Iron in PDB 5lwz: Cys-Gly Dipeptidase Glij (Space Group C2)

All present enzymatic activity of Cys-Gly Dipeptidase Glij (Space Group C2):
3.4.13.19;

The structure of Cys-Gly Dipeptidase Glij (Space Group C2), PDB code: 5lwz was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.800, 100.250, 106.640, 90.00, 90.27, 90.00
R / Rfree (%)	16.7 / 19.7

The binding sites of Iron atom in the Cys-Gly Dipeptidase Glij (Space Group C2) (pdb code 5lwz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cys-Gly Dipeptidase Glij (Space Group C2), PDB code: 5lwz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Cys-Gly Dipeptidase Glij (Space Group C2)


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 (Space Group C2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:50.1 occ:1.00 OE2 A:GLU134 2.0 43.0 1.0 O A:HOH586 2.3 51.6 1.0 NE2 A:HIS224 2.4 40.2 1.0 NE2 A:HIS203 2.4 46.6 1.0 O A:HOH535 2.5 51.4 1.0 CD A:GLU134 3.1 43.9 1.0 FE A:FE402 3.2 48.4 1.0 CD2 A:HIS203 3.3 45.2 1.0 CD2 A:HIS224 3.4 40.3 1.0 CE1 A:HIS224 3.4 40.7 1.0 CE1 A:HIS203 3.4 47.6 1.0 OE1 A:GLU134 3.6 43.5 1.0 O A:HOH603 3.9 45.3 1.0 OD1 A:ASP294 3.9 47.1 1.0 NE2 A:HIS161 4.0 53.0 1.0 CD2 A:HIS161 4.2 53.3 1.0 OD2 A:ASP294 4.2 47.3 1.0 NE2 A:HIS23 4.2 40.4 1.0 CG A:ASP294 4.3 44.1 1.0 CG A:GLU134 4.4 42.2 1.0 CG A:HIS203 4.5 46.3 1.0 NH1 A:ARG235 4.5 53.0 1.0 ND1 A:HIS224 4.5 39.9 1.0 ND1 A:HIS203 4.5 48.5 1.0 CG A:HIS224 4.5 39.9 1.0 CD2 A:HIS23 4.6 39.0 1.0 O A:HOH512 4.7 61.4 1.0 OD1 A:ASP25 4.8 43.5 1.0 CE1 A:HIS23 4.9 40.5 1.0

Iron binding site 2 out of 6 in the Cys-Gly Dipeptidase Glij (Space Group C2)


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 (Space Group C2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:48.4 occ:1.00 OE1 A:GLU134 2.2 43.5 1.0 OD1 A:ASP25 2.2 43.5 1.0 O A:HOH603 2.4 45.3 1.0 NE2 A:HIS23 2.4 40.4 1.0 OD2 A:ASP25 2.6 44.1 1.0 CG A:ASP25 2.7 42.7 1.0 CD A:GLU134 2.9 43.9 1.0 OE2 A:GLU134 3.0 43.0 1.0 FE A:FE401 3.2 50.1 1.0 CD2 A:HIS23 3.2 39.0 1.0 CE1 A:HIS23 3.5 40.5 1.0 OD1 A:ASP294 3.6 47.1 1.0 O A:HOH535 3.9 51.4 1.0 OG A:SER69 4.1 41.1 1.0 CB A:ASP25 4.2 42.1 1.0 NE2 A:HIS224 4.3 40.2 1.0 CG A:HIS23 4.4 39.1 1.0 CG A:GLU134 4.4 42.2 1.0 ND1 A:HIS23 4.5 39.9 1.0 CB A:PHE71 4.6 44.6 1.0 CB A:SER69 4.6 39.5 1.0 CG A:ASP294 4.7 44.1 1.0 CE1 A:HIS224 4.7 40.7 1.0 CG A:PHE71 4.8 45.8 1.0 O A:HOH586 4.8 51.6 1.0 CA A:GLY297 4.9 46.4 1.0 CB A:GLU134 4.9 41.7 1.0

Iron binding site 3 out of 6 in the Cys-Gly Dipeptidase Glij (Space Group C2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cys-Gly Dipeptidase Glij (Space Group C2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:51.1 occ:1.00 OE2 B:GLU134 2.0 44.6 1.0 O B:HOH558 2.3 50.1 1.0 O B:HOH518 2.4 53.5 1.0 NE2 B:HIS224 2.4 39.0 1.0 NE2 B:HIS203 2.5 49.4 1.0 CD B:GLU134 3.1 44.8 1.0 FE B:FE402 3.2 49.1 1.0 CD2 B:HIS203 3.3 47.3 1.0 CE1 B:HIS224 3.4 39.8 1.0 CD2 B:HIS224 3.4 39.8 1.0 CE1 B:HIS203 3.5 49.2 1.0 OE1 B:GLU134 3.7 43.9 1.0 O B:HOH597 3.9 46.4 1.0 NE2 B:HIS161 4.0 52.2 1.0 OD1 B:ASP294 4.1 46.4 1.0 OD2 B:ASP294 4.1 46.5 1.0 CD2 B:HIS161 4.1 52.3 1.0 NE2 B:HIS23 4.2 40.0 1.0 CG B:GLU134 4.4 43.8 1.0 CG B:ASP294 4.4 43.6 1.0 CG B:HIS203 4.5 48.1 1.0 ND1 B:HIS224 4.5 39.5 1.0 ND1 B:HIS203 4.5 50.1 1.0 CG B:HIS224 4.5 39.5 1.0 NH1 B:ARG235 4.6 54.4 1.0 CD2 B:HIS23 4.6 39.1 1.0 OD1 B:ASP25 4.9 46.6 1.0 CE1 B:HIS23 4.9 39.3 1.0

Iron binding site 4 out of 6 in the Cys-Gly Dipeptidase Glij (Space Group C2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cys-Gly Dipeptidase Glij (Space Group C2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:49.1 occ:1.00 OE1 B:GLU134 2.2 43.9 1.0 OD1 B:ASP25 2.3 46.6 1.0 O B:HOH597 2.4 46.4 1.0 NE2 B:HIS23 2.4 40.0 1.0 OD2 B:ASP25 2.5 45.0 1.0 CG B:ASP25 2.7 44.1 1.0 CD B:GLU134 2.9 44.8 1.0 OE2 B:GLU134 3.0 44.6 1.0 FE B:FE401 3.2 51.1 1.0 CD2 B:HIS23 3.2 39.1 1.0 CE1 B:HIS23 3.5 39.3 1.0 OD1 B:ASP294 3.7 46.4 1.0 O B:HOH518 3.8 53.5 1.0 OG B:SER69 4.1 40.0 1.0 CB B:ASP25 4.2 42.9 1.0 NE2 B:HIS224 4.4 39.0 1.0 CG B:HIS23 4.4 38.8 1.0 CG B:GLU134 4.4 43.8 1.0 ND1 B:HIS23 4.5 39.0 1.0 CB B:PHE71 4.6 44.2 1.0 CB B:SER69 4.6 38.5 1.0 CE1 B:HIS224 4.7 39.8 1.0 CG B:PHE71 4.7 45.6 1.0 CG B:ASP294 4.8 43.6 1.0 O B:HOH558 4.9 50.1 1.0 CA B:GLY297 4.9 45.8 1.0 CB B:GLU134 4.9 43.8 1.0 CD1 B:PHE71 4.9 46.0 1.0

Iron binding site 5 out of 6 in the Cys-Gly Dipeptidase Glij (Space Group C2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cys-Gly Dipeptidase Glij (Space Group C2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:49.7 occ:1.00 OE2 C:GLU134 2.0 42.8 1.0 O C:HOH595 2.2 54.1 1.0 O C:HOH526 2.4 51.8 1.0 NE2 C:HIS224 2.5 38.0 1.0 NE2 C:HIS203 2.5 48.4 1.0 FE C:FE402 3.1 47.5 1.0 CD C:GLU134 3.1 43.4 1.0 CE1 C:HIS203 3.3 48.5 1.0 CD2 C:HIS224 3.4 38.6 1.0 CD2 C:HIS203 3.4 46.4 1.0 CE1 C:HIS224 3.4 38.4 1.0 OE1 C:GLU134 3.7 41.5 1.0 O C:HOH605 3.9 45.2 1.0 NE2 C:HIS161 4.0 52.2 1.0 OD1 C:ASP294 4.0 47.9 1.0 CD2 C:HIS161 4.1 51.4 1.0 OD2 C:ASP294 4.2 49.1 1.0 NE2 C:HIS23 4.3 38.9 1.0 CG C:ASP294 4.4 44.4 1.0 CG C:GLU134 4.4 42.5 1.0 ND1 C:HIS203 4.4 49.1 1.0 CG C:HIS203 4.5 47.3 1.0 NH1 C:ARG235 4.5 54.3 1.0 ND1 C:HIS224 4.5 38.1 1.0 CG C:HIS224 4.6 38.1 1.0 CD2 C:HIS23 4.6 38.6 1.0 O C:HOH508 4.8 61.7 1.0 OD1 C:ASP25 4.8 48.7 1.0 CE1 C:HIS23 4.9 39.0 1.0

Iron binding site 6 out of 6 in the Cys-Gly Dipeptidase Glij (Space Group C2)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cys-Gly Dipeptidase Glij (Space Group C2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:47.5 occ:1.00 OD1 C:ASP25 2.1 48.7 1.0 OE1 C:GLU134 2.2 41.5 1.0 NE2 C:HIS23 2.4 38.9 1.0 O C:HOH605 2.4 45.2 1.0 CG C:ASP25 2.8 42.4 1.0 OD2 C:ASP25 2.8 43.8 1.0 CD C:GLU134 2.9 43.4 1.0 OE2 C:GLU134 3.0 42.8 1.0 FE C:FE401 3.1 49.7 1.0 CD2 C:HIS23 3.1 38.6 1.0 CE1 C:HIS23 3.4 39.0 1.0 OD1 C:ASP294 3.6 47.9 1.0 O C:HOH526 3.9 51.8 1.0 OG C:SER69 4.1 40.5 1.0 CB C:ASP25 4.2 42.3 1.0 NE2 C:HIS224 4.3 38.0 1.0 CG C:HIS23 4.3 38.2 1.0 CG C:GLU134 4.4 42.5 1.0 ND1 C:HIS23 4.4 38.4 1.0 CB C:PHE71 4.6 43.7 1.0 CB C:SER69 4.6 39.0 1.0 CE1 C:HIS224 4.7 38.4 1.0 CG C:PHE71 4.7 45.4 1.0 CG C:ASP294 4.7 44.4 1.0 O C:HOH595 4.8 54.1 1.0 CB C:GLU134 4.9 42.5 1.0 CA C:GLY297 5.0 46.9 1.0 CD1 C:PHE71 5.0 45.7 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