Zinc in PDB 8h3x: Bacteroide Fragilis Toxin in Complex with Nanobody 282

All present enzymatic activity of Bacteroide Fragilis Toxin in Complex with Nanobody 282:
3.4.24.74;

The structure of Bacteroide Fragilis Toxin in Complex with Nanobody 282, PDB code: 8h3x was solved by Y.Wen, Y.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.17 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.663, 78.212, 118.132, 90, 90, 90
R / Rfree (%)	18.3 / 21.6

The binding sites of Zinc atom in the Bacteroide Fragilis Toxin in Complex with Nanobody 282 (pdb code 8h3x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Bacteroide Fragilis Toxin in Complex with Nanobody 282, PDB code: 8h3x:

Zinc binding site 1 out of 1 in the Bacteroide Fragilis Toxin in Complex with Nanobody 282


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacteroide Fragilis Toxin in Complex with Nanobody 282 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:33.1 occ:1.00 NE2 C:HIS358 2.2 31.0 1.0 NE2 C:HIS352 2.2 27.4 1.0 OD1 C:ASP194 2.2 31.3 1.0 NE2 C:HIS348 2.2 25.9 1.0 OD2 C:ASP194 2.2 29.1 1.0 CG C:ASP194 2.5 27.1 1.0 CD2 C:HIS348 3.0 22.9 1.0 CE1 C:HIS358 3.0 33.4 1.0 CD2 C:HIS352 3.1 28.0 1.0 CD2 C:HIS358 3.2 31.1 1.0 CE1 C:HIS352 3.3 28.2 1.0 CE1 C:HIS348 3.3 29.0 1.0 CB C:TYR191 3.5 37.9 1.0 O C:TYR191 3.8 40.0 1.0 CB C:ASP194 4.0 31.5 1.0 CG C:TYR191 4.0 38.5 1.0 ND1 C:HIS358 4.1 34.2 1.0 CG C:HIS348 4.2 24.3 1.0 CG C:HIS358 4.2 32.5 1.0 CG C:HIS352 4.3 26.2 1.0 CD1 C:TYR191 4.3 32.9 1.0 ND1 C:HIS352 4.3 26.2 1.0 ND1 C:HIS348 4.4 24.0 1.0 OE2 C:GLU349 4.4 27.0 1.0 CD2 C:TYR195 4.4 31.8 1.0 CA C:TYR191 4.6 41.7 1.0 C C:TYR191 4.7 40.6 1.0 CE2 C:TYR195 4.7 31.4 1.0 CE C:MET366 4.7 25.7 1.0 CD2 C:TYR191 4.7 36.8 1.0 CA C:ASP194 4.9 32.7 1.0 O C:ASP194 5.0 27.1 1.0 N C:ASP194 5.0 33.4 1.0

Y.Guo, Z.Ouyang, W.He, J.Zhang, Q.Qin, M.Jiao, S.Muyldermans, F.Fang Zheng, Y.Wen. Screening and Epitope Characterization of Diagnostic Nanobody Against Total and Activated Bacteroide Fragilis Toxin. Front Immunol V. 14 2023.
ISSN: ESSN 1664-3224
DOI: 10.3389/FIMMU.2023.1065274