Iron in PDB 4ghe: Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution

Enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 Ang Resolution

All present enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 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 at 1.60 Ang Resolution, PDB code: 4ghe 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) 42.30 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.513, 150.116, 96.169, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.6

Other elements in 4ghe:

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.60 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 at 1.60 Ang Resolution (pdb code 4ghe). 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 at 1.60 Ang Resolution, PDB code: 4ghe:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4ghe

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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 in Complex with 4-Nitrocatechol at 1.60 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 at 1.60 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:24.9
occ:1.00
 OE1 A:GLU267 2.0 17.2 1.0
O A:HOH845 2.1 27.4 1.0
NE2 A:HIS214 2.2 18.5 1.0
NE2 A:HIS155 2.2 18.7 1.0
O A:HOH740 2.3 17.6 1.0
O A:HOH846 2.4 30.5 1.0
CE1 A:HIS214 3.1 18.3 1.0
CE1 A:HIS155 3.1 18.5 1.0
CD A:GLU267 3.1 17.3 1.0
CD2 A:HIS214 3.2 18.4 1.0
CD2 A:HIS155 3.2 19.3 1.0
OE2 A:GLU267 3.5 18.4 1.0
NE2 A:HIS200 3.7 25.6 1.0
ND1 A:HIS214 4.2 18.9 1.0
ND1 A:HIS155 4.2 18.3 1.0
O A:HOH848 4.3 33.6 1.0
CG A:HIS214 4.3 18.6 1.0
CG A:HIS155 4.3 19.4 1.0
CG A:GLU267 4.4 16.8 1.0
CE1 A:HIS200 4.5 24.3 1.0
ND2 A:ASN157 4.5 20.7 1.0
CB A:ALA216 4.5 17.1 1.0
CB A:GLU267 4.5 17.0 1.0
CB A:ASN157 4.6 20.3 1.0
CE1 A:PHE257 4.6 17.6 1.0
CZ A:PHE257 4.7 17.4 1.0
CD2 A:HIS200 4.7 25.6 1.0
CD1 A:TYR269 4.8 20.6 1.0
CE1 A:TYR269 4.9 21.1 1.0

Iron binding site 2 out of 4 in 4ghe

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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 in Complex with 4-Nitrocatechol at 1.60 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 at 1.60 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:23.2
occ:1.00
 OE1 B:GLU267 2.0 15.8 1.0
O B:HOH905 2.1 30.1 1.0
NE2 B:HIS155 2.2 15.6 1.0
NE2 B:HIS214 2.2 16.2 1.0
O B:HOH786 2.2 15.1 1.0
O B:HOH906 2.3 31.8 1.0
CE1 B:HIS214 3.1 16.2 1.0
CE1 B:HIS155 3.1 15.1 1.0
CD B:GLU267 3.1 15.7 1.0
CD2 B:HIS155 3.2 15.7 1.0
CD2 B:HIS214 3.2 15.9 1.0
OE2 B:GLU267 3.6 17.0 1.0
NE2 B:HIS200 3.7 23.2 1.0
ND1 B:HIS155 4.2 14.9 1.0
ND1 B:HIS214 4.2 16.1 1.0
CG B:HIS155 4.3 15.5 1.0
O B:HOH907 4.3 31.5 1.0
CG B:GLU267 4.3 14.6 1.0
CG B:HIS214 4.4 16.1 1.0
CE1 B:HIS200 4.5 22.8 1.0
CB B:GLU267 4.5 14.3 1.0
CB B:ALA216 4.5 14.5 1.0
ND2 B:ASN157 4.6 19.8 1.0
CE1 B:PHE257 4.7 14.0 1.0
CB B:ASN157 4.7 17.6 1.0
CZ B:PHE257 4.7 14.2 1.0
CD2 B:HIS200 4.7 23.5 1.0
CD1 B:TYR269 4.9 18.1 1.0
CE1 B:TYR269 5.0 18.2 1.0

Iron binding site 3 out of 4 in 4ghe

Go back to Iron Binding Sites List in 4ghe
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 at 1.60 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 at 1.60 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:21.3
occ:1.00
 OE1 C:GLU267 2.0 16.4 1.0
O8 C:4NC403 2.1 18.5 0.8
O7 C:4NC403 2.1 18.9 0.8
NE2 C:HIS214 2.2 12.4 1.0
NE2 C:HIS155 2.2 13.3 1.0
O C:HOH781 2.4 13.5 1.0
C2 C:4NC403 2.8 19.0 0.8
C1 C:4NC403 2.8 18.0 0.8
CE1 C:HIS214 2.9 12.9 1.0
CD C:GLU267 3.0 16.0 1.0
CE1 C:HIS155 3.1 12.4 1.0
CD2 C:HIS155 3.2 12.9 1.0
CD2 C:HIS214 3.3 12.1 1.0
OE2 C:GLU267 3.5 17.1 1.0
NE2 C:HIS200 3.7 18.9 1.0
C3 C:4NC403 4.1 19.8 0.8
ND1 C:HIS214 4.2 12.4 1.0
C6 C:4NC403 4.2 17.5 0.8
ND1 C:HIS155 4.3 12.2 1.0
CG C:GLU267 4.3 13.7 1.0
CG C:HIS214 4.3 12.4 1.0
CG C:HIS155 4.4 12.4 1.0
CE1 C:HIS200 4.4 19.1 1.0
CB C:GLU267 4.5 12.6 1.0
CB C:ALA216 4.5 12.4 1.0
CE1 C:PHE257 4.6 12.9 1.0
CZ C:PHE257 4.6 13.2 1.0
ND2 C:ASN157 4.7 18.2 1.0
CB C:ASN157 4.7 14.8 1.0
CD2 C:HIS200 4.8 18.7 1.0
CD1 C:TYR269 4.9 15.4 1.0
CE1 C:TYR269 5.0 16.0 1.0

Iron binding site 4 out of 4 in 4ghe

Go back to Iron Binding Sites List in 4ghe
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 at 1.60 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 at 1.60 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:19.7
occ:1.00
 OE1 D:GLU267 2.1 12.5 1.0
O D:HOH909 2.1 24.8 1.0
NE2 D:HIS214 2.1 12.6 1.0
NE2 D:HIS155 2.2 12.9 1.0
O D:HOH670 2.2 13.3 1.0
O D:HOH910 2.3 29.4 1.0
CE1 D:HIS214 3.0 13.4 1.0
CD D:GLU267 3.1 13.8 1.0
CE1 D:HIS155 3.1 14.0 1.0
CD2 D:HIS214 3.2 12.5 1.0
CD2 D:HIS155 3.2 13.1 1.0
OE2 D:GLU267 3.5 15.7 1.0
NE2 D:HIS200 3.6 20.6 1.0
ND1 D:HIS214 4.2 12.6 1.0
ND1 D:HIS155 4.3 14.1 1.0
CG D:HIS214 4.3 12.3 1.0
CE1 D:HIS200 4.3 20.1 1.0
CG D:HIS155 4.3 13.3 1.0
O D:HOH911 4.4 30.9 1.0
CG D:GLU267 4.4 12.1 1.0
ND2 D:ASN157 4.5 17.3 1.0
CB D:GLU267 4.5 11.5 1.0
CB D:ALA216 4.5 11.6 1.0
CB D:ASN157 4.6 13.5 1.0
CE1 D:PHE257 4.7 11.9 1.0
CD2 D:HIS200 4.7 20.1 1.0
CZ D:PHE257 4.7 11.9 1.0
CD1 D:TYR269 4.9 15.1 1.0
CE1 D:TYR269 4.9 15.3 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 15:35:33 2020

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