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Iron in PDB 4z6r: Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 Ang Resolution

Protein crystallography data

The structure of Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 Ang Resolution, PDB code: 4z6r 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) 29.43 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.457, 150.482, 95.957, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 17.4

Other elements in 4z6r:

The structure of Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 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 H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 Ang Resolution (pdb code 4z6r). 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 H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 Ang Resolution, PDB code: 4z6r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4z6r

Go back to Iron Binding Sites List in 4z6r
Iron binding site 1 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 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 H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:24.1
occ:0.90
 O A:HOH503 2.0 21.0 1.0
OE1 A:GLU267 2.1 18.1 1.0
NE2 A:HIS155 2.2 18.2 1.0
O A:HOH569 2.3 23.6 1.0
O A:HOH551 2.3 30.8 1.0
NE2 A:HIS214 2.3 18.4 1.0
CE1 A:HIS214 3.0 17.5 1.0
CE1 A:HIS155 3.1 18.8 1.0
CD A:GLU267 3.2 20.2 1.0
CD2 A:HIS155 3.3 19.5 1.0
CD2 A:HIS214 3.4 17.7 1.0
OE2 A:GLU267 3.6 20.5 1.0
OE1 A:GLU200 3.9 27.2 1.0
OH A:TYR257 4.0 17.4 1.0
OE2 A:GLU200 4.0 30.1 1.0
ND1 A:HIS214 4.2 18.5 1.0
O A:HOH734 4.2 35.9 1.0
ND1 A:HIS155 4.3 18.5 1.0
CD A:GLU200 4.3 29.9 1.0
CG A:HIS155 4.4 18.6 1.0
CG A:GLU267 4.4 17.0 1.0
CG A:HIS214 4.4 19.0 1.0
ND2 A:ASN157 4.5 20.7 1.0
CB A:GLU267 4.6 17.4 1.0
CB A:ALA216 4.6 16.3 1.0
CE1 A:TYR257 4.6 17.7 1.0
CB A:ASN157 4.7 19.0 1.0
CZ A:TYR257 4.8 17.4 1.0
CD1 A:TYR269 4.9 21.2 1.0
CE1 A:TYR269 4.9 21.4 1.0
NE2 A:HIS248 5.0 15.9 1.0

Iron binding site 2 out of 4 in 4z6r

Go back to Iron Binding Sites List in 4z6r
Iron binding site 2 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 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 H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:22.1
occ:0.90
 OE1 B:GLU267 2.1 13.3 1.0
O B:HOH546 2.1 13.9 1.0
O B:HOH681 2.1 27.8 1.0
O B:HOH503 2.2 20.6 1.0
NE2 B:HIS155 2.2 16.1 1.0
NE2 B:HIS214 2.3 16.1 1.0
CE1 B:HIS214 3.1 15.7 1.0
CE1 B:HIS155 3.1 16.7 1.0
CD B:GLU267 3.2 16.1 1.0
CD2 B:HIS155 3.3 18.3 1.0
CD2 B:HIS214 3.4 14.8 1.0
OE2 B:GLU267 3.7 18.5 1.0
OE1 B:GLU200 3.8 26.5 1.0
OE2 B:GLU200 4.1 29.8 1.0
OH B:TYR257 4.1 17.7 1.0
O B:HOH761 4.2 35.1 1.0
O B:HOH771 4.2 37.7 1.0
CD B:GLU200 4.2 27.5 1.0
ND1 B:HIS214 4.3 17.2 1.0
ND1 B:HIS155 4.3 16.1 1.0
CG B:GLU267 4.4 13.2 1.0
CG B:HIS155 4.4 17.3 1.0
ND2 B:ASN157 4.4 18.3 1.0
CG B:HIS214 4.5 14.6 1.0
CB B:GLU267 4.6 13.2 1.0
CE1 B:TYR257 4.7 15.1 1.0
CB B:ALA216 4.7 16.2 1.0
CB B:ASN157 4.7 15.9 1.0
CZ B:TYR257 4.9 15.1 1.0
CE1 B:TYR269 4.9 21.7 1.0
CD1 B:TYR269 5.0 21.5 1.0

Iron binding site 3 out of 4 in 4z6r

Go back to Iron Binding Sites List in 4z6r
Iron binding site 3 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 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 H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:22.7
occ:0.90
 OE1 C:GLU267 2.1 15.9 1.0
O7 C:4SX403 2.1 19.0 0.8
O8 C:4SX403 2.2 16.5 0.8
NE2 C:HIS214 2.2 14.0 1.0
O C:HOH609 2.3 14.4 1.0
NE2 C:HIS155 2.3 14.3 1.0
C2 C:4SX403 2.9 22.3 0.8
C1 C:4SX403 2.9 20.8 0.8
CE1 C:HIS214 3.0 15.3 1.0
CD C:GLU267 3.2 16.0 1.0
CE1 C:HIS155 3.2 14.2 1.0
CD2 C:HIS214 3.3 14.5 1.0
CD2 C:HIS155 3.4 13.8 1.0
OE2 C:GLU267 3.6 16.4 1.0
OE1 C:GLU200 3.9 22.6 1.0
OE2 C:GLU200 4.0 26.8 1.0
OH C:TYR257 4.1 16.1 1.0
ND1 C:HIS214 4.1 15.1 1.0
C3 C:4SX403 4.2 22.9 0.8
C6 C:4SX403 4.2 19.2 0.8
CD C:GLU200 4.3 23.9 1.0
ND1 C:HIS155 4.3 16.1 1.0
CG C:HIS214 4.4 14.2 1.0
CG C:GLU267 4.4 13.0 1.0
CG C:HIS155 4.4 14.9 1.0
CB C:GLU267 4.5 12.3 1.0
ND2 C:ASN157 4.5 22.2 1.0
CB C:ALA216 4.6 13.1 1.0
CE1 C:TYR257 4.6 14.3 1.0
CB C:ASN157 4.7 16.0 1.0
CZ C:TYR257 4.8 15.2 1.0
CE1 C:TYR269 4.9 18.3 1.0
CD1 C:TYR269 4.9 17.6 1.0

Iron binding site 4 out of 4 in 4z6r

Go back to Iron Binding Sites List in 4z6r
Iron binding site 4 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 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 H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Sulfonyl Catechol at 1.70 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:21.9
occ:0.90
 OE1 D:GLU267 2.1 15.5 1.0
O D:HOH507 2.1 22.4 1.0
NE2 D:HIS155 2.2 14.9 1.0
NE2 D:HIS214 2.2 13.2 1.0
O D:HOH504 2.3 23.8 1.0
O D:HOH644 2.3 19.1 1.0
CE1 D:HIS214 3.0 14.4 1.0
CE1 D:HIS155 3.0 15.1 1.0
CD D:GLU267 3.1 17.5 1.0
CD2 D:HIS155 3.3 14.6 1.0
CD2 D:HIS214 3.3 15.0 1.0
OE2 D:GLU267 3.5 18.0 1.0
OE1 D:GLU200 3.8 25.5 1.0
OE2 D:GLU200 4.0 26.5 1.0
OH D:TYR257 4.1 15.8 1.0
ND1 D:HIS214 4.2 14.6 1.0
ND1 D:HIS155 4.2 15.8 1.0
CD D:GLU200 4.2 27.0 1.0
CG D:HIS155 4.4 15.2 1.0
CG D:GLU267 4.4 14.1 1.0
CG D:HIS214 4.4 13.4 1.0
ND2 D:ASN157 4.5 17.1 1.0
CB D:ALA216 4.5 13.4 1.0
CB D:GLU267 4.5 12.6 1.0
CE1 D:TYR257 4.6 12.7 1.0
CB D:ASN157 4.7 15.0 1.0
CZ D:TYR257 4.9 14.4 1.0
CE1 D:TYR269 4.9 18.7 1.0
CD1 D:TYR269 5.0 16.1 1.0

Reference:

E.G.Kovaleva, M.S.Rogers, J.D.Lipscomb. Structural Basis For Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200. Biochemistry V. 54 5329 2015.
ISSN: ISSN 0006-2960
PubMed: 26267790
DOI: 10.1021/ACS.BIOCHEM.5B00709
Page generated: Mon Aug 5 18:05:53 2024

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