Zinc in PDB 8weo: Bacteroides Fragilis Toxin in Complex with Neutralization Nanobody

All present enzymatic activity of Bacteroides Fragilis Toxin in Complex with Neutralization Nanobody:
3.4.24.74;

The structure of Bacteroides Fragilis Toxin in Complex with Neutralization Nanobody, PDB code: 8weo 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)	30.42 / 1.50
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	121.678, 121.678, 84.143, 90, 90, 120
R / Rfree (%)	17.1 / 19.7

The binding sites of Zinc atom in the Bacteroides Fragilis Toxin in Complex with Neutralization Nanobody (pdb code 8weo). 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 in Complex with Neutralization Nanobody, PDB code: 8weo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bacteroides Fragilis Toxin in Complex with Neutralization Nanobody


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 in Complex with Neutralization Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:21.6 occ:1.00 OE1 C:GLU125 2.1 21.0 1.0 NE2 B:HIS348 2.2 17.3 1.0 O C:HOH261 2.2 22.9 1.0 NE2 B:HIS358 2.2 19.8 1.0 NE2 B:HIS352 2.2 19.3 1.0 OE2 C:GLU125 2.3 19.2 1.0 CD C:GLU125 2.5 19.5 1.0 CD2 B:HIS352 3.1 20.6 1.0 CD2 B:HIS348 3.1 17.0 1.0 CE1 B:HIS358 3.1 21.6 1.0 CE1 B:HIS348 3.2 18.2 1.0 CD2 B:HIS358 3.2 22.2 1.0 CE1 B:HIS352 3.3 20.8 1.0 O C:HOH212 4.0 27.0 1.0 CG C:GLU125 4.0 18.3 1.0 CB C:TYR124 4.2 16.4 1.0 CG B:HIS348 4.3 16.6 1.0 ND1 B:HIS358 4.3 21.3 1.0 CG B:HIS352 4.3 20.0 1.0 ND1 B:HIS348 4.3 16.2 1.0 CG B:HIS358 4.3 20.6 1.0 ND1 B:HIS352 4.4 19.4 1.0 O C:HOH332 4.4 23.4 1.0 CD1 C:TYR124 4.6 17.2 1.0 OE2 B:GLU349 4.7 19.0 1.0 N C:GLU125 4.7 16.2 1.0 CG C:TYR124 4.7 16.2 1.0 CB C:GLU125 4.8 16.7 1.0 O B:ALA368 4.8 19.3 1.0 CE B:MET366 4.9 19.4 1.0 CA B:ALA368 4.9 18.2 1.0

Zinc binding site 2 out of 2 in the Bacteroides Fragilis Toxin in Complex with Neutralization Nanobody


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 in Complex with Neutralization Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:23.2 occ:1.00 OE2 D:GLU125 2.1 21.2 1.0 NE2 A:HIS348 2.2 18.4 1.0 O D:HOH224 2.2 24.1 1.0 NE2 A:HIS352 2.2 21.8 1.0 NE2 A:HIS358 2.2 22.1 1.0 OE1 D:GLU125 2.3 21.6 1.0 CD D:GLU125 2.5 20.9 1.0 CD2 A:HIS352 3.1 19.3 1.0 CD2 A:HIS348 3.1 19.2 1.0 CE1 A:HIS358 3.2 23.4 1.0 CE1 A:HIS348 3.2 18.8 1.0 CD2 A:HIS358 3.3 20.6 1.0 CE1 A:HIS352 3.3 23.8 1.0 CG D:GLU125 4.0 18.8 1.0 CB D:TYR124 4.1 17.9 1.0 O D:HOH223 4.1 27.6 1.0 CG A:HIS348 4.3 16.4 1.0 CG A:HIS352 4.3 22.6 1.0 ND1 A:HIS348 4.3 18.0 1.0 ND1 A:HIS358 4.3 22.8 1.0 ND1 A:HIS352 4.3 22.6 1.0 O D:HOH285 4.4 26.1 1.0 CG A:HIS358 4.4 23.7 1.0 CD1 D:TYR124 4.6 16.4 1.0 CG D:TYR124 4.7 17.4 1.0 OE2 A:GLU349 4.7 19.9 1.0 N D:GLU125 4.7 18.5 1.0 CB D:GLU125 4.8 18.6 1.0 O A:ALA368 4.8 19.2 1.0 CA A:ALA368 5.0 20.3 1.0 CE A:MET366 5.0 20.3 1.0

Y.Guo, Y.Wen. Bacteroides Fragilis Toxin in Complex with Neutralization Nanobody To Be Published.