Zinc in PDB 5m0t: Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash

The structure of Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash, PDB code: 5m0t was solved by D.Jakubczyk, L.Caputi, C.E.M.Stevenson, D.M.Lawson, S.E.O'connor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.47 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.250, 100.170, 148.880, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 24.4

The structure of Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash (pdb code 5m0t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash, PDB code: 5m0t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:53.4 occ:1.00 OE1 A:GLU178 2.0 73.8 1.0 O A:HOH420 2.0 44.9 1.0 O1 A:AKG306 2.0 58.6 1.0 CD A:GLU178 2.6 60.2 1.0 OE2 A:GLU178 2.7 59.5 1.0 C1 A:AKG306 3.0 65.3 1.0 O2 A:AKG306 3.3 49.1 1.0 CG A:GLU178 4.1 54.2 1.0 C2 A:AKG306 4.4 56.2 1.0 CB A:GLU178 4.8 48.5 1.0 C3 A:AKG306 5.0 47.8 1.0

Zinc binding site 2 out of 4 in the Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:66.0 occ:1.00 O A:HOH401 2.0 50.2 1.0 O A:HOH407 2.0 30.9 0.5 OE2 A:GLU21 2.0 74.7 1.0 OE1 A:GLU21 2.0 63.4 1.0 CD A:GLU21 2.3 61.5 1.0 OD2 A:ASP20 3.5 55.9 1.0 O A:HOH407 3.8 10.4 0.5 CG A:GLU21 3.9 52.2 1.0 O A:HOH428 4.1 45.5 1.0 CG A:ASP20 4.4 50.2 1.0 O A:HOH423 4.5 31.4 1.0 NH2 A:ARG102 4.5 73.5 1.0 OD1 A:ASP20 4.7 49.3 1.0 CB A:GLU21 4.7 47.2 1.0 N A:GLU21 4.8 41.4 1.0 N A:ASP20 4.9 42.0 1.0

Zinc binding site 3 out of 4 in the Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:51.6 occ:1.00 OD2 A:ASP199 2.0 44.1 1.0 OE1 A:GLU36 2.0 69.1 1.0 O A:HOH408 2.0 53.0 1.0 CD A:GLU36 2.7 54.7 1.0 OE2 A:GLU36 2.8 50.4 1.0 CG A:ASP199 3.1 43.6 1.0 OD1 A:ASN196 3.6 47.1 1.0 OD1 A:ASP199 3.6 45.9 1.0 N A:ASN196 3.9 42.1 1.0 NH1 A:ARG13 4.1 43.3 1.0 CG A:GLU36 4.2 50.6 1.0 CB A:ASN196 4.2 44.6 1.0 CG A:ASN196 4.3 46.3 1.0 CB A:ASP199 4.3 39.3 1.0 CA A:MET195 4.6 39.9 1.0 CA A:ASN196 4.7 42.5 1.0 C A:MET195 4.8 41.5 1.0 CB A:GLU36 4.8 46.9 1.0

Zinc binding site 4 out of 4 in the Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alpha-Ketoglutarate-Dependent Non-Heme Iron Oxygenase Eash within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:74.7 occ:1.00 O B:HOH401 1.8 44.6 0.5 OE2 B:GLU21 2.0 85.6 1.0 O B:HOH402 2.0 48.9 1.0 OE1 B:GLU21 2.0 69.2 1.0 CD B:GLU21 2.3 64.8 1.0 OD2 B:ASP20 3.1 56.3 1.0 O B:HOH401 3.7 17.8 0.5 CG B:GLU21 3.8 58.8 1.0 CG B:ASP20 4.2 50.5 1.0 NH2 B:ARG102 4.3 58.7 1.0 OD1 B:ASP20 4.6 53.3 1.0 N B:GLU21 4.7 46.5 1.0 CB B:GLU21 4.7 53.0 1.0 O B:HOH413 4.7 39.1 1.0 N B:ASP20 4.9 43.5 1.0

D.Jakubczyk, L.Caputi, C.E.Stevenson, D.M.Lawson, S.E.O'connor. Structural Characterization of Eash (Aspergillus Japonicus) - An Oxidase Involved in Cycloclavine Biosynthesis. Chem. Commun. (Camb.) V. 52 14306 2016.
ISSN: ESSN 1364-548X
PubMed: 27885368
DOI: 10.1039/C6CC08438A