Atomistry » Iron » PDB 4g39-4gl5 » 4ghe
Atomistry »
  Iron »
    PDB 4g39-4gl5 »
      4ghe »

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

Go back to Iron Binding Sites List in 4ghe
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

Go back to Iron Binding Sites List in 4ghe
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: Mon Aug 5 02:42:34 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy