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Iron in PDB 4ghg: Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.50 Ang Resolution

Enzymatic activity of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.50 Ang Resolution

All present enzymatic activity of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.50 Ang Resolution:
1.13.11.15;

Protein crystallography data

The structure of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.50 Ang Resolution, PDB code: 4ghg 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) 45.86 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.540, 150.785, 96.276, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 16.1

Other elements in 4ghg:

The structure of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.50 Ang Resolution also contains other interesting chemical elements:

Chlorine (Cl) 3 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 Hpca at 1.50 Ang Resolution (pdb code 4ghg). 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 Hpca at 1.50 Ang Resolution, PDB code: 4ghg:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4ghg

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Iron binding site 1 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.50 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 Hpca at 1.50 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:16.6
occ:1.00
 OE1 A:GLU267 2.1 15.6 1.0
O A:HOH790 2.1 16.8 1.0
O A:HOH789 2.1 14.9 1.0
NE2 A:HIS214 2.2 14.7 1.0
NE2 A:HIS155 2.2 14.9 1.0
O A:HOH788 2.2 16.5 1.0
CE1 A:HIS214 3.1 14.3 1.0
CE1 A:HIS155 3.1 15.8 1.0
CD A:GLU267 3.1 16.0 1.0
CD2 A:HIS155 3.2 15.0 1.0
CD2 A:HIS214 3.2 15.2 1.0
OE2 A:GLU267 3.6 14.9 1.0
NE2 A:HIS200 3.8 17.2 1.0
OH A:TYR257 4.2 15.1 1.0
ND1 A:HIS155 4.2 15.5 1.0
ND1 A:HIS214 4.3 15.8 1.0
CG A:HIS155 4.3 16.0 1.0
CG A:HIS214 4.3 15.3 1.0
O A:HOH808 4.3 20.4 1.0
ND2 A:ASN157 4.4 16.8 1.0
CG A:GLU267 4.4 14.9 1.0
CE1 A:HIS200 4.5 15.1 1.0
CB A:GLU267 4.6 15.3 1.0
CB A:ASN157 4.6 15.1 1.0
CB A:ALA216 4.6 15.7 1.0
CE1 A:TYR257 4.6 15.6 1.0
CZ A:TYR257 4.9 13.8 1.0
CD2 A:HIS200 4.9 17.3 1.0

Iron binding site 2 out of 4 in 4ghg

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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 Hpca at 1.50 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 Hpca at 1.50 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:15.6
occ:1.00
 OE1 B:GLU267 2.0 15.3 1.0
O B:HOH827 2.2 15.8 1.0
O B:HOH828 2.2 17.1 1.0
O B:HOH826 2.2 14.2 1.0
NE2 B:HIS214 2.2 14.2 1.0
NE2 B:HIS155 2.2 12.6 1.0
CE1 B:HIS214 3.1 14.4 1.0
CD B:GLU267 3.1 14.4 1.0
CE1 B:HIS155 3.1 13.5 1.0
CD2 B:HIS155 3.2 13.3 1.0
CD2 B:HIS214 3.2 13.5 1.0
OE2 B:GLU267 3.6 15.6 1.0
NE2 B:HIS200 3.9 15.0 1.0
OH B:TYR257 4.2 14.3 1.0
ND1 B:HIS214 4.2 14.9 1.0
ND1 B:HIS155 4.3 13.1 1.0
CG B:HIS214 4.3 14.2 1.0
CG B:HIS155 4.3 14.1 1.0
CG B:GLU267 4.4 13.7 1.0
O B:HOH829 4.4 18.8 1.0
ND2 B:ASN157 4.4 15.8 1.0
CB B:GLU267 4.5 14.1 1.0
CE1 B:TYR257 4.5 13.4 1.0
CE1 B:HIS200 4.5 14.3 1.0
CB B:ALA216 4.6 14.0 1.0
CB B:ASN157 4.6 15.7 1.0
CZ B:TYR257 4.8 13.6 1.0
CD2 B:HIS200 4.9 15.9 1.0
CG B:ASN157 5.0 15.8 1.0

Iron binding site 3 out of 4 in 4ghg

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Iron binding site 3 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.50 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 Hpca at 1.50 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:14.6
occ:1.00
 OE1 C:GLU267 2.0 13.4 1.0
O3 C:DHY403 2.1 14.0 1.0
NE2 C:HIS214 2.2 12.0 1.0
NE2 C:HIS155 2.2 11.9 1.0
O4 C:DHY403 2.2 16.2 1.0
O C:HOH774 2.4 8.1 1.0
C3 C:DHY403 2.9 16.0 1.0
C4 C:DHY403 2.9 16.2 1.0
CE1 C:HIS214 3.0 13.5 1.0
CD C:GLU267 3.1 13.5 1.0
CE1 C:HIS155 3.1 12.8 1.0
CD2 C:HIS155 3.2 13.1 1.0
CD2 C:HIS214 3.2 12.9 1.0
OE2 C:GLU267 3.5 15.5 1.0
NE2 C:HIS200 3.8 16.1 1.0
OH C:TYR257 4.2 13.8 1.0
ND1 C:HIS214 4.2 13.2 1.0
C2 C:DHY403 4.2 17.9 1.0
ND1 C:HIS155 4.3 12.3 1.0
C5 C:DHY403 4.3 16.2 1.0
CG C:HIS214 4.3 12.7 1.0
CG C:HIS155 4.3 12.4 1.0
CG C:GLU267 4.3 12.9 1.0
CB C:GLU267 4.5 11.8 1.0
CB C:ALA216 4.6 11.4 1.0
CE1 C:TYR257 4.6 12.2 1.0
CD2 C:HIS200 4.7 16.8 1.0
CE1 C:HIS200 4.7 16.6 1.0
CB C:ASN157 4.7 13.9 1.0
ND2 C:ASN157 4.7 16.3 1.0
CZ C:TYR257 4.9 12.4 1.0

Iron binding site 4 out of 4 in 4ghg

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Iron binding site 4 out of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.50 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 Hpca at 1.50 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 12.9 1.0
NE2 D:HIS214 2.1 11.7 1.0
O D:HOH861 2.2 15.2 1.0
O D:HOH858 2.2 14.4 1.0
NE2 D:HIS155 2.2 11.4 1.0
O D:HOH791 2.2 10.8 1.0
CE1 D:HIS214 3.1 12.6 1.0
CD D:GLU267 3.1 13.1 1.0
CE1 D:HIS155 3.1 12.3 1.0
CD2 D:HIS214 3.2 11.6 1.0
CD2 D:HIS155 3.2 12.5 1.0
OE2 D:GLU267 3.6 12.9 1.0
NE2 D:HIS200 3.8 14.4 1.0
OH D:TYR257 4.2 13.1 1.0
ND1 D:HIS214 4.2 13.1 1.0
ND1 D:HIS155 4.3 12.6 1.0
CG D:HIS214 4.3 13.0 1.0
CG D:HIS155 4.4 11.7 1.0
CG D:GLU267 4.4 12.3 1.0
O D:HOH860 4.4 18.7 1.0
ND2 D:ASN157 4.5 15.2 1.0
CE1 D:HIS200 4.5 13.5 1.0
CB D:GLU267 4.5 12.6 1.0
CE1 D:TYR257 4.6 12.4 1.0
CB D:ASN157 4.6 13.4 1.0
CB D:ALA216 4.6 11.5 1.0
CZ D:TYR257 4.8 12.8 1.0
CD2 D:HIS200 4.9 14.1 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 10:40:01 2025

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