Zinc in PDB 5ns5: Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+

All present enzymatic activity of Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+:
3.4.13.19;

The structure of Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+, PDB code: 5ns5 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 / 2.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.000, 99.000, 106.490, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 18.9

The structure of Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+ also contains other interesting chemical elements:

Copper	(Cu)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Zinc atom in the Cys-Gly Dipeptidase Glij in Complex with CU2+ and ZN2+ (pdb code 5ns5). 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 CU2+ and ZN2+, PDB code: 5ns5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with CU2+ and 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 CU2+ and ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:59.8 occ:0.50 CU A:CU404 0.0 52.4 0.5 NE2 A:HIS203 2.0 48.6 1.0 OE2 A:GLU134 2.1 46.0 1.0 O A:HOH586 2.2 50.0 1.0 NE2 A:HIS224 2.2 38.1 1.0 O A:HOH638 2.8 69.7 1.0 CE1 A:HIS203 2.9 47.0 1.0 CD2 A:HIS203 3.0 49.1 1.0 CE1 A:HIS224 3.2 39.1 1.0 CD2 A:HIS224 3.2 36.2 1.0 CD A:GLU134 3.3 45.0 1.0 OE1 A:GLU134 3.8 46.8 1.0 ZN A:ZN402 3.8 67.1 0.5 CU A:CU403 3.9 68.1 0.5 ND1 A:HIS203 4.0 48.1 1.0 NH1 A:ARG235 4.1 51.5 1.0 NE2 A:HIS161 4.1 54.9 1.0 CG A:HIS203 4.1 49.1 1.0 CD2 A:HIS161 4.2 55.5 1.0 OD1 A:ASP294 4.3 48.2 1.0 ND1 A:HIS224 4.3 38.7 1.0 OD2 A:ASP294 4.4 49.0 1.0 NE2 A:HIS23 4.4 40.5 1.0 CG A:HIS224 4.4 38.2 1.0 CG A:GLU134 4.5 47.7 1.0 CG A:ASP294 4.6 47.9 1.0 CD2 A:HIS23 4.8 39.6 1.0 O A:HOH623 4.8 60.3 1.0 CZ A:ARG235 4.9 52.0 1.0 CE1 A:HIS23 4.9 41.2 1.0 NE A:ARG235 5.0 53.0 1.0

Zinc binding site 2 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with CU2+ and 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 CU2+ and ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:67.1 occ:0.50 CU A:CU403 0.1 68.1 0.5 OE1 A:GLU134 2.0 46.8 1.0 NE2 A:HIS23 2.0 40.5 1.0 OD1 A:ASP25 2.1 51.1 1.0 CG A:ASP25 2.7 48.6 1.0 OD2 A:ASP25 2.8 49.6 1.0 CD A:GLU134 2.9 45.0 1.0 CE1 A:HIS23 3.0 41.2 1.0 CD2 A:HIS23 3.1 39.6 1.0 OE2 A:GLU134 3.2 46.0 1.0 OG A:SER69 3.6 43.2 1.0 ZN A:ZN401 3.8 59.8 0.5 CU A:CU404 3.9 52.4 0.5 O A:HOH638 3.9 69.7 1.0 OD1 A:ASP294 4.0 48.2 1.0 ND1 A:HIS23 4.1 40.7 1.0 CG A:HIS23 4.2 39.8 1.0 CB A:SER69 4.2 43.7 1.0 CB A:ASP25 4.2 45.1 1.0 CG A:GLU134 4.2 47.7 1.0 CB A:PHE71 4.4 44.1 1.0 NE2 A:HIS224 4.5 38.1 1.0 CB A:GLU134 4.6 47.3 1.0 CG A:PHE71 4.7 45.9 1.0 CE1 A:HIS224 4.8 39.1 1.0 CD1 A:PHE71 5.0 47.1 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