Zinc in PDB 7poo: Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121.

The structure of Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121., PDB code: 7poo 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)	73.47 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.55, 83.06, 157.48, 90, 90, 90
R / Rfree (%)	21.6 / 24.3

The binding sites of Zinc atom in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121. (pdb code 7poo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121., PDB code: 7poo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121.


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 P212121. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:42.8 occ:0.22 OD1 A:ASP194 1.9 83.7 1.0 OD2 A:ASP194 2.0 84.4 1.0 NE2 A:HIS352 2.1 65.6 1.0 NE2 A:HIS348 2.2 56.8 1.0 CG A:ASP194 2.2 83.0 1.0 NE2 A:HIS358 2.4 79.7 1.0 CD2 A:HIS352 2.9 64.4 1.0 CD2 A:HIS348 3.0 55.0 1.0 CE1 A:HIS352 3.2 65.6 1.0 CE1 A:HIS358 3.2 79.7 1.0 CE1 A:HIS348 3.3 56.6 1.0 CD2 A:HIS358 3.3 78.0 1.0 CB A:TYR191 3.4 85.8 1.0 CB A:ASP194 3.7 78.9 1.0 O A:TYR191 3.8 85.9 1.0 CG A:TYR191 4.1 85.3 1.0 CG A:HIS352 4.1 62.8 1.0 CG A:HIS348 4.2 53.6 1.0 ND1 A:HIS352 4.3 65.0 1.0 ND1 A:HIS358 4.3 78.8 1.0 ND1 A:HIS348 4.3 55.7 1.0 CG A:HIS358 4.4 76.5 1.0 CD1 A:TYR191 4.4 85.4 1.0 OE1 A:GLU349 4.5 58.5 1.0 CA A:TYR191 4.5 86.5 1.0 C A:TYR191 4.6 85.5 1.0 CE A:MET366 4.6 55.9 1.0 CA A:ASP194 4.6 77.4 1.0 O A:ASP194 4.7 76.8 1.0 CD2 A:TYR195 4.7 79.0 1.0 C A:ASP194 4.7 77.2 1.0 CD2 A:TYR191 4.8 85.8 1.0 N A:ASP194 4.9 77.4 1.0 OE2 A:GLU349 4.9 57.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121.


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 P212121. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:99.2 occ:0.59 NE2 B:HIS358 2.6 92.5 1.0 NE2 B:HIS348 2.8 67.4 1.0 CB B:TYR191 2.9 104.5 1.0 NE2 B:HIS352 2.9 70.5 1.0 CG B:TYR191 3.1 104.7 1.0 CE1 B:HIS358 3.2 92.8 1.0 CD1 B:TYR191 3.4 105.3 1.0 CD2 B:HIS348 3.5 66.2 1.0 CD2 B:HIS352 3.7 69.4 1.0 CE1 B:HIS352 3.7 70.4 1.0 CD2 B:TYR191 3.8 105.4 1.0 CD2 B:HIS358 3.8 91.3 1.0 CE1 B:HIS348 3.9 67.7 1.0 CA B:TYR191 4.3 104.6 1.0 CE1 B:TYR191 4.3 105.9 1.0 ND1 B:HIS358 4.4 92.2 1.0 OE1 B:GLU349 4.5 77.4 1.0 CE2 B:TYR191 4.6 106.1 1.0 CG B:HIS358 4.7 90.0 1.0 CG B:HIS352 4.7 68.0 1.0 ND1 B:HIS352 4.7 69.8 1.0 CG B:HIS348 4.8 65.1 1.0 CZ B:TYR191 4.8 106.7 1.0 N B:ILE192 4.8 105.4 1.0 O B:SER368 4.9 78.7 1.0 ND1 B:HIS348 4.9 67.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:99.6 occ:0.81 OD2 B:ASP178 3.8 63.7 1.0 O B:GLY118 3.9 59.6 1.0 CZ B:TYR373 4.1 75.3 1.0 CE2 B:TYR373 4.2 73.9 1.0 OH B:TYR373 4.2 77.5 1.0 O B:THR371 4.3 76.3 1.0 CE1 B:TYR373 4.5 74.2 1.0 O B:GLY372 4.7 71.8 1.0 CD2 B:TYR373 4.7 72.6 1.0 C B:GLY372 4.8 71.6 1.0 CG B:ASP178 4.9 60.6 1.0 O B:HOH534 5.0 45.0 1.0 CD1 B:TYR373 5.0 73.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Profragilysin-3 (Probft-3) From Bacteroides Fragilis in Complex with Foliosidine in P212121. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:98.0 occ:0.72 CE2 B:TYR115 3.4 68.5 1.0 OH B:TYR115 3.4 71.8 1.0 CZ B:TYR115 3.4 69.8 1.0 CG B:LEU374 4.1 67.0 1.0 O B:GLY372 4.2 71.8 1.0 CD2 B:TYR115 4.2 67.0 1.0 CE1 B:TYR115 4.2 68.4 1.0 N B:LEU374 4.3 66.9 1.0 CD1 B:LEU374 4.3 67.7 1.0 CA B:TYR373 4.5 70.0 1.0 O B:HOH534 4.6 45.0 1.0 CB B:LEU374 4.7 65.9 1.0 CD1 B:TYR373 4.8 73.1 1.0 C B:TYR373 4.9 68.8 1.0 CG B:TYR115 4.9 65.0 1.0 CD1 B:TYR115 4.9 66.9 1.0 CE2 B:PHE375 4.9 64.7 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