Iron in PDB 4z6v: Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 Ang Resolution

The structure of Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 Ang Resolution, PDB code: 4z6v 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)	40.35 / 1.37
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.180, 150.635, 96.103, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 15.7

The structure of Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 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 H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 Ang Resolution (pdb code 4z6v). 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 H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 Ang Resolution, PDB code: 4z6v:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 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 H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.4 occ:1.00 OE1 A:GLU267 2.1 11.2 1.0 O A:HOH536 2.1 13.1 1.0 O A:HOH742 2.2 13.9 1.0 NE2 A:HIS214 2.2 13.6 1.0 NE2 A:HIS155 2.2 11.1 1.0 O A:HOH506 2.3 15.1 1.0 CE1 A:HIS214 3.0 11.3 1.0 CE1 A:HIS155 3.1 11.6 1.0 CD A:GLU267 3.1 11.4 1.0 CD2 A:HIS155 3.2 11.2 1.0 CD2 A:HIS214 3.3 13.0 1.0 OE2 A:GLU267 3.6 11.9 1.0 OE1 A:GLN200 4.0 14.4 1.0 NE2 A:GLN200 4.1 13.5 1.0 OH A:TYR257 4.2 11.9 1.0 ND1 A:HIS214 4.2 12.9 1.0 ND1 A:HIS155 4.3 11.6 1.0 O A:HOH828 4.3 23.7 1.0 ND2 A:ASN157 4.3 12.8 1.0 CG A:HIS214 4.3 12.6 1.0 CG A:HIS155 4.4 11.7 1.0 CD A:GLN200 4.4 12.6 1.0 CG A:GLU267 4.4 11.2 1.0 CB A:ASN157 4.6 12.7 1.0 CB A:GLU267 4.6 10.0 1.0 CE1 A:TYR257 4.7 10.9 1.0 CB A:ALA216 4.7 11.7 1.0 CZ A:TYR257 4.9 9.5 1.0 CG A:ASN157 5.0 13.5 1.0

Iron binding site 2 out of 4 in the Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 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 H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:11.2 occ:1.00 OE1 B:GLU267 2.0 11.0 1.0 O B:HOH536 2.1 10.8 1.0 O B:HOH509 2.2 12.8 1.0 NE2 B:HIS214 2.2 10.0 1.0 NE2 B:HIS155 2.2 9.9 1.0 O B:HOH708 2.2 12.8 1.0 CE1 B:HIS214 3.1 10.2 1.0 CD B:GLU267 3.1 9.7 1.0 CE1 B:HIS155 3.1 10.3 1.0 CD2 B:HIS155 3.2 10.5 1.0 CD2 B:HIS214 3.3 9.6 1.0 O B:HOH765 3.5 28.6 1.0 OE2 B:GLU267 3.5 11.4 1.0 OE1 B:GLN200 4.0 15.0 1.0 NE2 B:GLN200 4.1 13.0 1.0 OH B:TYR257 4.1 12.1 1.0 ND1 B:HIS214 4.2 10.4 1.0 ND1 B:HIS155 4.3 10.1 1.0 ND2 B:ASN157 4.3 10.9 1.0 O B:HOH853 4.3 23.4 1.0 CG B:HIS155 4.3 10.2 1.0 CG B:HIS214 4.3 10.7 1.0 CD B:GLN200 4.4 12.0 1.0 CG B:GLU267 4.4 9.5 1.0 CB B:ASN157 4.6 11.0 1.0 CB B:GLU267 4.6 10.1 1.0 CE1 B:TYR257 4.6 10.2 1.0 CB B:ALA216 4.7 10.5 1.0 CZ B:TYR257 4.8 10.4 1.0 CG B:ASN157 4.9 11.3 1.0

Iron binding site 3 out of 4 in the Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 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 H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:10.1 occ:1.00 OE1 C:GLU267 2.0 10.4 1.0 O8 C:4NC403 2.1 10.2 1.0 O7 C:4NC403 2.1 12.3 1.0 NE2 C:HIS214 2.2 8.8 1.0 NE2 C:HIS155 2.2 8.4 1.0 O C:HOH659 2.2 12.2 1.0 C2 C:4NC403 2.9 10.0 1.0 C1 C:4NC403 2.9 11.5 1.0 CE1 C:HIS214 3.1 8.8 1.0 CE1 C:HIS155 3.1 8.4 1.0 CD C:GLU267 3.1 9.6 1.0 CD2 C:HIS155 3.3 8.3 1.0 CD2 C:HIS214 3.3 9.2 1.0 OE2 C:GLU267 3.6 11.4 1.0 NE2 C:GLN200 4.1 10.6 1.0 OE1 C:GLN200 4.1 10.1 1.0 OH C:TYR257 4.2 10.6 1.0 ND1 C:HIS214 4.2 9.2 1.0 C3 C:4NC403 4.2 12.3 1.0 ND1 C:HIS155 4.2 8.0 1.0 C6 C:4NC403 4.2 10.6 1.0 CG C:HIS214 4.3 9.4 1.0 CG C:HIS155 4.4 8.4 1.0 CG C:GLU267 4.4 8.3 1.0 ND2 C:ASN157 4.4 13.4 1.0 CD C:GLN200 4.5 9.9 1.0 CB C:GLU267 4.5 8.1 1.0 CE2 C:TYR257 4.6 9.2 1.0 CB C:ASN157 4.6 11.2 1.0 CB C:ALA216 4.6 9.0 1.0 CZ C:TYR257 4.8 9.6 1.0 CD1 C:TYR269 4.9 9.5 1.0 NE1 C:TRP192 5.0 14.8 1.0 CE1 C:TYR269 5.0 9.2 1.0

Iron binding site 4 out of 4 in the Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 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 H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with 4-Nitrocatechol at 1.37 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:10.1 occ:1.00 OE1 D:GLU267 2.1 9.8 1.0 O D:HOH566 2.1 10.4 1.0 NE2 D:HIS214 2.2 8.5 1.0 O D:HOH711 2.2 12.8 1.0 O D:HOH504 2.2 13.0 1.0 NE2 D:HIS155 2.2 8.3 1.0 CE1 D:HIS214 3.1 9.8 1.0 CE1 D:HIS155 3.1 8.6 1.0 CD D:GLU267 3.1 10.9 1.0 CD2 D:HIS214 3.3 9.5 1.0 CD2 D:HIS155 3.3 7.7 1.0 OE2 D:GLU267 3.5 10.4 1.0 OE1 D:GLN200 4.0 13.2 1.0 OH D:TYR257 4.1 11.5 1.0 NE2 D:GLN200 4.1 12.4 1.0 ND1 D:HIS214 4.2 10.1 1.0 ND1 D:HIS155 4.3 8.8 1.0 ND2 D:ASN157 4.3 10.7 1.0 O D:HOH846 4.3 19.3 1.0 CG D:HIS214 4.3 9.3 1.0 CG D:HIS155 4.4 8.7 1.0 CD D:GLN200 4.4 10.5 1.0 CG D:GLU267 4.4 9.8 1.0 CB D:ASN157 4.6 9.6 1.0 CB D:GLU267 4.6 8.8 1.0 CE1 D:TYR257 4.6 8.9 1.0 CB D:ALA216 4.7 8.7 1.0 CZ D:TYR257 4.8 8.9 1.0 CG D:ASN157 4.9 9.5 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