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

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

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

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 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 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 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 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

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