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

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

The structure of Crystal Structure of the Anaerobic Desb-Gallate Complex, PDB code: 3wku 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)	20.00 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.435, 60.765, 117.986, 90.00, 98.58, 90.00
R / Rfree (%)	23.3 / 31.4

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

Iron binding site 1 out of 3 in the Crystal Structure of the Anaerobic 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 Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:0.5 occ:1.00 NE2 A:HIS59 2.1 61.8 1.0 OE1 A:GLU239 2.3 73.8 1.0 NE2 A:HIS12 2.5 90.0 1.0 OE2 A:GLU239 2.7 73.4 1.0 CD A:GLU239 2.9 74.2 1.0 OD1 A:ASN57 3.0 67.7 1.0 CD2 A:HIS59 3.0 61.5 1.0 CE1 A:HIS59 3.2 61.8 1.0 CD2 A:HIS12 3.3 89.7 1.0 CE1 A:HIS12 3.4 90.2 1.0 CG A:ASN57 4.0 66.1 1.0 NE2 A:HIS124 4.1 72.2 1.0 CG A:HIS59 4.2 60.9 1.0 ND1 A:HIS59 4.3 61.3 1.0 CG A:GLU239 4.3 75.2 1.0 CG A:HIS12 4.4 89.4 1.0 ND2 A:ASN57 4.4 66.2 1.0 ND1 A:HIS12 4.5 90.2 1.0 CE1 A:HIS124 4.8 73.0 1.0 CZ B:PHE374 4.9 60.0 1.0 CB A:GLU239 5.0 75.4 1.0 NE2 A:HIS192 5.0 77.6 1.0

Iron binding site 2 out of 3 in the Crystal Structure of the Anaerobic 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 Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:14.6 occ:0.50 FE B:FE501 0.0 14.6 0.5 FE B:FE501 1.8 23.6 0.5 OE1 B:GLU239 1.8 34.7 1.0 OD1 B:ASN57 1.9 31.2 1.0 O B:HOH602 2.0 28.8 1.0 NE2 B:HIS12 2.2 26.5 1.0 NE2 B:HIS59 2.2 33.5 1.0 CG B:ASN57 2.7 31.0 1.0 CE1 B:HIS59 2.8 34.2 1.0 CD B:GLU239 2.8 34.4 1.0 ND2 B:ASN57 3.0 29.1 1.0 CE1 B:HIS12 3.0 26.5 1.0 O B:HOH601 3.1 31.6 1.0 OE2 B:GLU239 3.1 31.3 1.0 CD2 B:HIS12 3.3 28.3 1.0 CD2 B:HIS59 3.4 34.1 1.0 OAE A:GDE502 3.9 30.4 1.0 ND1 B:HIS59 4.0 34.9 1.0 CG B:GLU239 4.1 36.6 1.0 CB B:ASN57 4.2 30.9 1.0 ND1 B:HIS12 4.2 26.5 1.0 CG B:HIS59 4.3 33.9 1.0 CG B:HIS12 4.4 27.0 1.0 O B:ASN57 4.4 31.3 1.0 CB B:GLU239 4.5 38.3 1.0 OAD A:GDE502 4.5 31.7 1.0 CE B:MET242 4.9 32.4 1.0 CA B:ASN57 4.9 31.5 1.0 C B:ASN57 4.9 31.1 1.0 CA B:GLY188 5.0 29.1 1.0 N B:ASN57 5.0 32.2 1.0

Iron binding site 3 out of 3 in the Crystal Structure of the Anaerobic Desb-Gallate Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Anaerobic Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:23.6 occ:0.50 FE B:FE501 0.0 23.6 0.5 FE B:FE501 1.8 14.6 0.5 O B:HOH601 2.0 31.6 1.0 NE2 B:HIS59 2.4 33.5 1.0 OAE A:GDE502 2.4 30.4 1.0 NE2 B:HIS12 2.6 26.5 1.0 O B:HOH602 2.6 28.8 1.0 OE1 B:GLU239 2.6 34.7 1.0 OE2 B:GLU239 2.7 31.3 1.0 OAD A:GDE502 2.8 31.7 1.0 CD2 B:HIS12 3.0 28.3 1.0 CD B:GLU239 3.0 34.4 1.0 CE1 B:HIS59 3.2 34.2 1.0 CD2 B:HIS59 3.4 34.1 1.0 CAL A:GDE502 3.4 28.8 1.0 CAJ A:GDE502 3.6 29.8 1.0 OD1 B:ASN57 3.6 31.2 1.0 CE1 B:HIS12 3.8 26.5 1.0 CG B:HIS12 4.3 27.0 1.0 ND1 B:HIS59 4.4 34.9 1.0 CG B:ASN57 4.4 31.0 1.0 ND2 B:ASN57 4.4 29.1 1.0 NE2 B:HIS124 4.5 33.2 1.0 NE2 B:HIS192 4.5 34.2 1.0 CG B:HIS59 4.5 33.9 1.0 CG B:GLU239 4.6 36.6 1.0 ND1 B:HIS12 4.7 26.5 1.0 CAI A:GDE502 4.7 28.4 1.0 CE1 B:HIS192 4.8 33.1 1.0 O B:HIS12 4.9 28.9 1.0 CAG A:GDE502 4.9 29.6 1.0 CD2 B:HIS124 5.0 33.4 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