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Zinc in PDB 4z9k: Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5)

Enzymatic activity of Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5)

All present enzymatic activity of Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5):
3.2.2.22;

Protein crystallography data

The structure of Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5), PDB code: 4z9k 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) 55.07 / 1.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 78.376, 107.085, 111.944, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.5

Other elements in 4z9k:

The structure of Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5) (pdb code 4z9k). 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 A Chain Bound to Camelid Nanobody (VHH2)(F5), PDB code: 4z9k:

Zinc binding site 1 out of 1 in 4z9k

Go back to Zinc Binding Sites List in 4z9k
Zinc binding site 1 out of 1 in the Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:24.4
occ:1.00
OE2 A:GLU103 2.0 23.3 1.0
NE2 A:HIS107 2.0 22.8 1.0
CL A:CL304 2.3 35.1 1.0
CD A:GLU103 2.8 22.7 1.0
CE1 A:HIS107 2.9 25.0 1.0
OE1 A:GLU103 3.0 23.7 1.0
CD2 A:HIS107 3.1 22.1 1.0
O A:HOH475 4.0 39.5 1.0
ND1 A:HIS107 4.1 23.8 1.0
CG A:HIS107 4.2 23.2 1.0
CG A:GLU103 4.2 22.0 1.0
O A:GLU103 4.4 19.3 1.0
OG1 A:THR106 4.7 23.8 1.0

Reference:

M.J.Rudolph, D.J.Vance, M.S.Cassidy, Y.Rong, C.B.Shoemaker, N.J.Mantis. Structural Analysis of Nested Neutralizing and Non-Neutralizing B Cell Epitopes on Ricin Toxin'S Enzymatic Subunit. Proteins V. 84 1162 2016.
ISSN: ESSN 1097-0134
PubMed: 27159829
DOI: 10.1002/PROT.25062
Page generated: Wed Dec 16 05:59:00 2020

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