Iron in PDB 5nrx: Cys-Gly Dipeptidase Glij in Complex with FE2+

All present enzymatic activity of Cys-Gly Dipeptidase Glij in Complex with FE2+:
3.4.13.19;

The structure of Cys-Gly Dipeptidase Glij in Complex with FE2+, PDB code: 5nrx 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 / 2.35
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.000, 99.000, 106.090, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 18.5

The structure of Cys-Gly Dipeptidase Glij in Complex with FE2+ also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Cys-Gly Dipeptidase Glij in Complex with FE2+ (pdb code 5nrx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Cys-Gly Dipeptidase Glij in Complex with FE2+, PDB code: 5nrx:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with FE2+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cys-Gly Dipeptidase Glij in Complex with FE2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:51.4 occ:1.00 OD1 A:ASP25 1.9 41.9 1.0 OE1 A:GLU134 2.1 41.9 1.0 NE2 A:HIS23 2.3 39.0 1.0 OD2 A:ASP25 2.3 43.3 1.0 CG A:ASP25 2.4 41.6 1.0 O A:HOH632 2.7 51.8 1.0 CD A:GLU134 3.0 42.2 1.0 CD2 A:HIS23 3.1 38.0 1.0 OE2 A:GLU134 3.2 42.7 1.0 CE1 A:HIS23 3.4 39.8 1.0 FE A:FE402 3.5 50.5 1.0 OD1 A:ASP294 3.8 45.2 1.0 CB A:ASP25 3.9 39.3 1.0 OG A:SER69 3.9 37.5 1.0 CG A:HIS23 4.3 38.2 1.0 CG A:GLU134 4.4 42.0 1.0 ND1 A:HIS23 4.4 39.3 1.0 CB A:SER69 4.4 37.0 1.0 O A:HOH611 4.5 57.2 1.0 NE2 A:HIS224 4.6 39.5 1.0 CB A:PHE71 4.6 39.5 1.0 CB A:GLU134 4.7 43.2 1.0 CG A:PHE71 4.8 40.8 1.0 CA A:ASP25 4.9 38.9 1.0 CA A:GLY297 4.9 46.5 1.0 CG A:ASP294 4.9 44.3 1.0 CE1 A:HIS224 4.9 39.5 1.0

Iron binding site 2 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with FE2+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cys-Gly Dipeptidase Glij in Complex with FE2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:50.5 occ:1.00 OE2 A:GLU134 1.9 42.7 1.0 NE2 A:HIS203 2.3 48.5 1.0 NE2 A:HIS224 2.4 39.5 1.0 O A:HOH583 2.5 44.0 1.0 O A:HOH611 2.8 57.2 1.0 CD A:GLU134 3.1 42.2 1.0 CE1 A:HIS203 3.2 47.6 1.0 CD2 A:HIS224 3.2 39.3 1.0 CD2 A:HIS203 3.3 47.2 1.0 CE1 A:HIS224 3.4 39.5 1.0 FE A:FE401 3.5 51.4 1.0 OE1 A:GLU134 3.6 41.9 1.0 OD1 A:ASP294 3.9 45.2 1.0 O A:HOH632 4.1 51.8 1.0 OD2 A:ASP294 4.1 45.7 1.0 NE2 A:HIS161 4.2 55.6 1.0 NH1 A:ARG235 4.2 55.4 1.0 CD2 A:HIS161 4.3 57.2 1.0 CG A:ASP294 4.3 44.3 1.0 NE2 A:HIS23 4.3 39.0 1.0 CG A:GLU134 4.3 42.0 1.0 ND1 A:HIS203 4.4 47.5 1.0 O A:HOH555 4.4 60.2 1.0 CG A:HIS203 4.4 47.0 1.0 CG A:HIS224 4.4 39.4 1.0 ND1 A:HIS224 4.5 39.8 1.0 CD2 A:HIS23 4.7 38.0 1.0 OD1 A:ASP25 4.8 41.9 1.0 CE1 A:HIS23 4.9 39.8 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