Zinc in PDB 8h3y: Bacteroide Fragilis Toxin in Complex with Nanobody 327

All present enzymatic activity of Bacteroide Fragilis Toxin in Complex with Nanobody 327:
3.4.24.74;

The structure of Bacteroide Fragilis Toxin in Complex with Nanobody 327, PDB code: 8h3y 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)	41.39 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.901, 82.984, 139.807, 90, 109.02, 90
R / Rfree (%)	20.4 / 24.4

The binding sites of Zinc atom in the Bacteroide Fragilis Toxin in Complex with Nanobody 327 (pdb code 8h3y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Bacteroide Fragilis Toxin in Complex with Nanobody 327, PDB code: 8h3y:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Bacteroide Fragilis Toxin in Complex with Nanobody 327


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 327 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:73.4 occ:1.00 OD1 A:ASP194 2.2 96.0 1.0 OD2 A:ASP194 2.2 87.3 1.0 NE2 A:HIS358 2.3 69.2 1.0 NE2 A:HIS348 2.3 51.2 1.0 NE2 A:HIS352 2.4 65.1 1.0 CG A:ASP194 2.5 91.7 1.0 CD2 A:HIS352 3.0 60.5 1.0 CD2 A:HIS358 3.1 63.0 1.0 CD2 A:HIS348 3.3 44.0 1.0 CE1 A:HIS348 3.3 44.8 1.0 CE1 A:HIS358 3.3 77.4 1.0 CE1 A:HIS352 3.5 75.8 1.0 CB A:TYR191 3.6 61.3 1.0 CB A:ASP194 4.0 81.8 1.0 CG A:TYR191 4.1 51.9 1.0 CD2 A:TYR191 4.2 53.7 1.0 O A:TYR191 4.2 71.6 1.0 CG A:HIS358 4.2 66.6 1.0 CG A:HIS352 4.2 56.7 1.0 CE A:MET366 4.3 43.8 1.0 ND1 A:HIS358 4.3 80.5 1.0 ND1 A:HIS348 4.4 47.1 1.0 CG A:HIS348 4.4 43.8 1.0 ND1 A:HIS352 4.4 64.8 1.0 CD1 A:TYR195 4.6 98.0 1.0 OE2 A:GLU349 4.6 50.6 1.0 CA A:ASP194 4.8 92.0 1.0 C A:TYR191 4.9 71.1 1.0 CD1 A:TYR191 4.9 52.0 1.0 N A:ASP194 4.9 91.7 1.0 CA A:TYR191 4.9 63.2 1.0 C A:ASP194 4.9 88.6 1.0

Zinc binding site 2 out of 3 in the Bacteroide Fragilis Toxin in Complex with Nanobody 327


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacteroide Fragilis Toxin in Complex with Nanobody 327 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:63.3 occ:1.00 OD1 B:ASP194 2.1 45.5 1.0 NE2 B:HIS358 2.3 41.7 1.0 NE2 B:HIS352 2.3 40.6 1.0 NE2 B:HIS348 2.3 42.3 1.0 OD2 B:ASP194 2.5 44.0 1.0 CG B:ASP194 2.6 39.9 1.0 CD2 B:HIS348 2.9 39.2 1.0 CE1 B:HIS358 3.0 39.8 1.0 CD2 B:HIS352 3.0 36.8 1.0 CD2 B:HIS358 3.3 41.3 1.0 CE1 B:HIS352 3.3 42.0 1.0 CB B:TYR191 3.4 38.2 1.0 CE1 B:HIS348 3.5 40.3 1.0 O B:TYR191 3.7 44.0 1.0 CB B:ASP194 4.0 43.1 1.0 CG B:TYR191 4.1 45.0 1.0 ND1 B:HIS358 4.1 47.1 1.0 CG B:HIS352 4.2 39.4 1.0 CG B:HIS348 4.2 42.0 1.0 CG B:HIS358 4.3 42.5 1.0 ND1 B:HIS352 4.3 37.3 1.0 CD2 B:TYR191 4.4 44.1 1.0 ND1 B:HIS348 4.4 46.7 1.0 CD1 B:TYR195 4.4 49.5 1.0 C B:TYR191 4.6 46.5 1.0 CA B:TYR191 4.6 46.4 1.0 OE2 B:GLU349 4.6 42.3 1.0 CE B:MET366 4.7 37.3 1.0 CA B:ASP194 4.8 47.0 1.0 O B:ASP194 4.8 44.9 1.0 N B:ASP194 4.9 42.4 1.0 C B:ASP194 4.9 43.2 1.0 CD1 B:TYR191 5.0 46.5 1.0

Zinc binding site 3 out of 3 in the Bacteroide Fragilis Toxin in Complex with Nanobody 327


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bacteroide Fragilis Toxin in Complex with Nanobody 327 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:50.2 occ:1.00 OD1 C:ASP194 2.1 40.7 1.0 NE2 C:HIS352 2.2 36.3 1.0 NE2 C:HIS358 2.2 36.3 1.0 NE2 C:HIS348 2.3 30.3 1.0 OD2 C:ASP194 2.4 36.6 1.0 CG C:ASP194 2.5 45.3 1.0 CE1 C:HIS358 3.0 43.5 1.0 CD2 C:HIS352 3.0 35.7 1.0 CD2 C:HIS348 3.0 34.8 1.0 CD2 C:HIS358 3.2 37.8 1.0 CE1 C:HIS352 3.4 36.8 1.0 CE1 C:HIS348 3.4 34.1 1.0 CB C:TYR191 3.5 45.0 1.0 O C:TYR191 3.6 47.1 1.0 CB C:ASP194 4.0 38.1 1.0 ND1 C:HIS358 4.0 46.7 1.0 CG C:HIS352 4.2 33.8 1.0 CG C:HIS358 4.2 42.9 1.0 CG C:TYR191 4.2 40.6 1.0 CG C:HIS348 4.2 36.4 1.0 CD2 C:TYR195 4.2 43.5 1.0 ND1 C:HIS352 4.4 40.9 1.0 ND1 C:HIS348 4.4 35.1 1.0 C C:TYR191 4.5 45.0 1.0 CE C:MET366 4.6 30.5 1.0 CD1 C:TYR191 4.6 38.2 1.0 CA C:TYR191 4.6 44.7 1.0 CE2 C:TYR195 4.6 44.7 1.0 OE2 C:GLU349 4.7 35.8 1.0 N C:ASP194 4.8 42.6 1.0 CA C:ASP194 4.8 38.3 1.0 C C:ASP194 4.9 38.8 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