Iron in PDB 4z6o: Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.63 Ang Resolution

The structure of Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.63 Ang Resolution, PDB code: 4z6o 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)	47.82 / 1.63
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.314, 150.478, 95.972, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.7

The structure of Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.63 Ang Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Iron atom in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.63 Ang Resolution (pdb code 4z6o). 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 Hpca at 1.63 Ang Resolution, PDB code: 4z6o:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.63 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 Hpca at 1.63 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.0 occ:0.80 OE1 A:GLU267 2.1 17.0 1.0 O A:HOH586 2.1 23.5 1.0 O A:HOH507 2.1 21.4 1.0 O A:HOH515 2.2 18.9 1.0 NE2 A:HIS214 2.2 17.1 1.0 NE2 A:HIS155 2.2 17.2 1.0 CE1 A:HIS214 2.9 16.7 1.0 CE1 A:HIS155 3.1 17.9 1.0 CD A:GLU267 3.2 16.8 1.0 CD2 A:HIS155 3.3 17.2 1.0 CD2 A:HIS214 3.3 16.3 1.0 OE2 A:GLU267 3.6 19.0 1.0 OE1 A:GLU200 3.8 23.3 1.0 OE2 A:GLU200 4.0 25.5 1.0 OH A:TYR257 4.1 17.2 1.0 ND1 A:HIS214 4.1 16.8 1.0 O A:HOH819 4.2 31.4 1.0 ND1 A:HIS155 4.2 16.6 1.0 CD A:GLU200 4.2 23.3 1.0 CG A:HIS214 4.4 16.6 1.0 CG A:HIS155 4.4 17.8 1.0 CG A:GLU267 4.4 15.7 1.0 ND2 A:ASN157 4.5 19.3 1.0 CB A:GLU267 4.6 14.8 1.0 CB A:ALA216 4.7 17.0 1.0 CE1 A:TYR257 4.7 15.8 1.0 CB A:ASN157 4.7 16.6 1.0 CZ A:TYR257 4.9 15.1 1.0 CE1 A:TYR269 4.9 19.8 1.0 CD1 A:TYR269 4.9 19.8 1.0

Iron binding site 2 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.63 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 Hpca at 1.63 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:19.9 occ:0.80 OE1 B:GLU267 2.1 16.0 1.0 O B:HOH549 2.1 15.2 1.0 O B:HOH505 2.2 22.4 1.0 NE2 B:HIS214 2.2 16.1 1.0 O B:HOH565 2.2 27.3 1.0 NE2 B:HIS155 2.2 16.5 1.0 CE1 B:HIS214 3.0 15.1 1.0 CE1 B:HIS155 3.1 16.6 1.0 CD B:GLU267 3.2 16.3 1.0 CD2 B:HIS155 3.3 17.4 1.0 CD2 B:HIS214 3.3 13.8 1.0 OE2 B:GLU267 3.7 19.4 1.0 OE1 B:GLU200 3.8 24.1 1.0 OE2 B:GLU200 3.9 26.1 1.0 OH B:TYR257 4.1 17.1 1.0 ND1 B:HIS214 4.1 15.4 1.0 CD B:GLU200 4.2 21.4 1.0 O B:HOH824 4.2 30.5 1.0 ND1 B:HIS155 4.2 15.2 1.0 O B:HOH830 4.3 36.5 1.0 CG B:HIS155 4.4 15.7 1.0 CG B:HIS214 4.4 14.2 1.0 CG B:GLU267 4.4 13.1 1.0 ND2 B:ASN157 4.5 17.1 1.0 CB B:GLU267 4.5 13.4 1.0 CE1 B:TYR257 4.6 15.5 1.0 CB B:ASN157 4.7 14.3 1.0 CB B:ALA216 4.7 14.4 1.0 CZ B:TYR257 4.9 16.0 1.0 CE1 B:TYR269 5.0 21.6 1.0

Iron binding site 3 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.63 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 Hpca at 1.63 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:18.7 occ:0.80 OE1 C:GLU267 2.0 16.5 1.0 O3 C:DHY403 2.0 12.6 0.8 O4 C:DHY403 2.1 12.8 0.8 NE2 C:HIS214 2.2 14.0 1.0 NE2 C:HIS155 2.3 15.0 1.0 O C:HOH563 2.4 14.9 1.0 C3 C:DHY403 2.8 15.3 0.8 C4 C:DHY403 2.8 14.7 0.8 CE1 C:HIS214 3.0 14.7 1.0 CD C:GLU267 3.1 14.8 1.0 CE1 C:HIS155 3.1 14.5 1.0 CD2 C:HIS155 3.3 13.9 1.0 CD2 C:HIS214 3.3 13.9 1.0 OE2 C:GLU267 3.6 15.4 1.0 OE1 C:GLU200 3.9 17.8 1.0 OE2 C:GLU200 4.0 21.0 1.0 C2 C:DHY403 4.1 14.2 0.8 ND1 C:HIS214 4.1 13.9 1.0 OH C:TYR257 4.2 14.4 1.0 C5 C:DHY403 4.2 12.5 0.8 ND1 C:HIS155 4.3 13.9 1.0 CD C:GLU200 4.3 18.0 1.0 CG C:GLU267 4.3 12.9 1.0 CG C:HIS214 4.3 13.0 1.0 CG C:HIS155 4.4 13.7 1.0 CB C:GLU267 4.5 12.0 1.0 ND2 C:ASN157 4.5 17.7 1.0 CE1 C:TYR257 4.6 13.1 1.0 CB C:ALA216 4.6 13.0 1.0 CB C:ASN157 4.7 14.5 1.0 CZ C:TYR257 4.8 13.4 1.0 CD1 C:TYR269 4.9 15.1 1.0 CE1 C:TYR269 4.9 16.0 1.0

Iron binding site 4 out of 4 in the Structure of H200E Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum in Complex with Hpca at 1.63 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 Hpca at 1.63 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:19.0 occ:0.80 OE1 D:GLU267 2.0 13.9 1.0 O3 D:DHY403 2.1 12.9 0.8 O4 D:DHY403 2.2 13.3 0.8 NE2 D:HIS214 2.2 12.5 1.0 O D:HOH584 2.3 15.7 1.0 NE2 D:HIS155 2.3 15.2 1.0 C3 D:DHY403 2.9 16.1 0.8 C4 D:DHY403 2.9 16.3 0.8 CE1 D:HIS214 3.0 14.5 1.0 CD D:GLU267 3.1 15.4 1.0 CE1 D:HIS155 3.1 15.0 1.0 CD2 D:HIS155 3.3 14.8 1.0 CD2 D:HIS214 3.3 14.0 1.0 OE2 D:GLU267 3.6 14.6 1.0 OE1 D:GLU200 3.9 19.9 1.0 OE2 D:GLU200 4.0 20.9 1.0 ND1 D:HIS214 4.2 13.5 1.0 OH D:TYR257 4.2 15.7 1.0 C2 D:DHY403 4.3 16.5 0.8 ND1 D:HIS155 4.3 15.2 1.0 CD D:GLU200 4.3 20.9 1.0 C5 D:DHY403 4.3 13.6 0.8 CG D:GLU267 4.3 12.8 1.0 CG D:HIS214 4.3 12.9 1.0 CG D:HIS155 4.4 14.5 1.0 CB D:GLU267 4.5 12.0 1.0 ND2 D:ASN157 4.6 17.8 1.0 CB D:ALA216 4.6 13.3 1.0 CE1 D:TYR257 4.6 13.6 1.0 CB D:ASN157 4.6 14.4 1.0 CZ D:TYR257 4.9 14.9 1.0 CD1 D:TYR269 4.9 14.9 1.0 CE1 D:TYR269 4.9 15.9 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