Zinc in PDB 6oq5: Structure of the Full-Length Clostridium Difficile Toxin B in Complex with 3 Vhhs

The structure of Structure of the Full-Length Clostridium Difficile Toxin B in Complex with 3 Vhhs, PDB code: 6oq5 was solved by P.Chen, K.Lam, R.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.91 / 3.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	149.619, 168.565, 179.921, 90.00, 90.00, 90.00
R / Rfree (%)	26.3 / 31.5

The structure of Structure of the Full-Length Clostridium Difficile Toxin B in Complex with 3 Vhhs also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Structure of the Full-Length Clostridium Difficile Toxin B in Complex with 3 Vhhs (pdb code 6oq5). 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 Structure of the Full-Length Clostridium Difficile Toxin B in Complex with 3 Vhhs, PDB code: 6oq5:

Zinc binding site 1 out of 1 in the Structure of the Full-Length Clostridium Difficile Toxin B in Complex with 3 Vhhs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Full-Length Clostridium Difficile Toxin B in Complex with 3 Vhhs within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2801 b:0.6 occ:1.00 OD2 A:ASP547 2.1 0.8 1.0 ND1 A:HIS654 2.3 0.6 1.0 SG A:CYS699 2.4 0.2 1.0 NE2 A:HIS758 2.5 0.3 1.0 CG A:HIS654 2.8 0.9 1.0 CG A:ASP547 2.8 0.6 1.0 CD2 A:HIS758 3.0 0.7 1.0 CB A:HIS654 3.0 0.6 1.0 OD1 A:ASP547 3.1 0.2 1.0 CB A:CYS699 3.1 0.9 1.0 CE1 A:HIS654 3.1 0.4 1.0 CE1 A:HIS758 3.6 0.7 1.0 CD2 A:HIS654 3.7 0.5 1.0 NE2 A:HIS654 3.9 0.3 1.0 CB A:ASP547 4.0 0.2 1.0 CA A:HIS654 4.0 0.9 1.0 CG A:HIS758 4.2 0.2 1.0 CA A:CYS699 4.4 0.0 1.0 N A:CYS699 4.4 0.6 1.0 ND1 A:HIS758 4.5 0.7 1.0 OE1 A:GLU546 4.7 0.5 1.0 C A:HIS654 4.9 0.3 1.0 N A:GLY655 5.0 0.1 1.0 O A:GLY655 5.0 0.4 1.0

P.Chen, K.H.Lam, Z.Liu, F.A.Mindlin, B.Chen, C.B.Gutierrez, L.Huang, Y.Zhang, T.Hamza, H.Feng, T.Matsui, M.E.Bowen, K.Perry, R.Jin. Structure of the Full-Length Clostridium Difficile Toxin B. Nat.Struct.Mol.Biol. V. 26 712 2019.
ISSN: ESSN 1545-9985
PubMed: 31308519
DOI: 10.1038/S41594-019-0268-0