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Iron in PDB 4z6w: Structure of H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 Ang Resolution

Protein crystallography data

The structure of Structure of H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 Ang Resolution, PDB code: 4z6w 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) 45.73 / 1.57
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.469, 150.646, 95.996, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 16.3

Other elements in 4z6w:

The structure of Structure of H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 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 H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 Ang Resolution (pdb code 4z6w). 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 H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 Ang Resolution, PDB code: 4z6w:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4z6w

Go back to Iron Binding Sites List in 4z6w
Iron binding site 1 out of 4 in the Structure of H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 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 H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:17.1
occ:1.00
 OE1 A:GLU267 2.0 16.3 1.0
O7 A:4NC403 2.1 16.2 0.8
O8 A:4NC403 2.2 14.6 0.8
NE2 A:HIS155 2.2 15.9 1.0
NE2 A:HIS214 2.2 16.3 1.0
O A:HOH694 2.5 18.7 1.0
C2 A:4NC403 2.8 16.2 0.8
C1 A:4NC403 2.8 17.6 0.8
CE1 A:HIS214 3.1 15.3 1.0
CE1 A:HIS155 3.1 16.5 1.0
CD A:GLU267 3.1 16.3 1.0
CD2 A:HIS155 3.2 16.6 1.0
CD2 A:HIS214 3.3 15.7 1.0
OE2 A:GLU267 3.5 17.1 1.0
OH A:TYR257 4.1 15.5 1.0
C3 A:4NC403 4.2 16.1 0.8
C6 A:4NC403 4.2 14.8 0.8
ND1 A:HIS214 4.2 16.0 1.0
ND1 A:HIS155 4.2 16.6 1.0
O A:HOH586 4.3 17.4 0.5
CG A:HIS155 4.3 16.8 1.0
CG A:HIS214 4.4 15.8 1.0
CG A:GLU267 4.4 15.9 1.0
ND2 A:ASN157 4.5 18.4 1.0
CB A:GLU267 4.6 14.6 1.0
CB A:ALA216 4.6 16.4 1.0
CE1 A:TYR257 4.7 15.4 1.0
CB A:ASN157 4.7 16.6 1.0
ND2 A:ASN200 4.7 17.6 0.5
CZ A:TYR257 4.8 14.6 1.0
NE1 A:TRP192 4.9 17.4 1.0
CD1 A:TYR269 4.9 17.9 1.0
CE1 A:TYR269 4.9 16.8 1.0

Iron binding site 2 out of 4 in 4z6w

Go back to Iron Binding Sites List in 4z6w
Iron binding site 2 out of 4 in the Structure of H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 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 H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:14.9
occ:1.00
 OE1 B:GLU267 2.0 14.9 1.0
O7 B:4NC406 2.1 16.3 0.7
O8 B:4NC406 2.1 11.2 0.7
NE2 B:HIS155 2.2 12.6 1.0
NE2 B:HIS214 2.2 14.7 1.0
O B:HOH692 2.3 18.0 1.0
C1 B:4NC406 2.8 16.6 0.7
C2 B:4NC406 2.8 15.1 0.7
CD B:GLU267 3.1 14.5 1.0
CE1 B:HIS214 3.1 13.8 1.0
CE1 B:HIS155 3.1 13.2 1.0
CD2 B:HIS155 3.2 13.2 1.0
CD2 B:HIS214 3.3 13.1 1.0
OE2 B:GLU267 3.5 15.9 1.0
OH B:TYR257 4.1 15.4 1.0
C6 B:4NC406 4.2 13.5 0.7
C3 B:4NC406 4.2 14.8 0.7
ND1 B:HIS214 4.2 14.2 1.0
ND1 B:HIS155 4.2 13.3 1.0
CG B:HIS155 4.3 13.6 1.0
O B:HOH673 4.3 21.0 0.5
CG B:GLU267 4.3 13.1 1.0
CG B:HIS214 4.4 13.3 1.0
ND2 B:ASN157 4.4 16.1 1.0
CB B:GLU267 4.6 13.1 1.0
CE1 B:TYR257 4.6 13.2 1.0
CB B:ALA216 4.6 12.3 1.0
CB B:ASN157 4.7 14.4 1.0
ND2 B:ASN200 4.7 15.3 0.5
CZ B:TYR257 4.8 14.1 1.0
NE1 B:TRP192 4.8 17.5 1.0
CE1 B:TYR269 5.0 15.1 1.0
CD1 B:TYR269 5.0 15.3 1.0

Iron binding site 3 out of 4 in 4z6w

Go back to Iron Binding Sites List in 4z6w
Iron binding site 3 out of 4 in the Structure of H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 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 H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:14.7
occ:1.00
 OE1 C:GLU267 2.0 13.6 1.0
O8 C:4NC403 2.1 12.1 0.8
O7 C:4NC403 2.1 11.5 0.8
NE2 C:HIS214 2.2 12.3 1.0
NE2 C:HIS155 2.3 13.8 1.0
O C:HOH719 2.5 11.7 1.0
C2 C:4NC403 2.8 10.9 0.8
C1 C:4NC403 2.9 11.2 0.8
CE1 C:HIS214 3.0 13.7 1.0
CD C:GLU267 3.1 12.8 1.0
CE1 C:HIS155 3.1 12.7 1.0
CD2 C:HIS214 3.3 12.8 1.0
CD2 C:HIS155 3.3 12.8 1.0
OE2 C:GLU267 3.5 14.5 1.0
OH C:TYR257 4.1 13.9 1.0
C3 C:4NC403 4.2 11.8 0.8
ND1 C:HIS214 4.2 13.1 1.0
C6 C:4NC403 4.2 10.7 0.8
ND1 C:HIS155 4.3 12.5 1.0
CG C:GLU267 4.3 12.3 1.0
O C:HOH672 4.3 19.4 0.7
CG C:HIS214 4.4 12.6 1.0
CG C:HIS155 4.4 12.8 1.0
CB C:GLU267 4.5 11.8 1.0
ND2 C:ASN157 4.5 16.7 1.0
CB C:ALA216 4.6 12.0 1.0
CE1 C:TYR257 4.6 13.2 1.0
ND2 C:ASN200 4.7 13.5 0.3
CB C:ASN157 4.7 14.0 1.0
CD2 C:TYR269 4.8 15.4 1.0
CZ C:TYR257 4.8 13.7 1.0
NE1 C:TRP192 4.9 17.3 1.0
CE2 C:TYR269 4.9 15.0 1.0

Iron binding site 4 out of 4 in 4z6w

Go back to Iron Binding Sites List in 4z6w
Iron binding site 4 out of 4 in the Structure of H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 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 H200N Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.57 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:14.2
occ:1.00
 OE1 D:GLU267 2.0 12.6 1.0
O8 D:4NC404 2.1 11.3 0.8
O7 D:4NC404 2.1 14.3 0.8
NE2 D:HIS214 2.2 11.7 1.0
NE2 D:HIS155 2.2 12.5 1.0
O D:HOH659 2.5 15.2 1.0
C2 D:4NC404 2.9 14.5 0.8
C1 D:4NC404 2.9 15.2 0.8
CE1 D:HIS214 3.0 12.9 1.0
CD D:GLU267 3.0 13.8 1.0
CE1 D:HIS155 3.1 12.9 1.0
CD2 D:HIS214 3.3 12.8 1.0
CD2 D:HIS155 3.3 13.0 1.0
OE2 D:GLU267 3.5 14.6 1.0
OH D:TYR257 4.1 14.2 1.0
ND1 D:HIS214 4.2 12.1 1.0
C3 D:4NC404 4.2 15.0 0.8
C6 D:4NC404 4.2 13.9 0.8
ND1 D:HIS155 4.3 13.1 1.0
O D:HOH533 4.3 17.5 0.5
CG D:GLU267 4.3 11.6 1.0
CG D:HIS214 4.3 11.9 1.0
CG D:HIS155 4.4 12.2 1.0
ND2 D:ASN157 4.5 15.6 1.0
CB D:GLU267 4.5 11.6 1.0
CB D:ALA216 4.6 12.5 1.0
CB D:ASN157 4.7 13.8 1.0
CE1 D:TYR257 4.7 12.5 1.0
ND2 D:ASN200 4.7 15.8 0.5
CZ D:TYR257 4.8 13.7 1.0
NE1 D:TRP192 4.9 16.0 1.0
CD1 D:TYR269 4.9 13.2 1.0
CE1 D:TYR269 4.9 14.1 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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