Iron in PDB 2wl9: Crystal Structure of Catechol 2,3-Dioxygenase

The structure of Crystal Structure of Catechol 2,3-Dioxygenase, PDB code: 2wl9 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)	142.17 / 1.90
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	102.562, 102.562, 142.132, 90.00, 90.00, 90.00
R / Rfree (%)	15.055 / 17.602

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

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Crystal Structure of Catechol 2,3-Dioxygenase (pdb code 2wl9). 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: 2wl9:
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:Fe1301 b:33.9 occ:1.00 OE1 A:GLU263 2.2 18.2 1.0 NE2 A:HIS149 2.4 15.0 1.0 O A:HOH2078 2.5 25.7 1.0 NE2 A:HIS212 2.5 17.1 1.0 OH A:TYR253 2.9 17.8 1.0 CD A:GLU263 3.1 19.1 1.0 CE1 A:HIS212 3.2 18.9 1.0 CE1 A:HIS149 3.3 15.8 1.0 OE2 A:GLU263 3.3 18.6 1.0 CD2 A:HIS149 3.5 15.2 1.0 CD2 A:HIS212 3.6 18.5 1.0 CZ A:TYR253 3.8 18.9 1.0 CE1 A:TYR253 4.1 19.0 1.0 CB A:MET214 4.2 21.8 1.0 NE2 A:HIS197 4.4 12.8 1.0 ND1 A:HIS212 4.4 18.7 1.0 ND1 A:HIS149 4.5 15.3 1.0 CG A:GLU263 4.5 18.0 1.0 CG A:HIS212 4.6 17.9 1.0 CG A:HIS149 4.6 15.7 1.0 NE2 A:HIS244 4.7 21.7 1.0 CD2 A:HIS244 4.7 20.1 1.0 CG A:MET214 4.8 21.7 1.0 CE1 A:HIS197 4.8 14.9 1.0 CB A:GLU263 4.9 16.9 1.0 OD2 A:ASP247 4.9 21.9 1.0 CE2 A:TYR253 4.9 18.2 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:Fe1300 b:35.3 occ:1.00 OA2 B:MBD1301 2.2 31.5 1.0 OE1 B:GLU263 2.3 19.9 1.0 NE2 B:HIS212 2.5 16.2 1.0 O B:HOH2064 2.5 19.1 1.0 NE2 B:HIS149 2.6 20.2 1.0 OH B:TYR253 2.8 22.2 1.0 CD B:GLU263 3.2 18.2 1.0 CE1 B:HIS212 3.2 19.1 1.0 OE2 B:GLU263 3.3 19.3 1.0 CE1 B:HIS149 3.4 19.9 1.0 CA2 B:MBD1301 3.5 31.6 1.0 CD2 B:HIS212 3.6 17.9 1.0 CD2 B:HIS149 3.6 19.5 1.0 CZ B:TYR253 3.7 22.5 1.0 CE1 B:TYR253 4.0 22.5 1.0 OA1 B:MBD1301 4.3 31.2 1.0 CA1 B:MBD1301 4.4 31.4 1.0 ND1 B:HIS212 4.4 18.4 1.0 CA3 B:MBD1301 4.4 31.5 1.0 CB3 B:MBD1301 4.4 31.9 1.0 CE1 B:HIS197 4.5 22.3 1.0 CB B:MET214 4.5 16.9 1.0 CG B:GLU263 4.6 17.1 1.0 CG B:HIS212 4.6 18.7 1.0 ND1 B:HIS149 4.6 17.8 1.0 NE2 B:HIS244 4.7 23.8 1.0 NE2 B:HIS197 4.7 23.0 1.0 CG B:HIS149 4.7 19.3 1.0 CD2 B:HIS244 4.8 22.4 1.0 CG B:MET214 4.8 16.7 1.0 CE2 B:TYR253 4.9 22.0 1.0 CB B:GLU263 5.0 17.7 1.0 OD2 B:ASP247 5.0 22.2 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:Fe1300 b:36.2 occ:1.00 OE1 C:GLU263 2.3 21.2 1.0 NE2 C:HIS149 2.3 19.7 1.0 NE2 C:HIS212 2.4 20.3 1.0 OH C:TYR253 2.8 22.6 1.0 CE1 C:HIS212 3.1 20.2 1.0 CE1 C:HIS149 3.1 19.8 1.0 CD C:GLU263 3.2 19.9 1.0 CD2 C:HIS149 3.5 20.2 1.0 OE2 C:GLU263 3.5 19.2 1.0 CD2 C:HIS212 3.5 20.2 1.0 CZ C:TYR253 3.8 22.2 1.0 CE1 C:TYR253 4.1 21.9 1.0 ND1 C:HIS212 4.2 20.6 1.0 CE1 C:HIS197 4.3 17.3 1.0 ND1 C:HIS149 4.3 19.6 1.0 O C:HOH2067 4.4 34.9 1.0 CB C:MET214 4.5 19.5 1.0 CG C:HIS212 4.5 20.5 1.0 CG C:HIS149 4.5 19.2 1.0 NE2 C:HIS244 4.6 25.0 1.0 NE2 C:HIS197 4.6 19.8 1.0 CG C:GLU263 4.6 19.6 1.0 CG C:MET214 4.7 22.2 1.0 CD2 C:HIS244 4.8 23.2 1.0 OD2 C:ASP247 4.9 22.6 1.0 CE2 C:TYR253 5.0 21.2 1.0 CB C:GLU263 5.0 18.8 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:Fe1301 b:39.0 occ:1.00 OE1 D:GLU263 2.3 20.5 1.0 O D:HOH2062 2.4 26.6 1.0 NE2 D:HIS212 2.5 20.3 1.0 NE2 D:HIS149 2.5 18.5 1.0 OA2 D:MBD1303 2.6 37.0 1.0 OH D:TYR253 2.9 21.8 1.0 CE1 D:HIS212 3.1 19.5 1.0 CD D:GLU263 3.1 20.0 1.0 OE2 D:GLU263 3.3 21.4 1.0 CE1 D:HIS149 3.4 19.9 1.0 CD2 D:HIS149 3.5 18.9 1.0 CD2 D:HIS212 3.5 20.1 1.0 CA2 D:MBD1303 3.9 34.7 1.0 CZ D:TYR253 3.9 22.5 1.0 CE1 D:TYR253 4.2 21.9 1.0 ND1 D:HIS212 4.3 19.6 1.0 CB D:MET214 4.3 21.8 1.0 CE1 D:HIS197 4.4 21.9 1.0 CG D:HIS212 4.5 19.8 1.0 OA1 D:MBD1303 4.5 36.1 1.0 ND1 D:HIS149 4.5 19.0 1.0 CG D:GLU263 4.6 18.9 1.0 CG D:HIS149 4.6 19.2 1.0 CB3 D:MBD1303 4.6 35.0 1.0 CD2 D:HIS244 4.7 24.4 1.0 NE2 D:HIS197 4.7 23.9 1.0 CG D:MET214 4.7 21.7 1.0 NE2 D:HIS244 4.7 25.7 1.0 CA3 D:MBD1303 4.7 34.8 1.0 CA1 D:MBD1303 4.7 35.2 1.0 OD2 D:ASP247 4.9 21.8 1.0 CB D:GLU263 5.0 18.1 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