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Iron in PDB 4ghc: Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution

Enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution

All present enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution:
1.13.11.15;

Protein crystallography data

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution, PDB code: 4ghc 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) 22.47 / 1.55
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.356, 151.736, 96.335, 90.00, 90.00, 90.00
R / Rfree (%) 11.7 / 14.8

Other elements in 4ghc:

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 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 Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution (pdb code 4ghc). 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 Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution, PDB code: 4ghc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4ghc

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Iron binding site 1 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 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 Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:10.0
occ:1.00
 OE1 A:GLU267 2.0 9.6 1.0
O A:HOH866 2.1 9.5 1.0
NE2 A:HIS214 2.2 8.2 1.0
O A:HOH865 2.2 11.7 1.0
NE2 A:HIS155 2.2 7.9 1.0
O A:HOH867 2.3 13.9 1.0
CE1 A:HIS214 3.1 8.8 1.0
CD A:GLU267 3.1 8.9 1.0
CE1 A:HIS155 3.1 8.5 1.0
CD2 A:HIS155 3.2 8.6 1.0
CD2 A:HIS214 3.2 8.4 1.0
OE2 A:GLU267 3.5 9.5 1.0
NE2 A:HIS200 3.8 10.6 1.0
ND1 A:HIS214 4.3 8.7 1.0
ND1 A:HIS155 4.3 8.7 1.0
ND2 A:ASN157 4.3 9.8 1.0
CG A:HIS214 4.3 8.6 1.0
CG A:HIS155 4.3 8.7 1.0
CG A:GLU267 4.4 8.5 1.0
O A:HOH868 4.4 17.1 1.0
CE1 A:HIS200 4.5 10.3 1.0
CE1 A:PHE257 4.6 8.8 1.0
CB A:ALA216 4.6 8.3 1.0
CB A:GLU267 4.6 8.5 1.0
CB A:ASN157 4.6 9.3 1.0
CZ A:PHE257 4.7 9.0 1.0
CD2 A:HIS200 4.9 10.8 1.0
CD1 A:TYR269 5.0 9.6 1.0

Iron binding site 2 out of 4 in 4ghc

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Iron binding site 2 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 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 Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:8.6
occ:1.00
 OE1 B:GLU267 2.0 8.9 1.0
O B:HOH904 2.1 8.1 1.0
NE2 B:HIS214 2.2 7.1 1.0
O B:HOH905 2.2 11.6 1.0
NE2 B:HIS155 2.2 7.1 1.0
O B:HOH906 2.3 11.6 1.0
CE1 B:HIS214 3.0 7.1 1.0
CE1 B:HIS155 3.1 7.6 1.0
CD B:GLU267 3.1 7.9 1.0
CD2 B:HIS214 3.2 7.4 1.0
CD2 B:HIS155 3.3 7.4 1.0
OE2 B:GLU267 3.6 8.4 1.0
NE2 B:HIS200 3.8 9.0 1.0
ND1 B:HIS214 4.2 6.9 1.0
ND1 B:HIS155 4.3 7.1 1.0
CG B:HIS214 4.3 7.2 1.0
ND2 B:ASN157 4.3 8.2 1.0
CG B:HIS155 4.4 7.1 1.0
CG B:GLU267 4.4 7.0 1.0
O B:HOH907 4.4 16.7 1.0
CE1 B:HIS200 4.4 9.0 1.0
CE1 B:PHE257 4.5 7.9 1.0
CB B:GLU267 4.6 7.0 1.0
CB B:ALA216 4.6 7.4 1.0
CZ B:PHE257 4.6 8.3 1.0
CB B:ASN157 4.7 8.2 1.0
CD2 B:HIS200 4.9 9.7 1.0

Iron binding site 3 out of 4 in 4ghc

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Iron binding site 3 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 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 Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:10.2
occ:1.00
 OE1 C:GLU267 2.1 10.1 1.0
O C:HOH829 2.2 9.2 1.0
NE2 C:HIS214 2.2 8.8 1.0
NE2 C:HIS155 2.2 8.7 1.0
O C:HOH830 2.2 13.2 1.0
O C:HOH831 2.3 13.4 1.0
CE1 C:HIS214 3.1 8.8 1.0
CE1 C:HIS155 3.1 8.6 1.0
CD C:GLU267 3.1 9.4 1.0
CD2 C:HIS214 3.2 8.5 1.0
CD2 C:HIS155 3.2 8.6 1.0
OE2 C:GLU267 3.5 10.6 1.0
NE2 C:HIS200 3.8 10.1 1.0
ND1 C:HIS214 4.2 8.4 1.0
ND1 C:HIS155 4.3 8.5 1.0
ND2 C:ASN157 4.3 10.4 1.0
CG C:HIS214 4.3 8.6 1.0
CG C:HIS155 4.3 8.6 1.0
CG C:GLU267 4.4 8.3 1.0
O C:HOH832 4.4 18.7 1.0
CE1 C:HIS200 4.5 10.2 1.0
CB C:GLU267 4.5 8.1 1.0
CE1 C:PHE257 4.6 8.5 1.0
CB C:ALA216 4.6 8.2 1.0
CB C:ASN157 4.6 9.5 1.0
CZ C:PHE257 4.6 8.7 1.0
CD2 C:HIS200 4.9 10.7 1.0
CG C:ASN157 5.0 10.3 1.0
CD1 C:TYR269 5.0 10.4 1.0

Iron binding site 4 out of 4 in 4ghc

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Iron binding site 4 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 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 Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.55 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:9.5
occ:1.00
 OE1 D:GLU267 2.0 9.6 1.0
O D:HOH822 2.1 9.0 1.0
NE2 D:HIS214 2.2 7.9 1.0
NE2 D:HIS155 2.2 7.9 1.0
O D:HOH824 2.2 12.4 1.0
O D:HOH823 2.3 13.2 1.0
CE1 D:HIS214 3.1 8.8 1.0
CE1 D:HIS155 3.1 8.1 1.0
CD D:GLU267 3.1 9.1 1.0
CD2 D:HIS214 3.2 7.8 1.0
CD2 D:HIS155 3.2 8.0 1.0
OE2 D:GLU267 3.5 10.1 1.0
NE2 D:HIS200 3.8 9.4 1.0
ND1 D:HIS214 4.2 8.6 1.0
ND1 D:HIS155 4.2 8.0 1.0
CG D:HIS214 4.3 8.3 1.0
CG D:HIS155 4.3 8.5 1.0
ND2 D:ASN157 4.4 10.1 1.0
CG D:GLU267 4.4 8.8 1.0
O D:HOH825 4.5 15.8 1.0
CE1 D:HIS200 4.5 9.6 1.0
CE1 D:PHE257 4.5 8.6 1.0
CB D:GLU267 4.6 8.4 1.0
CB D:ALA216 4.6 7.9 1.0
CZ D:PHE257 4.6 9.0 1.0
CB D:ASN157 4.6 9.2 1.0
CD2 D:HIS200 4.9 9.9 1.0

Reference:

E.G.Kovaleva, J.D.Lipscomb. Structural Basis For the Role of Tyrosine 257 of Homoprotocatechuate 2,3-Dioxygenase in Substrate and Oxygen Activation. Biochemistry V. 51 8755 2012.
ISSN: ISSN 0006-2960
PubMed: 23066739
DOI: 10.1021/BI301115C
Page generated: Tue Aug 5 10:38:37 2025

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