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Iron in PDB 4ghh: Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.55 Ang Resolution

Enzymatic activity of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.55 Ang Resolution

All present enzymatic activity of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.55 Ang Resolution:
1.13.11.15;

Protein crystallography data

The structure of Structure of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.55 Ang Resolution, PDB code: 4ghh 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) 47.83 / 1.55
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.246, 150.509, 96.243, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 16.5

Other elements in 4ghh:

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

Iron binding site 1 out of 4 in 4ghh

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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 4-Nitrocatechol 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 Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.55 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:19.2
occ:1.00
 OE1 A:GLU267 2.1 17.3 1.0
O A:HOH873 2.1 23.6 1.0
NE2 A:HIS214 2.2 18.0 1.0
NE2 A:HIS155 2.2 17.8 1.0
O A:HOH872 2.2 19.9 1.0
O A:HOH859 2.4 15.9 1.0
CE1 A:HIS214 3.0 16.4 1.0
CE1 A:HIS155 3.1 17.4 1.0
CD A:GLU267 3.1 17.4 1.0
CD2 A:HIS155 3.2 18.7 1.0
CD2 A:HIS214 3.2 17.2 1.0
OE2 A:GLU267 3.6 17.1 1.0
NE2 A:HIS200 3.8 22.8 1.0
OH A:TYR257 4.2 17.8 1.0
ND1 A:HIS214 4.2 18.5 1.0
ND1 A:HIS155 4.2 17.9 1.0
O A:HOH874 4.2 25.4 1.0
CG A:HIS155 4.3 19.2 1.0
CG A:HIS214 4.3 17.7 1.0
CG A:GLU267 4.4 16.5 1.0
CE1 A:HIS200 4.5 20.4 1.0
CB A:ALA216 4.5 18.6 1.0
CB A:GLU267 4.5 16.6 1.0
ND2 A:ASN157 4.6 22.1 1.0
CE1 A:TYR257 4.6 15.8 1.0
CB A:ASN157 4.7 18.7 1.0
CD2 A:HIS200 4.8 20.9 1.0
CZ A:TYR257 4.9 17.0 1.0
CD1 A:TYR269 4.9 18.7 1.0
CE1 A:TYR269 5.0 17.7 1.0

Iron binding site 2 out of 4 in 4ghh

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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-Nitrocatechol 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 Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.55 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:18.0
occ:1.00
 OE1 B:GLU267 2.0 17.5 1.0
O B:HOH841 2.1 18.1 1.0
NE2 B:HIS214 2.2 15.1 1.0
NE2 B:HIS155 2.2 14.2 1.0
O B:HOH843 2.2 21.6 1.0
O B:HOH842 2.2 15.2 1.0
CD B:GLU267 3.1 15.8 1.0
CE1 B:HIS214 3.1 15.6 1.0
CE1 B:HIS155 3.1 15.6 1.0
CD2 B:HIS155 3.2 15.6 1.0
CD2 B:HIS214 3.2 15.2 1.0
OE2 B:GLU267 3.6 18.0 1.0
NE2 B:HIS200 3.8 19.0 1.0
OH B:TYR257 4.2 16.9 1.0
ND1 B:HIS214 4.2 16.9 1.0
ND1 B:HIS155 4.3 14.9 1.0
CG B:HIS214 4.3 15.5 1.0
CG B:HIS155 4.3 14.9 1.0
O B:HOH845 4.3 24.2 1.0
CG B:GLU267 4.3 15.1 1.0
ND2 B:ASN157 4.5 20.3 1.0
CB B:GLU267 4.5 15.3 1.0
CE1 B:HIS200 4.5 19.5 1.0
CB B:ALA216 4.6 16.9 1.0
CE1 B:TYR257 4.6 15.3 1.0
CB B:ASN157 4.7 17.5 1.0
CD2 B:HIS200 4.8 18.6 1.0
CZ B:TYR257 4.9 15.7 1.0

Iron binding site 3 out of 4 in 4ghh

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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 4-Nitrocatechol 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 Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.55 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:16.1
occ:1.00
 OE1 C:GLU267 2.0 15.4 1.0
O7 C:4NC403 2.1 16.0 0.8
O8 C:4NC403 2.2 12.8 0.8
NE2 C:HIS214 2.2 12.9 1.0
NE2 C:HIS155 2.2 13.3 1.0
O C:HOH869 2.4 12.1 1.0
C1 C:4NC403 2.9 16.7 0.8
C2 C:4NC403 2.9 17.1 0.8
CE1 C:HIS214 3.0 14.8 1.0
CE1 C:HIS155 3.1 12.9 1.0
CD C:GLU267 3.1 14.4 1.0
CD2 C:HIS155 3.2 13.7 1.0
CD2 C:HIS214 3.2 14.2 1.0
OE2 C:GLU267 3.5 15.9 1.0
NE2 C:HIS200 3.8 18.1 1.0
OH C:TYR257 4.2 15.2 1.0
ND1 C:HIS214 4.2 13.9 1.0
ND1 C:HIS155 4.2 12.9 1.0
C3 C:4NC403 4.3 19.6 0.8
C6 C:4NC403 4.3 15.2 0.8
CG C:HIS214 4.3 13.7 1.0
CG C:GLU267 4.3 13.2 1.0
CG C:HIS155 4.3 13.5 1.0
CB C:GLU267 4.5 13.0 1.0
CB C:ALA216 4.6 12.5 1.0
CE1 C:TYR257 4.6 13.1 1.0
CE1 C:HIS200 4.6 19.9 1.0
ND2 C:ASN157 4.7 17.6 1.0
CB C:ASN157 4.7 15.8 1.0
CD2 C:HIS200 4.7 17.2 1.0
CZ C:TYR257 4.8 13.6 1.0
CD1 C:TYR269 4.9 16.0 1.0

Iron binding site 4 out of 4 in 4ghh

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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 4-Nitrocatechol 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 Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.55 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:15.1
occ:1.00
 OE1 D:GLU267 2.0 14.5 1.0
O7 D:4NC403 2.1 16.6 0.6
O D:HOH916 2.1 14.7 0.4
NE2 D:HIS214 2.1 13.6 1.0
O D:HOH915 2.2 12.9 0.4
O8 D:4NC403 2.2 15.6 0.6
NE2 D:HIS155 2.2 12.3 1.0
O D:HOH900 2.3 11.8 1.0
C1 D:4NC403 2.9 16.4 0.6
C2 D:4NC403 2.9 16.6 0.6
CE1 D:HIS214 3.1 13.6 1.0
CD D:GLU267 3.1 13.9 1.0
CE1 D:HIS155 3.1 13.9 1.0
CD2 D:HIS214 3.2 13.9 1.0
CD2 D:HIS155 3.2 12.3 1.0
OE2 D:GLU267 3.5 14.9 1.0
NE2 D:HIS200 3.8 17.5 1.0
OH D:TYR257 4.1 14.4 1.0
ND1 D:HIS214 4.2 12.7 1.0
ND1 D:HIS155 4.3 14.8 1.0
C6 D:4NC403 4.3 17.4 0.6
C3 D:4NC403 4.3 16.9 0.6
CG D:HIS214 4.3 13.7 1.0
CG D:HIS155 4.3 13.1 1.0
CG D:GLU267 4.4 13.6 1.0
O D:HOH917 4.5 14.0 0.4
CB D:GLU267 4.5 12.7 1.0
CE1 D:HIS200 4.6 18.5 1.0
ND2 D:ASN157 4.6 17.2 1.0
CE1 D:TYR257 4.6 12.5 1.0
CB D:ALA216 4.6 12.5 1.0
CB D:ASN157 4.7 14.1 1.0
CD2 D:HIS200 4.7 18.2 1.0
CZ D:TYR257 4.8 13.1 1.0
CD1 D:TYR269 5.0 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: Mon Aug 5 02:44:08 2024

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