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Iron in PDB 4ghd: Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.85 Ang Resolution

Enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.85 Ang Resolution

All present enzymatic activity of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.85 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 Hpca at 1.85 Ang Resolution, PDB code: 4ghd 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) 48.05 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.163, 150.701, 96.107, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 18.9

Other elements in 4ghd:

The structure of Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.85 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 Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.85 Ang Resolution (pdb code 4ghd). 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 Hpca at 1.85 Ang Resolution, PDB code: 4ghd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4ghd

Go back to Iron Binding Sites List in 4ghd
Iron binding site 1 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.85 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 Hpca at 1.85 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:38.6
occ:1.00
 OE1 A:GLU267 2.1 23.6 1.0
NE2 A:HIS214 2.2 22.3 1.0
O A:HOH723 2.2 38.3 1.0
NE2 A:HIS155 2.3 22.3 1.0
O A:HOH722 2.3 21.6 1.0
O A:HOH724 2.7 42.7 1.0
CE1 A:HIS214 3.1 21.6 1.0
CD A:GLU267 3.1 23.8 1.0
CE1 A:HIS155 3.2 22.9 1.0
CD2 A:HIS214 3.2 23.3 1.0
CD2 A:HIS155 3.3 23.2 1.0
OE2 A:GLU267 3.6 25.9 1.0
NE2 A:HIS200 3.8 29.3 1.0
ND1 A:HIS214 4.2 23.9 1.0
O A:HOH735 4.3 34.1 1.0
CG A:HIS214 4.4 22.3 1.0
ND1 A:HIS155 4.4 23.2 1.0
CG A:GLU267 4.4 21.2 1.0
CG A:HIS155 4.4 23.6 1.0
ND2 A:ASN157 4.5 24.4 1.0
CB A:GLU267 4.5 20.2 1.0
CB A:ALA216 4.6 20.4 1.0
CE1 A:HIS200 4.6 28.1 1.0
CE1 A:PHE257 4.6 21.3 1.0
CZ A:PHE257 4.7 20.7 1.0
CB A:ASN157 4.7 22.5 1.0
CD2 A:HIS200 4.8 30.0 1.0
CD1 A:TYR269 4.9 25.7 1.0
NE2 A:HIS248 5.0 21.4 1.0
CE1 A:TYR269 5.0 25.7 1.0

Iron binding site 2 out of 4 in 4ghd

Go back to Iron Binding Sites List in 4ghd
Iron binding site 2 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.85 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 Hpca at 1.85 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:38.1
occ:1.00
 OE1 B:GLU267 2.1 21.3 1.0
NE2 B:HIS155 2.2 20.8 1.0
O B:HOH752 2.3 16.6 1.0
O B:HOH756 2.3 36.0 1.0
NE2 B:HIS214 2.3 20.4 1.0
O B:HOH759 2.5 35.1 1.0
CE1 B:HIS155 3.1 21.7 1.0
CE1 B:HIS214 3.1 20.7 1.0
CD B:GLU267 3.1 21.9 1.0
CD2 B:HIS155 3.2 21.7 1.0
CD2 B:HIS214 3.3 20.8 1.0
OE2 B:GLU267 3.6 23.4 1.0
NE2 B:HIS200 3.7 26.3 1.0
O B:HOH769 4.2 35.6 1.0
ND1 B:HIS155 4.2 20.7 1.0
CG B:HIS155 4.3 21.1 1.0
ND1 B:HIS214 4.3 21.8 1.0
CG B:GLU267 4.4 20.8 1.0
CG B:HIS214 4.4 20.2 1.0
CE1 B:HIS200 4.4 24.6 1.0
ND2 B:ASN157 4.5 25.0 1.0
CB B:GLU267 4.5 20.0 1.0
CB B:ASN157 4.6 22.3 1.0
CB B:ALA216 4.6 19.7 1.0
CE1 B:PHE257 4.7 18.8 1.0
CD2 B:HIS200 4.7 26.5 1.0
CZ B:PHE257 4.8 19.5 1.0
CD1 B:TYR269 5.0 27.2 1.0

Iron binding site 3 out of 4 in 4ghd

Go back to Iron Binding Sites List in 4ghd
Iron binding site 3 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.85 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 Hpca at 1.85 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:34.1
occ:1.00
 O3 C:DHY403 2.1 23.7 1.0
OE1 C:GLU267 2.1 20.3 1.0
O4 C:DHY403 2.2 26.3 1.0
NE2 C:HIS155 2.2 18.5 1.0
NE2 C:HIS214 2.3 18.6 1.0
O C:HOH729 2.4 14.4 1.0
C3 C:DHY403 2.8 27.2 1.0
C4 C:DHY403 2.8 26.2 1.0
CE1 C:HIS214 3.0 19.0 1.0
CE1 C:HIS155 3.1 19.9 1.0
CD C:GLU267 3.2 20.9 1.0
CD2 C:HIS155 3.2 19.2 1.0
CD2 C:HIS214 3.4 19.1 1.0
OE2 C:GLU267 3.6 21.0 1.0
NE2 C:HIS200 3.7 26.5 1.0
C2 C:DHY403 4.1 26.1 1.0
ND1 C:HIS214 4.2 19.2 1.0
C5 C:DHY403 4.2 24.9 1.0
ND1 C:HIS155 4.3 19.3 1.0
CG C:HIS155 4.4 19.8 1.0
CG C:GLU267 4.4 18.6 1.0
CG C:HIS214 4.4 18.5 1.0
CB C:GLU267 4.5 18.1 1.0
CE1 C:HIS200 4.5 26.4 1.0
CB C:ALA216 4.6 18.6 1.0
ND2 C:ASN157 4.6 20.3 1.0
CE1 C:PHE257 4.6 18.4 1.0
CB C:ASN157 4.7 19.5 1.0
CD2 C:HIS200 4.7 26.1 1.0
CZ C:PHE257 4.7 18.7 1.0
CD1 C:TYR269 5.0 19.6 1.0
NE1 C:TRP192 5.0 23.6 1.0

Iron binding site 4 out of 4 in 4ghd

Go back to Iron Binding Sites List in 4ghd
Iron binding site 4 out of 4 in the Structure of Y257F Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.85 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 Hpca at 1.85 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:34.6
occ:1.00
 OE1 D:GLU267 2.1 18.3 1.0
NE2 D:HIS214 2.2 15.9 1.0
O D:HOH752 2.2 29.2 1.0
O D:HOH748 2.3 15.1 1.0
NE2 D:HIS155 2.3 18.5 1.0
O D:HOH765 2.4 27.4 1.0
CE1 D:HIS214 2.9 16.6 1.0
CD D:GLU267 3.1 20.9 1.0
CE1 D:HIS155 3.2 18.6 1.0
CD2 D:HIS214 3.3 16.3 1.0
CD2 D:HIS155 3.3 18.4 1.0
OE2 D:GLU267 3.6 21.5 1.0
NE2 D:HIS200 3.8 23.7 1.0
ND1 D:HIS214 4.2 17.2 1.0
O D:HOH762 4.3 30.6 1.0
ND1 D:HIS155 4.3 20.0 1.0
CG D:HIS214 4.3 16.9 1.0
CG D:GLU267 4.4 19.2 1.0
CG D:HIS155 4.4 18.9 1.0
ND2 D:ASN157 4.5 19.0 1.0
CE1 D:HIS200 4.5 25.1 1.0
CE1 D:PHE257 4.5 17.6 1.0
CB D:GLU267 4.6 17.9 1.0
CB D:ASN157 4.6 18.9 1.0
CZ D:PHE257 4.6 17.4 1.0
CB D:ALA216 4.6 18.4 1.0
CD2 D:HIS200 4.8 23.1 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 02:42:24 2024

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