Manganese in PDB 5nrz: Cys-Gly Dipeptidase Glij in Complex with MN2+

All present enzymatic activity of Cys-Gly Dipeptidase Glij in Complex with MN2+:
3.4.13.19;

The structure of Cys-Gly Dipeptidase Glij in Complex with MN2+, PDB code: 5nrz 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 / 2.05
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.270, 98.270, 106.010, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 19.2

The structure of Cys-Gly Dipeptidase Glij in Complex with MN2+ also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Manganese atom in the Cys-Gly Dipeptidase Glij in Complex with MN2+ (pdb code 5nrz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Cys-Gly Dipeptidase Glij in Complex with MN2+, PDB code: 5nrz:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cys-Gly Dipeptidase Glij in Complex with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:39.5 occ:1.00 OE1 A:GLU134 2.1 40.6 1.0 NE2 A:HIS203 2.1 40.2 1.0 NE2 A:HIS224 2.3 33.5 1.0 O A:HOH639 2.3 39.5 1.0 O A:HOH502 2.4 39.3 1.0 CD2 A:HIS203 3.1 40.3 1.0 O A:HOH691 3.1 48.0 1.0 CE1 A:HIS203 3.1 40.1 1.0 CD2 A:HIS224 3.2 33.8 1.0 CD A:GLU134 3.3 40.2 1.0 CE1 A:HIS224 3.3 33.6 1.0 MN A:MN402 3.5 43.5 1.0 OE2 A:GLU134 3.8 40.4 1.0 NE2 A:HIS161 4.1 45.4 1.0 OD1 A:ASP294 4.1 37.7 1.0 CD2 A:HIS161 4.2 45.3 1.0 OD2 A:ASP294 4.2 38.7 1.0 ND1 A:HIS203 4.2 40.2 1.0 NH1 A:ARG235 4.2 41.8 1.0 NE2 A:HIS23 4.2 33.6 1.0 CG A:HIS203 4.2 40.2 1.0 O A:HOH676 4.2 44.9 1.0 ND1 A:HIS224 4.4 33.4 1.0 CG A:HIS224 4.4 33.8 1.0 CG A:ASP294 4.4 38.3 1.0 CG A:GLU134 4.5 40.3 1.0 CD2 A:HIS23 4.7 33.3 1.0 CE1 A:HIS23 4.8 34.3 1.0 O A:HOH690 4.9 49.9 1.0

Manganese binding site 2 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cys-Gly Dipeptidase Glij in Complex with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:43.5 occ:1.00 NE2 A:HIS23 2.1 33.6 1.0 OE2 A:GLU134 2.2 40.4 1.0 OD1 A:ASP25 2.2 41.7 1.0 O A:HOH502 2.3 39.3 1.0 O A:HOH676 2.5 44.9 1.0 OD2 A:ASP25 2.8 38.1 1.0 CG A:ASP25 2.9 37.8 1.0 CD A:GLU134 3.0 40.2 1.0 CD2 A:HIS23 3.0 33.3 1.0 OE1 A:GLU134 3.1 40.6 1.0 CE1 A:HIS23 3.1 34.3 1.0 MN A:MN401 3.5 39.5 1.0 OD1 A:ASP294 3.7 37.7 1.0 OG A:SER69 3.9 36.3 1.0 O A:HOH691 4.2 48.0 1.0 CG A:HIS23 4.2 33.1 1.0 ND1 A:HIS23 4.2 34.2 1.0 NE2 A:HIS224 4.3 33.5 1.0 CB A:ASP25 4.3 35.6 1.0 CG A:GLU134 4.4 40.3 1.0 CB A:SER69 4.4 36.0 1.0 CB A:PHE71 4.5 35.3 1.0 CE1 A:HIS224 4.7 33.6 1.0 CG A:PHE71 4.8 36.6 1.0 CG A:ASP294 4.8 38.3 1.0 CB A:GLU134 4.8 39.6 1.0 O A:HOH776 4.9 59.0 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