Zinc in PDB 8wem: Bacteroides Fragilis Toxin 1

All present enzymatic activity of Bacteroides Fragilis Toxin 1:
3.4.24.74;

The structure of Bacteroides Fragilis Toxin 1, PDB code: 8wem was solved by Y.Guo, Y.Wen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.37 / 1.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.672, 82.672, 280.068, 90, 90, 90
R / Rfree (%)	17.6 / 20.2

The binding sites of Zinc atom in the Bacteroides Fragilis Toxin 1 (pdb code 8wem). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bacteroides Fragilis Toxin 1, PDB code: 8wem:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bacteroides Fragilis Toxin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacteroides Fragilis Toxin 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:33.4 occ:1.00 NE2 C:HIS358 2.0 29.6 1.0 NE2 C:HIS352 2.0 31.7 1.0 OD1 C:ASP194 2.1 42.2 1.0 NE2 C:HIS348 2.1 31.5 1.0 OD2 C:ASP194 2.5 38.5 1.0 CG C:ASP194 2.6 40.9 1.0 CE1 C:HIS358 3.0 38.0 1.0 CD2 C:HIS352 3.0 32.8 1.0 CD2 C:HIS348 3.0 33.2 1.0 CD2 C:HIS358 3.0 32.9 1.0 CE1 C:HIS352 3.1 34.5 1.0 CE1 C:HIS348 3.2 34.4 1.0 CB C:TYR191 3.7 48.1 1.0 CB C:ASP194 4.1 40.5 1.0 ND1 C:HIS358 4.1 34.6 1.0 O C:TYR191 4.1 58.2 1.0 CG C:TYR191 4.1 45.1 1.0 CG C:HIS358 4.1 37.0 1.0 CG C:HIS352 4.2 32.8 1.0 ND1 C:HIS352 4.2 32.9 1.0 CG C:HIS348 4.2 33.8 1.0 ND1 C:HIS348 4.2 31.5 1.0 CD2 C:TYR195 4.3 48.3 1.0 CD1 C:TYR191 4.4 42.8 1.0 CE C:MET366 4.5 30.4 1.0 CE2 C:TYR195 4.6 51.5 1.0 OE2 C:GLU349 4.8 35.8 1.0 CD2 C:TYR191 4.8 40.6 1.0 CA C:ASP194 4.9 44.7 1.0 CA C:TYR191 4.9 51.9 1.0 C C:TYR191 4.9 57.4 1.0 N C:ASP194 5.0 48.9 1.0

Zinc binding site 2 out of 2 in the Bacteroides Fragilis Toxin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacteroides Fragilis Toxin 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:34.5 occ:1.00 OD1 A:ASP194 2.0 38.6 1.0 NE2 A:HIS352 2.1 34.5 1.0 NE2 A:HIS358 2.1 34.0 1.0 NE2 A:HIS348 2.1 34.7 1.0 OD2 A:ASP194 2.6 32.7 1.0 CG A:ASP194 2.6 33.8 1.0 CD2 A:HIS358 3.0 34.9 1.0 CD2 A:HIS348 3.0 32.5 1.0 CD2 A:HIS352 3.0 30.9 1.0 CE1 A:HIS352 3.1 34.2 1.0 CE1 A:HIS358 3.1 34.5 1.0 CE1 A:HIS348 3.2 34.6 1.0 CB A:TYR191 3.5 33.2 1.0 CD1 A:TYR195 4.1 33.1 1.0 CG A:TYR191 4.1 31.4 1.0 O A:TYR191 4.1 33.0 1.0 CG A:HIS358 4.1 35.7 1.0 CB A:ASP194 4.1 34.3 1.0 CG A:HIS348 4.2 33.4 1.0 ND1 A:HIS358 4.2 34.0 1.0 ND1 A:HIS352 4.2 34.7 1.0 CG A:HIS352 4.2 35.1 1.0 ND1 A:HIS348 4.2 31.0 1.0 CD1 A:TYR191 4.3 35.3 1.0 CE1 A:TYR195 4.3 33.6 1.0 CE A:MET366 4.5 32.7 1.0 N A:ASP194 4.7 33.1 1.0 CA A:TYR191 4.8 34.5 1.0 CA A:ASP194 4.8 35.6 1.0 C A:ASP194 4.9 39.5 1.0 C A:TYR191 4.9 35.6 1.0 CD2 A:TYR191 4.9 34.0 1.0 OE2 A:GLU349 5.0 37.3 1.0

Y.Guo, Y.Wen. Bacteroides Fragilis Toxin 1 To Be Published.