Iron in PDB 3wra: Crystal Structure of the Desb-Gallate Complex Exposed to Aerobic Atomosphere

All present enzymatic activity of Crystal Structure of the Desb-Gallate Complex Exposed to Aerobic Atomosphere:
1.13.11.58;

The structure of Crystal Structure of the Desb-Gallate Complex Exposed to Aerobic Atomosphere, PDB code: 3wra was solved by K.Sugimoto, M.Senda, D.Kasai, M.Fukuda, E.Masai, T.Senda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.372, 64.857, 117.656, 90.00, 96.24, 90.00
R / Rfree (%)	21 / 25.6

The binding sites of Iron atom in the Crystal Structure of the Desb-Gallate Complex Exposed to Aerobic Atomosphere (pdb code 3wra). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of the Desb-Gallate Complex Exposed to Aerobic Atomosphere, PDB code: 3wra:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of the Desb-Gallate Complex Exposed to Aerobic Atomosphere


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Desb-Gallate Complex Exposed to Aerobic Atomosphere within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:40.5 occ:1.00 OE1 A:GLU239 2.1 33.0 1.0 OD1 A:ASN57 2.2 31.9 1.0 O A:HOH621 2.2 36.8 1.0 NE2 A:HIS59 2.2 32.1 1.0 O A:HOH625 2.3 36.0 1.0 NE2 A:HIS12 2.4 38.6 1.0 CE1 A:HIS59 3.0 31.9 1.0 CD A:GLU239 3.1 33.0 1.0 CG A:ASN57 3.1 30.4 1.0 OE2 A:GLU239 3.3 33.2 1.0 CE1 A:HIS12 3.3 38.5 1.0 ND2 A:ASN57 3.3 33.1 1.0 CD2 A:HIS59 3.3 28.7 1.0 CD2 A:HIS12 3.4 36.8 1.0 O A:HOH649 4.1 34.1 1.0 ND1 A:HIS59 4.2 31.5 1.0 CG A:HIS59 4.4 30.1 1.0 CG A:GLU239 4.4 32.6 1.0 ND1 A:HIS12 4.4 37.4 1.0 CB A:ASN57 4.5 28.8 1.0 CG A:HIS12 4.5 39.0 1.0 O A:ASN57 4.5 27.9 1.0 CE A:MET242 4.6 28.2 1.0 O A:HOH638 4.7 27.8 1.0 CB A:GLU239 4.8 33.5 1.0 CA A:GLY188 4.8 32.7 1.0 N A:ASN57 5.0 27.2 1.0

Iron binding site 2 out of 2 in the Crystal Structure of the Desb-Gallate Complex Exposed to Aerobic Atomosphere


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Desb-Gallate Complex Exposed to Aerobic Atomosphere within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:23.2 occ:1.00 O B:HOH604 2.0 21.7 1.0 OE1 B:GLU239 2.1 27.0 1.0 NE2 B:HIS59 2.2 24.5 1.0 OD1 B:ASN57 2.2 20.6 1.0 O B:HOH610 2.2 27.2 1.0 NE2 B:HIS12 2.3 26.4 1.0 CE1 B:HIS59 2.9 25.2 1.0 CD B:GLU239 3.1 24.2 1.0 CG B:ASN57 3.1 20.2 1.0 CE1 B:HIS12 3.2 24.1 1.0 CD2 B:HIS12 3.3 23.6 1.0 CD2 B:HIS59 3.3 25.0 1.0 ND2 B:ASN57 3.3 22.1 1.0 OE2 B:GLU239 3.4 22.0 1.0 ND1 B:HIS59 4.1 24.9 1.0 O B:HOH635 4.1 27.7 1.0 O B:HOH645 4.1 27.1 1.0 ND1 B:HIS12 4.3 23.0 1.0 CG B:HIS59 4.3 25.6 1.0 CG B:HIS12 4.4 26.0 1.0 O B:HOH619 4.5 30.6 1.0 CG B:GLU239 4.5 22.6 1.0 CB B:ASN57 4.5 22.0 1.0 O B:ASN57 4.5 22.1 1.0 CE B:MET242 4.7 26.9 1.0 CA B:GLY188 4.8 23.8 1.0 CB B:GLU239 4.8 23.3 1.0

K.Sugimoto, M.Senda, D.Kasai, M.Fukuda, E.Masai, T.Senda. Molecular Mechanism of Strict Substrate Specificity of An Extradiol Dioxygenase, Desb, Derived From Sphingobium Sp. Syk-6 Plos One V. 9 92249 2014.
ISSN: ESSN 1932-6203
PubMed: 24657997
DOI: 10.1371/JOURNAL.PONE.0092249