6 49.8 1.0 CD2 B:HIS358 2.9 36.0 1.0 CE1 B:HIS358 3.0 37.1 1.0 CD2 B:HIS348 3.0 29.4 1.0 CD2 B:HIS352 3.0 31.1 1.0 CE1 B:HIS348 3.0 31.3 1.0 CE1 B:HIS352 3.0 32.2 1.0 CB B:TYR191 3.8 62.7 1.0 O B:TYR191 3.8 67.0 1.0 CG B:HIS358 4.0 35.5 1.0 ND1 B:HIS358 4.1 36.7 1.0 CB B:ASP194 4.1 51.8 1.0 CG B:HIS348 4.1 28.8 1.0 ND1 B:HIS348 4.1 30.8 1.0 CG B:HIS352 4.1 29.8 1.0 ND1 B:HIS352 4.2 31.2 1.0 CG B:TYR191 4.3 61.7 1.0 CD2 B:TYR195 4.5 61.1 1.0 CE B:MET366 4.5 29.9 1.0 CD1 B:TYR191 4.6 62.0 1.0 C B:TYR191 4.7 66.0 1.0 CA B:TYR191 4.8 64.0 1.0 OE1 B:GLU349 4.8 32.6 1.0 C B:ASP194 4.8 54.8 1.0 CA B:ASP194 4.9 54.0 1.0 O B:ASP194 4.9 54.2 1.0 CD2 B:TYR191 4.9 61.8 1.0 N B:ASP194 5.0 55.9 1.0

A.Jimenez-Alesanco, U.Eckhard, M.Asencio Del Rio, S.Vega, T.Guevara, A.Velazquez-Campoy, F.X.Gomis-Ruth, O.Abian. Repositioning Small Molecule Drugs As Allosteric Inhibitors of the Bft-3 Toxin From Enterotoxigenic Bacteroides Fragilis. Protein Sci. V. 31 E4427 2022.
ISSN: ESSN 1469-896X
PubMed: 36173175
DOI: 10.1002/PRO.4427