Iron in PDB 3wrb: Crystal Structure of the Anaerobic H124F Desb-Gallate Complex

All present enzymatic activity of Crystal Structure of the Anaerobic H124F Desb-Gallate Complex:
1.13.11.58;

The structure of Crystal Structure of the Anaerobic H124F Desb-Gallate Complex, PDB code: 3wrb 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)	58.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.349, 65.519, 117.875, 90.00, 96.93, 90.00
R / Rfree (%)	19.2 / 24.3

The binding sites of Iron atom in the Crystal Structure of the Anaerobic H124F Desb-Gallate Complex (pdb code 3wrb). 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 Anaerobic H124F Desb-Gallate Complex, PDB code: 3wrb:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of the Anaerobic H124F Desb-Gallate Complex


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 Anaerobic H124F Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.8 occ:1.00 O A:HOH644 2.1 16.3 1.0 OE1 A:GLU239 2.1 22.6 1.0 NE2 A:HIS59 2.2 16.8 1.0 NE2 A:HIS12 2.2 21.8 1.0 OD1 A:ASN57 2.3 18.1 1.0 O A:HOH638 2.5 27.1 1.0 CE1 A:HIS59 3.0 17.1 1.0 CD A:GLU239 3.0 22.0 1.0 CE1 A:HIS12 3.2 22.7 1.0 CG A:ASN57 3.2 17.1 1.0 CD2 A:HIS12 3.3 22.1 1.0 OE2 A:GLU239 3.3 21.3 1.0 CD2 A:HIS59 3.3 17.2 1.0 ND2 A:ASN57 3.5 15.6 1.0 O B:HOH779 3.9 23.9 1.0 ND1 A:HIS59 4.2 17.4 1.0 ND1 A:HIS12 4.3 22.5 1.0 CG A:HIS59 4.4 15.4 1.0 CG A:HIS12 4.4 23.8 1.0 CG A:GLU239 4.4 20.3 1.0 O A:ASN57 4.6 17.2 1.0 CB A:ASN57 4.6 16.8 1.0 O B:HOH707 4.7 36.3 1.0 O A:HOH856 4.7 20.7 1.0 CE A:MET242 4.8 19.9 1.0 CB A:GLU239 4.8 19.9 1.0 CA A:GLY188 4.9 19.3 1.0 OAE B:GDE502 5.0 34.6 1.0

Iron binding site 2 out of 2 in the Crystal Structure of the Anaerobic H124F Desb-Gallate Complex


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 Anaerobic H124F Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:13.2 occ:1.00 OE1 B:GLU239 2.1 13.7 1.0 O B:HOH602 2.2 17.0 1.0 NE2 B:HIS12 2.2 12.7 1.0 NE2 B:HIS59 2.2 11.8 1.0 OD1 B:ASN57 2.3 9.6 1.0 O B:HOH663 2.3 14.5 1.0 CE1 B:HIS59 3.1 10.8 1.0 CD B:GLU239 3.1 13.4 1.0 CE1 B:HIS12 3.1 13.1 1.0 CG B:ASN57 3.2 11.3 1.0 CD2 B:HIS12 3.3 11.0 1.0 CD2 B:HIS59 3.3 10.4 1.0 OE2 B:GLU239 3.3 12.0 1.0 ND2 B:ASN57 3.4 10.5 1.0 O A:HOH650 4.0 18.8 1.0 ND1 B:HIS59 4.2 9.8 1.0 ND1 B:HIS12 4.3 10.6 1.0 CG B:HIS59 4.3 10.6 1.0 CG B:HIS12 4.4 12.2 1.0 O B:HOH628 4.4 16.7 1.0 CG B:GLU239 4.5 12.1 1.0 O B:ASN57 4.6 13.4 1.0 CB B:ASN57 4.6 11.5 1.0 CE B:MET242 4.8 12.0 1.0 O A:HOH747 4.9 22.4 1.0 CB B:GLU239 4.9 12.1 1.0 CA B:GLY188 4.9 12.2 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