Chlorine in PDB 4z9k: 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;

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

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

Zinc

(Zn)

1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5), PDB code: 4z9k:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl304 b:35.1 occ:1.00 ZN A:ZN303 2.3 24.4 1.0 OE2 A:GLU103 3.4 23.3 1.0 NE2 A:HIS107 3.6 22.8 1.0 CE1 A:HIS107 3.9 25.0 1.0 O A:HOH475 4.3 39.5 1.0 CD A:GLU103 4.5 22.7 1.0 CD2 A:HIS107 4.9 22.1 1.0 OE1 A:GLU103 5.0 23.7 1.0

Chlorine binding site 2 out of 2 in the Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ricin A Chain Bound to Camelid Nanobody (VHH2)(F5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:36.2 occ:1.00 O A:HOH530 2.3 34.9 1.0 N A:GLU136 3.0 15.1 1.0 OE2 A:GLU136 3.1 44.2 1.0 CG A:GLU136 3.2 24.4 1.0 CB A:GLU136 3.4 18.9 1.0 CB A:LEU134 3.5 17.4 1.0 N A:ARG135 3.6 14.7 1.0 CD1 A:ILE206 3.6 25.1 1.0 CD A:GLU136 3.6 42.8 1.0 O A:HOH630 3.7 40.0 1.0 CA A:GLU136 3.8 15.4 1.0 C A:ARG135 3.9 16.2 1.0 CB A:ARG135 4.0 14.9 1.0 CA A:ARG135 4.0 15.3 1.0 OE2 A:GLU128 4.1 15.9 1.0 C A:LEU134 4.1 16.0 1.0 CD1 A:LEU134 4.3 23.5 1.0 CA A:LEU134 4.4 16.9 1.0 CG A:LEU134 4.4 19.3 1.0 CG1 A:ILE206 4.5 21.0 1.0 CD2 A:LEU134 4.6 20.1 1.0 CG2 A:ILE206 4.7 19.2 1.0 OE1 A:GLU136 4.9 41.3 1.0 O A:LEU134 4.9 17.0 1.0 C A:GLU136 4.9 17.3 1.0 NE A:ARG135 5.0 14.2 1.0 CD A:GLU128 5.0 15.4 1.0

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