Zinc in PDB 5nru: Cys-Gly Dipeptidase Glij in Complex with ZN2+

All present enzymatic activity of Cys-Gly Dipeptidase Glij in Complex with ZN2+:
3.4.13.19;

The structure of Cys-Gly Dipeptidase Glij in Complex with ZN2+, PDB code: 5nru was solved by M.Groll, E.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.15
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.210, 99.210, 106.670, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 21.1

The structure of Cys-Gly Dipeptidase Glij in Complex with ZN2+ also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Cys-Gly Dipeptidase Glij in Complex with ZN2+ (pdb code 5nru). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cys-Gly Dipeptidase Glij in Complex with ZN2+, PDB code: 5nru:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cys-Gly Dipeptidase Glij in Complex with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:47.7 occ:1.00 OE2 A:GLU134 1.9 34.5 1.0 NE2 A:HIS203 2.1 46.8 1.0 NE2 A:HIS224 2.2 40.5 1.0 O A:HOH618 2.3 43.4 1.0 CE1 A:HIS203 3.0 47.0 1.0 O A:HOH643 3.0 70.3 1.0 CD A:GLU134 3.1 33.8 1.0 CD2 A:HIS224 3.1 40.6 1.0 CD2 A:HIS203 3.2 45.6 1.0 CE1 A:HIS224 3.2 40.1 1.0 ZN A:ZN402 3.4 45.0 1.0 OE1 A:GLU134 3.6 33.1 1.0 OD1 A:ASP294 4.0 45.3 1.0 NH1 A:ARG235 4.1 43.8 1.0 ND1 A:HIS203 4.2 46.8 1.0 OD2 A:ASP294 4.2 45.9 1.0 NE2 A:HIS23 4.2 38.4 1.0 CG A:GLU134 4.2 38.4 1.0 CG A:HIS224 4.2 40.1 1.0 CG A:HIS203 4.3 45.6 1.0 NE2 A:HIS161 4.3 49.6 1.0 ND1 A:HIS224 4.3 39.9 1.0 CG A:ASP294 4.3 44.5 1.0 CD2 A:HIS161 4.4 50.1 1.0 O A:HOH582 4.5 57.9 1.0 CD2 A:HIS23 4.6 38.0 1.0 CE1 A:HIS23 4.7 38.2 1.0 OD1 A:ASP25 4.9 40.8 1.0 CZ A:ARG235 5.0 45.9 1.0

Zinc binding site 2 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cys-Gly Dipeptidase Glij in Complex with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:45.0 occ:1.00 OD1 A:ASP25 1.9 40.8 1.0 OE1 A:GLU134 2.0 33.1 1.0 NE2 A:HIS23 2.2 38.4 1.0 CG A:ASP25 2.7 39.0 1.0 CD A:GLU134 2.8 33.8 1.0 OE2 A:GLU134 2.9 34.5 1.0 OD2 A:ASP25 3.0 39.9 1.0 CD2 A:HIS23 3.1 38.0 1.0 CE1 A:HIS23 3.2 38.2 1.0 ZN A:ZN401 3.4 47.7 1.0 OD1 A:ASP294 3.6 45.3 1.0 O A:HOH643 3.6 70.3 1.0 CB A:ASP25 4.1 37.9 1.0 CG A:GLU134 4.2 38.4 1.0 NE2 A:HIS224 4.2 40.5 1.0 ND1 A:HIS23 4.3 37.8 1.0 CG A:HIS23 4.3 37.5 1.0 OG A:SER69 4.3 42.9 1.0 CE1 A:HIS224 4.7 40.1 1.0 CB A:GLU134 4.7 41.0 1.0 CG A:ASP294 4.7 44.5 1.0 CB A:SER69 4.7 42.5 1.0 CB A:PHE71 4.8 40.4 1.0 CG A:PHE71 5.0 42.1 1.0 CD2 A:HIS224 5.0 40.6 1.0 CA A:GLY297 5.0 47.8 1.0 O A:HOH672 5.0 75.8 1.0

A.Marion, M.Groll, D.H.Scharf, K.Scherlach, M.Glaser, H.Sievers, M.Schuster, C.Hertweck, A.A.Brakhage, I.Antes, E.M.Huber. Gliotoxin Biosynthesis: Structure, Mechanism, and Metal Promiscuity of Carboxypeptidase Glij. Acs Chem. Biol. V. 12 1874 2017.
ISSN: ESSN 1554-8937
PubMed: 28525266
DOI: 10.1021/ACSCHEMBIO.6B00847