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

Protein crystallography data

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

Other elements in 2wl9:

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

Magnesium (Mg) 1 atom

Iron Binding Sites:

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 2wl9

Go back to Iron Binding Sites List in 2wl9
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 2wl9

Go back to Iron Binding Sites List in 2wl9
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 2wl9

Go back to Iron Binding Sites List in 2wl9
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 2wl9

Go back to Iron Binding Sites List in 2wl9
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

Reference:

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
Page generated: Sun Aug 4 04:04:45 2024

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