Nickel in PDB 5ns1: Cys-Gly Dipeptidase Glij in Complex with NI2+

All present enzymatic activity of Cys-Gly Dipeptidase Glij in Complex with NI2+:
3.4.13.19;

The structure of Cys-Gly Dipeptidase Glij in Complex with NI2+, PDB code: 5ns1 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 / 2.40
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.350, 99.350, 107.370, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 20.1

The structure of Cys-Gly Dipeptidase Glij in Complex with NI2+ also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Cys-Gly Dipeptidase Glij in Complex with NI2+ (pdb code 5ns1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Cys-Gly Dipeptidase Glij in Complex with NI2+, PDB code: 5ns1:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Cys-Gly Dipeptidase Glij in Complex with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:58.4 occ:1.00 OE2 A:GLU134 1.8 48.9 1.0 NE2 A:HIS203 2.1 69.3 1.0 NE2 A:HIS224 2.2 53.7 1.0 O A:HOH564 2.6 57.7 1.0 CD A:GLU134 3.0 49.2 1.0 CE1 A:HIS203 3.0 70.7 1.0 CD2 A:HIS203 3.1 65.8 1.0 CE1 A:HIS224 3.2 54.2 1.0 CD2 A:HIS224 3.2 53.2 1.0 OE1 A:GLU134 3.5 48.5 1.0 NI A:NI402 3.6 58.2 1.0 OD1 A:ASP294 3.9 60.0 1.0 ND1 A:HIS203 4.1 66.4 1.0 NE2 A:HIS161 4.2 72.2 1.0 CG A:HIS203 4.2 63.3 1.0 CG A:GLU134 4.2 50.6 1.0 NE2 A:HIS23 4.2 53.2 1.0 OD2 A:ASP294 4.3 61.7 1.0 ND1 A:HIS224 4.3 53.7 1.0 CD2 A:HIS161 4.3 72.7 1.0 CG A:HIS224 4.3 52.9 1.0 NH1 A:ARG235 4.3 60.4 1.0 CG A:ASP294 4.4 60.0 1.0 CD2 A:HIS23 4.7 52.3 1.0 CE1 A:HIS23 4.7 53.0 1.0 OD1 A:ASP25 4.9 56.8 1.0

Nickel binding site 2 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Cys-Gly Dipeptidase Glij in Complex with NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:58.2 occ:1.00 OD1 A:ASP25 1.9 56.8 1.0 OE1 A:GLU134 2.0 48.5 1.0 NE2 A:HIS23 2.1 53.2 1.0 CG A:ASP25 2.5 56.1 1.0 OD2 A:ASP25 2.5 58.5 1.0 CD A:GLU134 2.9 49.2 1.0 CD2 A:HIS23 3.1 52.3 1.0 CE1 A:HIS23 3.1 53.0 1.0 OE2 A:GLU134 3.2 48.9 1.0 O A:HOH564 3.4 57.7 1.0 NI A:NI401 3.6 58.4 1.0 OG A:SER69 3.7 52.8 1.0 OD1 A:ASP294 3.9 60.0 1.0 CB A:ASP25 3.9 54.1 1.0 ND1 A:HIS23 4.2 51.8 1.0 CG A:HIS23 4.2 51.0 1.0 CB A:SER69 4.3 53.1 1.0 CG A:GLU134 4.3 50.6 1.0 CB A:PHE71 4.5 56.0 1.0 NE2 A:HIS224 4.5 53.7 1.0 CB A:GLU134 4.6 54.6 1.0 CG A:PHE71 4.7 58.2 1.0 CE1 A:HIS224 4.7 54.2 1.0 CA A:ASP25 4.9 54.8 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