Iron in PDB 5nry: Cys-Gly Dipeptidase Glij in Complex with FE3+

All present enzymatic activity of Cys-Gly Dipeptidase Glij in Complex with FE3+:
3.4.13.19;

The structure of Cys-Gly Dipeptidase Glij in Complex with FE3+, PDB code: 5nry 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 / 1.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.990, 98.990, 106.300, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 19

The structure of Cys-Gly Dipeptidase Glij in Complex with FE3+ also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Iron atom in the Cys-Gly Dipeptidase Glij in Complex with FE3+ (pdb code 5nry). 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 FE3+, PDB code: 5nry:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with FE3+


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 FE3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:45.7 occ:1.00 OD1 A:ASP25 2.1 35.5 1.0 OE1 A:GLU134 2.2 34.1 1.0 NE2 A:HIS23 2.2 29.1 1.0 O A:HOH742 2.3 44.7 1.0 OD2 A:ASP25 2.6 33.4 1.0 CG A:ASP25 2.7 32.3 1.0 CD A:GLU134 3.0 34.8 1.0 OE2 A:GLU134 3.1 35.8 1.0 CD2 A:HIS23 3.1 28.9 1.0 CE1 A:HIS23 3.2 29.3 1.0 FE A:FE402 3.5 40.1 1.0 OD1 A:ASP294 3.8 32.0 1.0 OG A:SER69 3.9 29.5 1.0 O A:HOH618 3.9 47.5 1.0 CB A:ASP25 4.2 29.9 1.0 ND1 A:HIS23 4.3 28.6 1.0 CG A:HIS23 4.3 27.9 1.0 CB A:SER69 4.4 28.5 1.0 CG A:GLU134 4.4 34.0 1.0 NE2 A:HIS224 4.4 29.8 1.0 CB A:PHE71 4.5 32.1 1.0 CG A:PHE71 4.7 33.3 1.0 CE1 A:HIS224 4.8 29.9 1.0 CG A:ASP294 4.9 31.5 1.0 CB A:GLU134 4.9 33.0 1.0 O A:HOH860 4.9 59.9 1.0 CD1 A:PHE71 5.0 34.7 1.0

Iron binding site 2 out of 2 in the Cys-Gly Dipeptidase Glij in Complex with FE3+


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 FE3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:40.1 occ:1.00 OE2 A:GLU134 2.1 35.8 1.0 NE2 A:HIS203 2.1 39.2 1.0 NE2 A:HIS224 2.2 29.8 1.0 O A:HOH655 2.3 45.4 1.0 O A:HOH618 2.6 47.5 1.0 CD2 A:HIS203 3.1 37.9 1.0 CE1 A:HIS203 3.1 39.4 1.0 CE1 A:HIS224 3.2 29.9 1.0 CD2 A:HIS224 3.2 29.9 1.0 CD A:GLU134 3.2 34.8 1.0 FE A:FE401 3.5 45.7 1.0 OE1 A:GLU134 3.7 34.1 1.0 O A:HOH742 4.0 44.7 1.0 OD1 A:ASP294 4.1 32.0 1.0 NE2 A:HIS161 4.1 41.4 1.0 CD2 A:HIS161 4.2 41.1 1.0 NE2 A:HIS23 4.2 29.1 1.0 OD2 A:ASP294 4.2 34.4 1.0 ND1 A:HIS203 4.2 38.6 1.0 CG A:HIS203 4.2 37.4 1.0 ND1 A:HIS224 4.3 29.2 1.0 NH1 A:ARG235 4.3 42.2 1.0 CG A:HIS224 4.4 29.1 1.0 CG A:ASP294 4.4 31.5 1.0 CG A:GLU134 4.4 34.0 1.0 CD2 A:HIS23 4.6 28.9 1.0 CE1 A:HIS23 4.7 29.3 1.0 O A:HOH699 4.9 47.9 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