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Iron in PDB 4z6l: Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.65 Ang Resolution

Protein crystallography data

The structure of Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.65 Ang Resolution, PDB code: 4z6l 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) 45.61 / 1.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.346, 150.594, 96.175, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.8

Other elements in 4z6l:

The structure of Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.65 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 at 1.65 Ang Resolution (pdb code 4z6l). 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 at 1.65 Ang Resolution, PDB code: 4z6l:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4z6l

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Iron binding site 1 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.65 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 at 1.65 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:30.0
occ:1.00
 O A:HOH501 2.1 27.5 1.0
OE1 A:GLU267 2.1 19.5 1.0
O A:HOH516 2.2 19.0 1.0
O A:HOH540 2.3 29.3 1.0
NE2 A:HIS155 2.3 20.7 1.0
NE2 A:HIS214 2.3 22.2 1.0
CE1 A:HIS214 3.0 21.7 1.0
CE1 A:HIS155 3.1 21.3 1.0
CD A:GLU267 3.2 21.2 1.0
CD2 A:HIS155 3.3 21.4 1.0
CD2 A:HIS214 3.4 21.2 1.0
OE2 A:GLU267 3.6 23.1 1.0
OE1 A:GLU200 3.8 31.0 1.0
OE2 A:GLU200 4.0 31.0 1.0
OH A:TYR257 4.0 20.7 1.0
O A:HOH774 4.2 32.4 1.0
ND1 A:HIS214 4.2 21.9 1.0
ND1 A:HIS155 4.2 21.1 1.0
CD A:GLU200 4.2 28.6 1.0
CG A:HIS155 4.4 21.4 1.0
CG A:HIS214 4.4 21.1 1.0
CG A:GLU267 4.4 19.2 1.0
ND2 A:ASN157 4.5 22.2 1.0
CB A:GLU267 4.6 19.4 1.0
CE1 A:TYR257 4.6 18.8 1.0
CB A:ALA216 4.6 20.5 1.0
CB A:ASN157 4.7 21.3 1.0
CZ A:TYR257 4.8 19.6 1.0
CD1 A:TYR269 5.0 22.3 1.0
CE1 A:TYR269 5.0 22.3 1.0

Iron binding site 2 out of 4 in 4z6l

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Iron binding site 2 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.65 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 at 1.65 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:27.7
occ:1.00
 OE1 B:GLU267 2.1 18.0 1.0
O B:HOH506 2.1 22.9 1.0
O B:HOH511 2.1 15.7 1.0
O B:HOH656 2.2 35.2 1.0
NE2 B:HIS155 2.2 18.5 1.0
NE2 B:HIS214 2.3 18.2 1.0
CE1 B:HIS214 3.0 17.2 1.0
CE1 B:HIS155 3.2 17.9 1.0
CD2 B:HIS155 3.2 18.9 1.0
CD B:GLU267 3.2 20.1 1.0
CD2 B:HIS214 3.4 17.0 1.0
OE2 B:GLU267 3.7 22.7 1.0
OE1 B:GLU200 3.8 29.6 1.0
OE2 B:GLU200 3.9 31.3 1.0
OH B:TYR257 4.2 19.9 1.0
CD B:GLU200 4.2 28.4 1.0
ND1 B:HIS214 4.2 18.2 1.0
O B:HOH805 4.2 40.4 1.0
O B:HOH796 4.3 40.4 1.0
ND1 B:HIS155 4.3 17.6 1.0
CG B:HIS155 4.3 18.2 1.0
CG B:HIS214 4.4 17.3 1.0
CG B:GLU267 4.4 17.6 1.0
ND2 B:ASN157 4.4 21.2 1.0
CB B:GLU267 4.5 16.8 1.0
CE1 B:TYR257 4.6 16.9 1.0
CB B:ASN157 4.7 19.1 1.0
CB B:ALA216 4.7 16.4 1.0
CZ B:TYR257 4.9 18.4 1.0
CE1 B:TYR269 5.0 23.9 1.0

Iron binding site 3 out of 4 in 4z6l

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Iron binding site 3 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.65 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 at 1.65 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:27.3
occ:1.00
 OE1 C:GLU267 2.1 19.5 1.0
O C:HOH502 2.1 25.6 1.0
O C:HOH597 2.2 15.8 1.0
O C:HOH605 2.2 28.6 1.0
NE2 C:HIS214 2.3 15.9 1.0
NE2 C:HIS155 2.3 17.1 1.0
CE1 C:HIS214 3.0 16.5 1.0
CE1 C:HIS155 3.2 17.1 1.0
CD C:GLU267 3.2 19.3 1.0
CD2 C:HIS155 3.3 16.8 1.0
CD2 C:HIS214 3.4 15.9 1.0
OE2 C:GLU267 3.7 21.5 1.0
OE1 C:GLU200 3.9 25.3 1.0
OE2 C:GLU200 4.0 31.0 1.0
OH C:TYR257 4.2 17.9 1.0
ND1 C:HIS214 4.2 16.4 1.0
O C:HOH790 4.2 40.9 1.0
O C:HOH781 4.3 30.5 1.0
CD C:GLU200 4.3 26.9 1.0
ND1 C:HIS155 4.3 16.4 1.0
CG C:GLU267 4.4 17.2 1.0
ND2 C:ASN157 4.4 19.4 1.0
CG C:HIS214 4.4 16.0 1.0
CG C:HIS155 4.4 16.9 1.0
CB C:GLU267 4.5 15.9 1.0
CE1 C:TYR257 4.6 17.8 1.0
CB C:ASN157 4.6 17.1 1.0
CB C:ALA216 4.7 15.1 1.0
CZ C:TYR257 4.8 17.8 1.0
CD1 C:TYR269 5.0 21.5 1.0
CE1 C:TYR269 5.0 21.2 1.0

Iron binding site 4 out of 4 in 4z6l

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Iron binding site 4 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.65 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 at 1.65 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:26.5
occ:1.00
 O D:HOH502 2.1 25.4 1.0
OE1 D:GLU267 2.1 18.6 1.0
O D:HOH617 2.2 16.3 1.0
NE2 D:HIS214 2.2 15.4 1.0
NE2 D:HIS155 2.2 17.2 1.0
O D:HOH536 2.3 27.4 1.0
CE1 D:HIS214 3.0 16.4 1.0
CE1 D:HIS155 3.1 17.0 1.0
CD D:GLU267 3.2 18.6 1.0
CD2 D:HIS155 3.3 17.6 1.0
CD2 D:HIS214 3.4 17.5 1.0
OE2 D:GLU267 3.6 19.2 1.0
OE1 D:GLU200 3.9 30.6 1.0
OE2 D:GLU200 4.0 32.9 1.0
OH D:TYR257 4.1 18.2 1.0
O D:HOH812 4.1 45.8 1.0
ND1 D:HIS214 4.2 17.7 1.0
O D:HOH800 4.2 29.9 1.0
ND1 D:HIS155 4.3 18.2 1.0
CD D:GLU200 4.3 31.0 1.0
CG D:HIS155 4.4 17.0 1.0
CG D:HIS214 4.4 16.3 1.0
CG D:GLU267 4.4 16.3 1.0
ND2 D:ASN157 4.5 20.7 1.0
CB D:GLU267 4.6 15.4 1.0
CE1 D:TYR257 4.6 17.1 1.0
CB D:ALA216 4.6 16.1 1.0
CB D:ASN157 4.7 17.9 1.0
CZ D:TYR257 4.8 17.9 1.0
CE1 D:TYR269 4.9 18.5 1.0
CD1 D:TYR269 5.0 18.0 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: Sun Dec 13 15:54:09 2020

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