Zinc in PDB 7pnd: Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis at 1.85 A Resolution.

The structure of Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis at 1.85 A Resolution., PDB code: 7pnd 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)	63.07 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.72, 82.74, 158.9, 90, 90, 90
R / Rfree (%)	18.9 / 21.1

The structure of Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis at 1.85 A Resolution. also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis at 1.85 A Resolution. (pdb code 7pnd). 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 at 1.85 A Resolution., PDB code: 7pnd:
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 at 1.85 A Resolution.


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 at 1.85 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:25.4 occ:1.00 OD1 A:ASP194 1.9 31.1 1.0 NE2 A:HIS358 1.9 27.5 1.0 NE2 A:HIS348 2.0 23.6 1.0 NE2 A:HIS352 2.0 26.2 1.0 CG A:ASP194 2.6 31.0 1.0 OD2 A:ASP194 2.6 32.5 1.0 CD2 A:HIS358 2.9 26.5 1.0 CD2 A:HIS348 3.0 22.9 1.0 CE1 A:HIS358 3.0 27.7 1.0 CE1 A:HIS348 3.0 23.4 1.0 CD2 A:HIS352 3.0 24.4 1.0 CE1 A:HIS352 3.0 25.9 1.0 CG A:HIS358 4.0 26.1 1.0 CB A:ASP194 4.0 30.6 1.0 ND1 A:HIS358 4.1 27.0 1.0 CG A:HIS348 4.1 21.8 1.0 ND1 A:HIS348 4.1 23.0 1.0 CG A:HIS352 4.2 23.5 1.0 ND1 A:HIS352 4.2 25.0 1.0 CB A:TYR191 4.3 60.1 1.0 CG A:TYR191 4.4 58.6 1.0 CD2 A:TYR195 4.5 34.6 1.0 CE A:MET366 4.6 20.4 1.0 O A:ASP194 4.6 29.1 1.0 N A:ASP194 4.7 35.7 1.0 CD2 A:TYR191 4.7 58.5 1.0 CA A:ASP194 4.7 32.0 1.0 CD1 A:TYR191 4.7 58.6 1.0 C A:ASP194 4.7 29.9 1.0 OE1 A:GLU349 4.8 24.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis at 1.85 A Resolution.


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 at 1.85 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:31.4 occ:1.00 NE2 B:HIS358 1.9 33.8 1.0 NE2 B:HIS352 2.0 29.4 1.0 OD1 B:ASP194 2.0 34.5 1.0 NE2 B:HIS348 2.0 27.6 1.0 OD2 B:ASP194 2.6 34.0 1.0 CG B:ASP194 2.6 34.8 1.0 CD2 B:HIS358 2.9 33.4 1.0 CD2 B:HIS352 2.9 28.5 1.0 CE1 B:HIS358 2.9 34.5 1.0 CD2 B:HIS348 3.0 26.4 1.0 CE1 B:HIS352 3.0 28.6 1.0 CE1 B:HIS348 3.1 27.6 1.0 CB B:TYR191 3.7 44.8 1.0 O B:TYR191 3.8 47.3 1.0 CG B:HIS358 4.0 33.9 1.0 ND1 B:HIS358 4.1 34.7 1.0 CB B:ASP194 4.1 33.5 1.0 CG B:HIS352 4.1 27.6 1.0 ND1 B:HIS352 4.1 28.4 1.0 CG B:HIS348 4.1 26.0 1.0 ND1 B:HIS348 4.2 26.9 1.0 CG B:TYR191 4.2 42.9 1.0 CD1 B:TYR191 4.5 42.2 1.0 CE B:MET366 4.6 27.3 1.0 O B:ASP194 4.6 35.3 1.0 C B:TYR191 4.7 47.1 1.0 CA B:TYR191 4.7 47.0 1.0 OE1 B:GLU349 4.7 29.1 1.0 C B:ASP194 4.8 36.2 1.0 CA B:ASP194 4.8 35.1 1.0 N B:ASP194 4.9 35.8 1.0 CD2 B:TYR195 5.0 43.4 1.0 OE2 B:GLU349 5.0 29.9 1.0 CD2 B:TYR191 5.0 42.3 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