Iron in PDB 3wr8: Crystal Structure of Desb From Sphingobium Sp. Strain Syk-6

All present enzymatic activity of Crystal Structure of Desb From Sphingobium Sp. Strain Syk-6:
1.13.11.58;

The structure of Crystal Structure of Desb From Sphingobium Sp. Strain Syk-6, PDB code: 3wr8 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)	56.63 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.420, 64.916, 116.247, 90.00, 94.83, 90.00
R / Rfree (%)	19.1 / 23.9

The binding sites of Iron atom in the Crystal Structure of Desb From Sphingobium Sp. Strain Syk-6 (pdb code 3wr8). 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 Desb From Sphingobium Sp. Strain Syk-6, PDB code: 3wr8:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Desb From Sphingobium Sp. Strain Syk-6


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 Desb From Sphingobium Sp. Strain Syk-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:23.0 occ:1.00 OE1 A:GLU239 2.1 19.2 1.0 O A:HOH702 2.1 20.1 1.0 NE2 A:HIS12 2.2 19.8 1.0 OD1 A:ASN57 2.3 20.4 1.0 NE2 A:HIS59 2.4 19.0 1.0 O A:HOH689 2.4 24.1 1.0 CD A:GLU239 3.0 19.2 1.0 CE1 A:HIS12 3.0 20.5 1.0 CE1 A:HIS59 3.1 19.6 1.0 CG A:ASN57 3.2 16.8 1.0 CD2 A:HIS12 3.3 20.7 1.0 OE2 A:GLU239 3.3 21.7 1.0 CD2 A:HIS59 3.4 18.8 1.0 ND2 A:ASN57 3.5 17.1 1.0 O A:HOH617 4.1 17.9 1.0 ND1 A:HIS12 4.2 21.3 1.0 ND1 A:HIS59 4.3 21.2 1.0 CG A:HIS12 4.4 21.5 1.0 CG A:GLU239 4.4 18.2 1.0 CG A:HIS59 4.4 18.4 1.0 O A:ASN57 4.6 16.0 1.0 CB A:ASN57 4.6 15.8 1.0 O A:HOH680 4.6 27.6 1.0 CB A:GLU239 4.7 16.8 1.0 CA A:GLY188 4.8 16.1 1.0 CE A:MET242 4.8 17.6 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Desb From Sphingobium Sp. Strain Syk-6


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 Desb From Sphingobium Sp. Strain Syk-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:18.9 occ:1.00 OE1 B:GLU239 2.1 18.9 1.0 NE2 B:HIS12 2.2 18.7 1.0 O B:HOH703 2.2 19.3 1.0 NE2 B:HIS59 2.3 19.5 1.0 OD1 B:ASN57 2.3 13.9 1.0 O B:HOH673 2.3 19.4 1.0 CD B:GLU239 3.0 18.6 1.0 CE1 B:HIS59 3.2 20.2 1.0 CE1 B:HIS12 3.2 17.3 1.0 CD2 B:HIS12 3.2 18.4 1.0 CG B:ASN57 3.2 13.1 1.0 OE2 B:GLU239 3.2 19.1 1.0 CD2 B:HIS59 3.3 17.3 1.0 ND2 B:ASN57 3.4 14.1 1.0 ND1 B:HIS12 4.3 18.2 1.0 ND1 B:HIS59 4.3 18.9 1.0 CG B:HIS12 4.3 18.9 1.0 CG B:GLU239 4.4 18.9 1.0 CG B:HIS59 4.4 18.1 1.0 O B:HOH621 4.5 25.0 1.0 CB B:ASN57 4.6 14.2 1.0 O B:ASN57 4.6 15.5 1.0 CE B:MET242 4.8 11.1 1.0 CB B:GLU239 4.8 17.8 1.0 CA B:GLY188 4.8 14.9 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