Iron in PDB 2wl3: Crystal Structure of Catechol 2,3-Dioxygenase

The structure of Crystal Structure of Catechol 2,3-Dioxygenase, PDB code: 2wl3 was solved by H.J.Cho, K.J.Kim, B.S.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.24 / 2.20
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	102.373, 102.373, 142.399, 90.00, 90.00, 90.00
R / Rfree (%)	15.526 / 17.816

The structure of Crystal Structure of Catechol 2,3-Dioxygenase also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Crystal Structure of Catechol 2,3-Dioxygenase (pdb code 2wl3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Catechol 2,3-Dioxygenase, PDB code: 2wl3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Catechol 2,3-Dioxygenase


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 Catechol 2,3-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1289 b:45.0 occ:1.00 NE2 A:HIS149 2.3 26.5 1.0 O A:HOH2046 2.3 21.9 1.0 OE1 A:GLU263 2.3 26.5 1.0 NE2 A:HIS212 2.5 25.7 1.0 O A:HOH2072 2.7 27.1 1.0 OH A:TYR253 3.1 33.2 1.0 CE1 A:HIS212 3.1 26.2 1.0 CE1 A:HIS149 3.2 25.0 1.0 CD A:GLU263 3.3 25.1 1.0 CD2 A:HIS149 3.3 23.4 1.0 OE2 A:GLU263 3.5 27.3 1.0 CD2 A:HIS212 3.6 26.4 1.0 CZ A:TYR253 4.1 35.2 1.0 CB A:MSE214 4.2 22.0 1.0 ND1 A:HIS212 4.3 27.5 1.0 ND1 A:HIS149 4.4 23.7 1.0 NE2 A:HIS197 4.4 24.3 1.0 CE1 A:TYR253 4.4 34.9 1.0 CG A:HIS149 4.5 21.9 1.0 CG A:HIS212 4.6 25.0 1.0 NE2 A:HIS244 4.6 41.8 1.0 O A:HOH2070 4.6 37.5 1.0 CG A:GLU263 4.7 23.8 1.0 CG A:MSE214 4.7 25.6 1.0 CE1 A:HIS197 4.7 25.6 1.0 CD2 A:HIS244 4.8 41.1 1.0 OD2 A:ASP247 4.9 37.5 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Catechol 2,3-Dioxygenase


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 Catechol 2,3-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1288 b:42.3 occ:1.00 NE2 B:HIS149 2.3 23.8 1.0 NE2 B:HIS212 2.4 21.9 1.0 OE1 B:GLU263 2.5 23.6 1.0 O B:HOH2059 2.8 22.1 1.0 CE1 B:HIS149 3.1 22.8 1.0 OH B:TYR253 3.1 27.6 1.0 CE1 B:HIS212 3.1 23.3 1.0 CD2 B:HIS149 3.4 21.7 1.0 CD B:GLU263 3.4 24.0 1.0 CD2 B:HIS212 3.5 22.6 1.0 OE2 B:GLU263 3.7 26.8 1.0 CZ B:TYR253 4.0 28.1 1.0 CE1 B:TYR253 4.3 28.2 1.0 ND1 B:HIS212 4.3 24.0 1.0 ND1 B:HIS149 4.3 22.7 1.0 O B:HOH2057 4.3 44.6 1.0 CE1 B:HIS197 4.4 20.1 1.0 CB B:MSE214 4.4 21.3 1.0 CG B:HIS149 4.5 20.4 1.0 CG B:HIS212 4.5 22.9 1.0 NE2 B:HIS244 4.5 31.2 1.0 CG B:MSE214 4.7 25.6 1.0 CD2 B:HIS244 4.8 30.3 1.0 CG B:GLU263 4.8 20.6 1.0 NE2 B:HIS197 4.8 21.5 1.0 OD2 B:ASP247 4.9 30.7 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Catechol 2,3-Dioxygenase


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 Catechol 2,3-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1286 b:51.9 occ:1.00 OE1 C:GLU263 2.2 30.7 1.0 NE2 C:HIS149 2.2 26.9 1.0 NE2 C:HIS212 2.3 31.5 1.0 O C:HOH2048 2.8 44.2 1.0 CE1 C:HIS212 2.8 31.7 1.0 CD C:GLU263 3.2 29.9 1.0 CD2 C:HIS149 3.2 25.9 1.0 CE1 C:HIS149 3.2 26.8 1.0 OH C:TYR253 3.2 38.7 1.0 OE2 C:GLU263 3.4 32.4 1.0 CD2 C:HIS212 3.5 30.4 1.0 O C:HOH2046 3.9 41.2 1.0 ND1 C:HIS212 4.0 31.6 1.0 CZ C:TYR253 4.1 40.0 1.0 CB C:MSE214 4.2 24.0 1.0 ND1 C:HIS149 4.3 26.8 1.0 CG C:HIS149 4.3 23.1 1.0 CE1 C:HIS197 4.3 28.8 1.0 CG C:HIS212 4.4 28.6 1.0 NE2 C:HIS197 4.5 29.5 1.0 CE1 C:TYR253 4.5 38.4 1.0 CG C:GLU263 4.6 26.6 1.0 CG C:MSE214 4.6 27.9 1.0 OD2 C:ASP247 4.7 45.2 1.0 NE2 C:HIS244 4.8 48.9 1.0 CD2 C:HIS244 4.9 48.5 1.0 CB C:GLU263 4.9 23.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Catechol 2,3-Dioxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Catechol 2,3-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1287 b:55.2 occ:1.00 OE1 D:GLU263 2.3 31.7 1.0 NE2 D:HIS149 2.3 26.6 1.0 NE2 D:HIS212 2.6 28.8 1.0 CD D:GLU263 3.2 29.9 1.0 CE1 D:HIS212 3.2 29.8 1.0 CE1 D:HIS149 3.2 24.6 1.0 OH D:TYR253 3.2 37.0 1.0 CD2 D:HIS149 3.3 23.6 1.0 OE2 D:GLU263 3.3 33.0 1.0 CD2 D:HIS212 3.7 28.5 1.0 O D:HOH2051 4.2 37.9 1.0 CZ D:TYR253 4.3 38.8 1.0 CB D:MSE214 4.3 22.7 1.0 ND1 D:HIS149 4.4 24.0 1.0 CE1 D:HIS244 4.4 41.1 1.0 ND1 D:HIS212 4.4 30.2 1.0 CE1 D:HIS197 4.4 30.6 1.0 CG D:HIS149 4.5 21.8 1.0 CG D:MSE214 4.6 26.4 1.0 NE2 D:HIS197 4.6 31.7 1.0 CG D:GLU263 4.6 27.1 1.0 ND1 D:HIS244 4.6 41.5 1.0 OD2 D:ASP247 4.7 44.0 1.0 CG D:HIS212 4.7 27.5 1.0 CE1 D:TYR253 4.8 37.5 1.0

H.J.Cho, K.Kim, S.Y.Sohn, H.Y.Cho, K.J.Kim, M.H.Kim, D.Kim, E.Kim, B.S.Kang. Substrate-Binding Mechanism of A Type I Extradiol Dioxygenase. J.Biol.Chem. V. 285 34643 2010.
ISSN: ISSN 0021-9258
PubMed: 20810655
DOI: 10.1074/JBC.M110.130310