Zinc in PDB 7kd0: Ricin Bound to Vhh Antibody V2C11

All present enzymatic activity of Ricin Bound to Vhh Antibody V2C11:
3.2.2.22;

The structure of Ricin Bound to Vhh Antibody V2C11, PDB code: 7kd0 was solved by M.J.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.43 / 2.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.223, 100.817, 129.712, 90, 90, 90
R / Rfree (%)	20.7 / 25.5

The structure of Ricin Bound to Vhh Antibody V2C11 also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Zinc atom in the Ricin Bound to Vhh Antibody V2C11 (pdb code 7kd0). 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 Ricin Bound to Vhh Antibody V2C11, PDB code: 7kd0:

Zinc binding site 1 out of 1 in the Ricin Bound to Vhh Antibody V2C11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ricin Bound to Vhh Antibody V2C11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:39.1 occ:1.00 OE2 A:GLU102 2.1 52.0 1.0 NE2 A:HIS106 2.1 45.5 1.0 OE1 A:GLU102 2.6 50.6 1.0 CD A:GLU102 2.6 45.9 1.0 O A:HOH478 2.8 23.9 1.0 CE1 A:HIS106 2.8 46.3 1.0 CD2 A:HIS106 3.2 42.6 1.0 ND1 A:HIS106 4.0 42.5 1.0 CG A:GLU102 4.1 46.6 1.0 O A:HOH437 4.1 53.8 1.0 CG A:HIS106 4.2 37.3 1.0 CL A:CL307 4.3 73.2 1.0 O A:GLU102 4.5 39.6 1.0 OG1 A:THR105 4.7 38.0 1.0

M.J.Rudolph, A.Y.Poon, S.Kavaliauskiene, A.G.Myrann, C.Reynolds-Peterson, S.A.Davis, K.Sandvig, D.J.Vance, N.J.Mantis. Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies That Bridge Ricin'S A-B Subunit Interface. J.Mol.Biol. V. 433 67086 2021.
ISSN: ESSN 1089-8638
PubMed: 34089718
DOI: 10.1016/J.JMB.2021.167086