Iron in PDB 4ghf: Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution

Enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution

All present enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution:
1.13.11.15;

Protein crystallography data

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution, PDB code: 4ghf 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) 89.04 / 1.67
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.519, 150.318, 96.105, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18.1

Other elements in 4ghf:

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 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 in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution (pdb code 4ghf). 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 in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution, PDB code: 4ghf:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4ghf

Go back to Iron Binding Sites List in 4ghf
Iron binding site 1 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 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 in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:23.6
occ:1.00
 O8 A:4NC402 2.1 21.5 0.7
OE1 A:GLU267 2.1 22.1 1.0
O7 A:4NC402 2.1 20.2 0.7
NE2 A:HIS214 2.2 21.5 1.0
NE2 A:HIS155 2.2 21.6 1.0
O A:HOH682 2.4 20.6 1.0
C2 A:4NC402 2.8 22.3 0.7
C1 A:4NC402 2.8 23.3 0.7
CE1 A:HIS214 3.1 19.6 1.0
CD A:GLU267 3.1 22.4 1.0
CE1 A:HIS155 3.1 22.5 1.0
CD2 A:HIS214 3.2 20.8 1.0
CD2 A:HIS155 3.2 22.8 1.0
OE2 A:GLU267 3.5 24.2 1.0
NE2 A:HIS200 3.8 32.0 1.0
C3 A:4NC402 4.1 24.4 0.7
C6 A:4NC402 4.1 21.8 0.7
ND1 A:HIS214 4.2 21.0 1.0
ND1 A:HIS155 4.3 21.6 1.0
CG A:HIS214 4.3 21.4 1.0
CG A:HIS155 4.4 22.9 1.0
CG A:GLU267 4.4 20.5 1.0
CB A:ALA216 4.5 21.2 1.0
ND2 A:ASN157 4.5 28.7 1.0
CZ A:PHE257 4.5 19.9 1.0
CE1 A:HIS200 4.6 27.4 1.0
CB A:GLU267 4.6 20.8 1.0
CE1 A:PHE257 4.6 19.6 1.0
CB A:ASN157 4.7 23.6 1.0
CD2 A:HIS200 4.8 30.6 1.0
CD1 A:TYR269 4.9 25.9 1.0
CE1 A:TYR269 5.0 25.0 1.0

Iron binding site 2 out of 4 in 4ghf

Go back to Iron Binding Sites List in 4ghf
Iron binding site 2 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 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 in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:21.1
occ:1.00
 OE1 B:GLU267 2.0 17.9 1.0
O B:HOH796 2.1 28.2 1.0
NE2 B:HIS214 2.2 18.8 1.0
O B:HOH795 2.2 26.7 1.0
NE2 B:HIS155 2.2 19.1 1.0
O B:HOH738 2.2 19.8 1.0
CE1 B:HIS214 3.0 17.8 1.0
CD B:GLU267 3.1 18.6 1.0
CE1 B:HIS155 3.1 19.5 1.0
CD2 B:HIS155 3.2 19.9 1.0
CD2 B:HIS214 3.2 16.9 1.0
OE2 B:GLU267 3.6 20.5 1.0
NE2 B:HIS200 3.8 27.1 1.0
O B:HOH797 4.2 31.4 1.0
ND1 B:HIS214 4.2 18.0 1.0
ND1 B:HIS155 4.3 19.4 1.0
CG B:HIS214 4.3 17.2 1.0
CG B:HIS155 4.3 19.7 1.0
CG B:GLU267 4.4 17.2 1.0
ND2 B:ASN157 4.5 25.1 1.0
CB B:GLU267 4.6 17.6 1.0
CE1 B:HIS200 4.6 25.7 1.0
CB B:ALA216 4.6 18.2 1.0
CE1 B:PHE257 4.6 17.5 1.0
CZ B:PHE257 4.7 18.1 1.0
CB B:ASN157 4.7 20.6 1.0
CD2 B:HIS200 4.8 28.1 1.0
CD1 B:TYR269 5.0 22.6 1.0

Iron binding site 3 out of 4 in 4ghf

Go back to Iron Binding Sites List in 4ghf
Iron binding site 3 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 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 in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:21.2
occ:1.00
 O8 C:4NC402 2.0 21.0 0.9
OE1 C:GLU267 2.0 17.7 1.0
O7 C:4NC402 2.1 20.9 0.9
NE2 C:HIS214 2.2 16.0 1.0
NE2 C:HIS155 2.2 17.6 1.0
O C:HOH792 2.3 10.8 0.5
O2 C:OXY405 2.5 22.2 0.5
C2 C:4NC402 2.8 21.9 0.9
C1 C:4NC402 2.9 20.9 0.9
O1 C:OXY405 3.0 20.7 0.5
CE1 C:HIS214 3.0 17.3 1.0
CD C:GLU267 3.1 17.0 1.0
CE1 C:HIS155 3.1 18.7 1.0
CD2 C:HIS155 3.2 17.5 1.0
CD2 C:HIS214 3.3 17.5 1.0
OE2 C:GLU267 3.5 20.3 1.0
NE2 C:HIS200 3.8 29.0 1.0
C3 C:4NC402 4.2 21.9 0.9
ND1 C:HIS214 4.2 17.9 1.0
C6 C:4NC402 4.2 20.7 0.9
ND1 C:HIS155 4.3 18.1 1.0
CG C:HIS214 4.3 16.6 1.0
CG C:HIS155 4.3 19.0 1.0
CG C:GLU267 4.3 16.0 1.0
CB C:GLU267 4.5 15.2 1.0
CB C:ALA216 4.5 16.8 1.0
CE1 C:HIS200 4.6 27.0 1.0
CE1 C:PHE257 4.6 18.9 1.0
CZ C:PHE257 4.6 18.2 1.0
ND2 C:ASN157 4.7 25.2 1.0
CB C:ASN157 4.7 20.9 1.0
CD2 C:HIS200 4.8 26.6 1.0
CD1 C:TYR269 4.9 22.1 1.0

Iron binding site 4 out of 4 in 4ghf

Go back to Iron Binding Sites List in 4ghf
Iron binding site 4 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol and Dioxygen at 1.67 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 in Complex with 4-Nitrocatechol and Dioxygen at 1.67 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:20.6
occ:1.00
 OE1 D:GLU267 2.1 18.9 1.0
O8 D:4NC402 2.1 19.6 0.7
NE2 D:HIS214 2.1 14.3 1.0
O7 D:4NC402 2.2 17.7 0.7
NE2 D:HIS155 2.2 18.1 1.0
O D:HOH812 2.3 10.0 0.5
O1 D:OXY404 2.3 26.6 0.5
O2 D:OXY404 2.7 26.8 0.5
C2 D:4NC402 2.9 21.0 0.7
C1 D:4NC402 2.9 19.6 0.7
CD D:GLU267 3.1 17.6 1.0
CE1 D:HIS214 3.1 15.7 1.0
CE1 D:HIS155 3.1 18.3 1.0
CD2 D:HIS214 3.2 16.0 1.0
CD2 D:HIS155 3.3 18.4 1.0
OE2 D:GLU267 3.5 18.5 1.0
NE2 D:HIS200 3.7 25.8 1.0
C3 D:4NC402 4.2 22.1 0.7
ND1 D:HIS214 4.2 14.7 1.0
C6 D:4NC402 4.3 18.9 0.7
ND1 D:HIS155 4.3 19.2 1.0
CG D:HIS214 4.3 15.7 1.0
CG D:GLU267 4.3 16.4 1.0
CG D:HIS155 4.4 17.6 1.0
CB D:GLU267 4.6 15.3 1.0
CE1 D:HIS200 4.6 27.5 1.0
ND2 D:ASN157 4.6 23.8 1.0
CB D:ALA216 4.6 17.3 1.0
CE1 D:PHE257 4.6 16.3 1.0
CD2 D:HIS200 4.6 27.5 1.0
CZ D:PHE257 4.7 17.3 1.0
CB D:ASN157 4.7 19.0 1.0
CD1 D:TYR269 5.0 21.0 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: Sun Dec 13 15:35:32 2020

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