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Iron in PDB 4z6z: Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution

Protein crystallography data

The structure of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution, PDB code: 4z6z was solved by E.G.Kovaleva, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.51 / 1.52
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.399, 151.247, 96.158, 90.00, 90.00, 90.00
R / Rfree (%) 12.1 / 16.1

Other elements in 4z6z:

The structure of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution (pdb code 4z6z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution, PDB code: 4z6z:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4z6z

Go back to Iron Binding Sites List in 4z6z
Iron binding site 1 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:16.8
occ:1.00
 OE1 A:GLU267 2.1 15.2 1.0
O A:HOH728 2.1 21.8 1.0
O A:HOH501 2.2 17.3 1.0
NE2 A:HIS214 2.2 16.6 1.0
NE2 A:HIS155 2.2 15.2 1.0
O A:HOH635 2.3 17.0 1.0
CE1 A:HIS214 3.1 16.2 1.0
CE1 A:HIS155 3.1 16.0 1.0
CD A:GLU267 3.1 16.4 1.0
CD2 A:HIS155 3.2 16.2 1.0
CD2 A:HIS214 3.3 15.9 1.0
OE2 A:GLU267 3.5 15.5 1.0
NE2 A:HIS200 3.8 20.1 1.0
OH A:TYR257 4.1 15.5 1.0
ND1 A:HIS214 4.2 16.9 1.0
ND1 A:HIS155 4.2 15.3 1.0
CG A:HIS155 4.3 15.9 1.0
CG A:HIS214 4.3 16.3 1.0
O A:HOH765 4.4 23.4 1.0
CG A:GLU267 4.4 14.5 1.0
CE1 A:HIS200 4.5 20.0 1.0
CB A:GLU267 4.5 13.6 1.0
ND2 A:ASN157 4.6 20.5 1.0
CB A:ALA216 4.6 17.3 1.0
CE1 A:TYR257 4.6 15.4 1.0
CB A:ASN157 4.7 17.3 1.0
CZ A:TYR257 4.8 15.5 1.0
CD2 A:HIS200 4.9 20.0 1.0
CD1 A:TYR269 5.0 18.7 1.0

Iron binding site 2 out of 4 in 4z6z

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Iron binding site 2 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:14.9
occ:1.00
 OE1 B:GLU267 2.0 13.7 1.0
O B:HOH624 2.1 15.7 1.0
O B:HOH507 2.2 16.6 1.0
O B:HOH709 2.2 18.4 1.0
NE2 B:HIS214 2.2 13.2 1.0
NE2 B:HIS155 2.2 13.5 1.0
CE1 B:HIS214 3.0 13.1 1.0
CD B:GLU267 3.1 13.8 1.0
CE1 B:HIS155 3.1 13.3 1.0
CD2 B:HIS155 3.2 13.8 1.0
CD2 B:HIS214 3.3 12.7 1.0
O B:HOH803 3.5 30.9 1.0
OE2 B:GLU267 3.6 15.1 1.0
NE2 B:HIS200 3.8 17.4 1.0
OH B:TYR257 4.1 15.2 1.0
ND1 B:HIS214 4.2 14.1 1.0
ND1 B:HIS155 4.2 13.2 1.0
CG B:HIS214 4.3 13.6 1.0
CG B:HIS155 4.3 13.2 1.0
CG B:GLU267 4.4 12.6 1.0
O B:HOH790 4.4 23.4 1.0
ND2 B:ASN157 4.4 17.7 1.0
CE1 B:HIS200 4.5 16.5 1.0
CB B:GLU267 4.5 12.3 1.0
CE1 B:TYR257 4.5 13.7 1.0
CB B:ALA216 4.6 13.7 1.0
CB B:ASN157 4.7 13.8 1.0
CZ B:TYR257 4.8 13.0 1.0
CD2 B:HIS200 4.9 16.9 1.0

Iron binding site 3 out of 4 in 4z6z

Go back to Iron Binding Sites List in 4z6z
Iron binding site 3 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:15.1
occ:1.00
 OE1 C:GLU267 2.0 13.7 1.0
O7 C:4SX403 2.1 14.0 0.8
O8 C:4SX403 2.1 13.1 0.8
NE2 C:HIS214 2.2 12.5 1.0
NE2 C:HIS155 2.2 13.7 1.0
O C:HOH644 2.4 13.3 1.0
C2 C:4SX403 2.8 16.7 0.8
C1 C:4SX403 2.8 16.0 0.8
CE1 C:HIS214 3.0 13.3 1.0
CD C:GLU267 3.1 14.4 1.0
CE1 C:HIS155 3.1 12.8 1.0
CD2 C:HIS155 3.2 12.6 1.0
CD2 C:HIS214 3.3 13.4 1.0
OE2 C:GLU267 3.5 15.1 1.0
NE2 C:HIS200 3.8 18.9 1.0
OH C:TYR257 4.1 14.6 1.0
ND1 C:HIS214 4.2 13.9 1.0
C3 C:4SX403 4.2 19.3 0.8
C6 C:4SX403 4.2 12.0 0.8
ND1 C:HIS155 4.2 12.1 1.0
CG C:HIS214 4.3 13.8 1.0
CG C:HIS155 4.3 12.5 1.0
CG C:GLU267 4.4 13.7 1.0
CE1 C:HIS200 4.5 17.6 1.0
CB C:GLU267 4.5 11.6 1.0
CB C:ALA216 4.6 12.3 1.0
CE1 C:TYR257 4.6 12.3 1.0
ND2 C:ASN157 4.6 18.5 1.0
CB C:ASN157 4.7 14.0 1.0
CZ C:TYR257 4.8 12.2 1.0
CD1 C:TYR269 4.9 14.4 1.0
CD2 C:HIS200 4.9 18.0 1.0

Iron binding site 4 out of 4 in 4z6z

Go back to Iron Binding Sites List in 4z6z
Iron binding site 4 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.52 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:14.0
occ:1.00
 OE1 D:GLU267 2.0 13.4 1.0
O8 D:4SX403 2.1 10.0 0.7
O7 D:4SX403 2.1 15.7 0.7
O D:HOH643 2.2 12.4 0.3
NE2 D:HIS214 2.2 12.6 1.0
NE2 D:HIS155 2.2 11.7 1.0
O D:HOH688 2.3 14.2 1.0
C2 D:4SX403 2.9 17.6 0.7
C1 D:4SX403 2.9 16.9 0.7
CE1 D:HIS155 3.1 13.2 1.0
CE1 D:HIS214 3.1 12.3 1.0
CD D:GLU267 3.1 12.6 1.0
CD2 D:HIS214 3.2 12.3 1.0
CD2 D:HIS155 3.3 11.5 1.0
OE2 D:GLU267 3.5 13.4 1.0
NE2 D:HIS200 3.8 16.8 1.0
OH D:TYR257 4.1 13.7 1.0
ND1 D:HIS214 4.2 12.4 1.0
ND1 D:HIS155 4.2 13.4 1.0
C3 D:4SX403 4.2 18.9 0.7
C6 D:4SX403 4.3 16.3 0.7
CG D:HIS214 4.3 11.6 1.0
CG D:HIS155 4.3 11.9 1.0
CG D:GLU267 4.3 12.6 1.0
O D:HOH770 4.4 14.5 0.3
CE1 D:HIS200 4.5 18.5 1.0
CB D:GLU267 4.5 11.3 1.0
CE1 D:TYR257 4.5 12.1 1.0
CB D:ALA216 4.6 12.8 1.0
ND2 D:ASN157 4.7 17.9 1.0
CB D:ASN157 4.7 13.5 1.0
CZ D:TYR257 4.8 13.1 1.0
CD2 D:HIS200 4.9 17.8 1.0
CD2 D:TYR269 4.9 13.6 1.0

Reference:

E.G.Kovaleva, M.S.Rogers, J.D.Lipscomb. Structural Basis For Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200. Biochemistry V. 54 5329 2015.
ISSN: ISSN 0006-2960
PubMed: 26267790
DOI: 10.1021/ACS.BIOCHEM.5B00709
Page generated: Mon Aug 5 18:05:53 2024

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