Zinc in PDB 4lgr: Ricin A Chain Bound to Camelid Nanobody (VHH3)

All present enzymatic activity of Ricin A Chain Bound to Camelid Nanobody (VHH3):
3.2.2.22;

The structure of Ricin A Chain Bound to Camelid Nanobody (VHH3), PDB code: 4lgr was solved by M.J.Rudolph, J.Cheung, M.Franklin, F.Burshteyn, M.Cassidy, E.Gary, N.Mantis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.22 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.345, 77.423, 121.805, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.4

The structure of Ricin A Chain Bound to Camelid Nanobody (VHH3) also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Zinc atom in the Ricin A Chain Bound to Camelid Nanobody (VHH3) (pdb code 4lgr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Ricin A Chain Bound to Camelid Nanobody (VHH3), PDB code: 4lgr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


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 (VHH3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.2 occ:1.00 OE2 A:GLU102 1.9 23.9 1.0 OXT A:ACY302 2.0 27.0 1.0 NE2 A:HIS106 2.1 22.1 1.0 CD A:GLU102 2.7 24.3 1.0 C A:ACY302 2.9 33.0 1.0 OE1 A:GLU102 3.0 22.7 1.0 CE1 A:HIS106 3.0 29.7 1.0 O A:ACY302 3.0 30.2 1.0 CD2 A:HIS106 3.1 20.0 1.0 O A:HOH456 4.0 32.9 1.0 ND1 A:HIS106 4.1 21.4 1.0 CG A:GLU102 4.1 24.0 1.0 CG A:HIS106 4.2 19.5 1.0 CH3 A:ACY302 4.3 36.4 1.0 OG1 A:THR105 4.5 20.1 1.0 O A:GLU102 4.5 18.8 1.0

Zinc binding site 2 out of 3 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:28.7 occ:1.00 ND1 B:HIS121 2.1 31.8 1.0 O B:HOH304 2.1 25.3 1.0 O B:HOH302 2.1 25.2 1.0 O B:HOH301 2.2 28.8 1.0 O B:HOH303 2.2 19.0 1.0 CE1 B:HIS121 3.0 30.8 1.0 CG B:HIS121 3.1 32.7 1.0 CB B:HIS121 3.5 34.2 1.0 O B:HOH353 3.9 35.4 1.0 NE2 B:HIS121 4.1 36.2 1.0 OG B:SER123 4.1 37.7 1.0 CD2 B:HIS121 4.2 35.7 1.0 CA B:HIS121 5.0 36.3 1.0

Zinc binding site 3 out of 3 in the Ricin A Chain Bound to Camelid Nanobody (VHH3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ricin A Chain Bound to Camelid Nanobody (VHH3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:38.8 occ:1.00 ND1 B:HIS21 2.0 44.3 0.5 O B:HOH388 2.2 28.1 0.6 ND1 B:HIS21 2.2 48.4 0.5 OD1 B:ASP79 2.3 34.1 1.0 OXT B:ACY203 2.3 55.3 1.0 OD2 B:ASP79 2.4 40.4 1.0 O B:ACY203 2.5 66.9 1.0 CG B:ASP79 2.7 25.4 1.0 C B:ACY203 2.7 63.5 1.0 O B:HOH388 2.7 28.1 0.4 CE1 B:HIS21 2.9 49.2 0.5 CG B:HIS21 3.0 37.1 0.5 CG B:HIS21 3.1 36.5 0.5 CE1 B:HIS21 3.1 50.1 0.5 CB B:HIS21 3.4 30.7 0.5 CB B:HIS21 3.4 30.6 0.5 CA B:HIS21 4.0 27.1 0.5 NE2 B:HIS21 4.0 40.3 0.5 CA B:HIS21 4.0 26.9 0.5 CD2 B:HIS21 4.1 40.0 0.5 CH3 B:ACY203 4.2 64.6 1.0 NE2 B:HIS21 4.2 37.0 0.5 CD2 B:HIS21 4.2 37.0 0.5 CB B:ASP79 4.2 28.0 1.0 NE B:ARG19 4.5 53.1 1.0 O B:HOH316 4.8 33.1 1.0 O B:LEU20 4.8 26.4 1.0 CA B:ASP79 5.0 27.8 1.0

M.J.Rudolph, D.J.Vance, J.Cheung, M.C.Franklin, F.Burshteyn, M.S.Cassidy, E.N.Gary, C.Herrera, C.B.Shoemaker, N.J.Mantis. Crystal Structures of Ricin Toxin'S Enzymatic Subunit (Rta) in Complex with Neutralizing and Non-Neutralizing Single-Chain Antibodies. J.Mol.Biol. V. 426 3057 2014.
ISSN: ISSN 0022-2836
PubMed: 24907552
DOI: 10.1016/J.JMB.2014.05.026