Iron in PDB 4z6m: Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.35 Ang Resolution

The structure of Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.35 Ang Resolution, PDB code: 4z6m 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)	48.09 / 1.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.485, 152.089, 96.188, 90.00, 90.00, 90.00
R / Rfree (%)	11.2 / 14

The structure of Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.35 Ang Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	4 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 at 1.35 Ang Resolution (pdb code 4z6m). 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 at 1.35 Ang Resolution, PDB code: 4z6m:
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 at 1.35 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 at 1.35 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:8.0 occ:1.00 OE1 A:GLU267 2.1 7.7 1.0 O A:HOH725 2.2 9.1 1.0 O A:HOH516 2.2 7.2 1.0 O A:HOH512 2.2 10.3 1.0 NE2 A:HIS155 2.2 6.2 1.0 NE2 A:HIS214 2.2 7.1 1.0 CE1 A:HIS214 3.1 7.8 1.0 CE1 A:HIS155 3.1 6.1 1.0 CD A:GLU267 3.1 7.8 1.0 CD2 A:HIS155 3.2 6.9 1.0 CD2 A:HIS214 3.3 7.0 1.0 OE2 A:GLU267 3.6 7.8 1.0 OE1 A:GLN200 4.0 10.2 1.0 NE2 A:GLN200 4.1 10.5 1.0 OH A:TYR257 4.2 9.0 1.0 ND1 A:HIS214 4.2 7.3 1.0 ND1 A:HIS155 4.3 6.4 1.0 ND2 A:ASN157 4.3 8.8 1.0 CG A:HIS214 4.4 6.9 1.0 CG A:HIS155 4.4 6.7 1.0 O A:HOH850 4.4 16.7 1.0 CD A:GLN200 4.4 9.8 1.0 CG A:GLU267 4.4 6.9 1.0 CE1 A:TYR257 4.6 7.2 1.0 CB A:ASN157 4.6 7.3 1.0 CB A:GLU267 4.6 6.8 1.0 CB A:ALA216 4.7 6.6 1.0 CZ A:TYR257 4.9 7.3 1.0 CG A:ASN157 5.0 8.2 1.0

Iron binding site 2 out of 4 in the Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.35 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 at 1.35 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:6.7 occ:1.00 OE1 B:GLU267 2.0 6.9 1.0 O B:HOH528 2.2 5.7 1.0 O B:HOH749 2.2 8.6 1.0 NE2 B:HIS214 2.2 5.5 1.0 NE2 B:HIS155 2.2 5.4 1.0 O B:HOH507 2.2 8.9 1.0 CE1 B:HIS214 3.1 5.8 1.0 CD B:GLU267 3.1 5.6 1.0 CE1 B:HIS155 3.1 5.5 1.0 CD2 B:HIS155 3.2 5.3 1.0 CD2 B:HIS214 3.2 5.1 1.0 OE2 B:GLU267 3.5 7.0 1.0 OE1 B:GLN200 4.0 9.2 1.0 NE2 B:GLN200 4.1 8.9 1.0 OH B:TYR257 4.1 7.4 1.0 ND1 B:HIS214 4.2 5.5 1.0 ND1 B:HIS155 4.3 5.1 1.0 CG B:HIS214 4.3 5.2 1.0 CG B:HIS155 4.4 5.2 1.0 O B:HOH870 4.4 16.4 1.0 ND2 B:ASN157 4.4 7.0 1.0 CG B:GLU267 4.4 5.2 1.0 CD B:GLN200 4.4 8.0 1.0 CB B:ASN157 4.6 6.0 1.0 CB B:GLU267 4.6 5.4 1.0 CE1 B:TYR257 4.6 6.3 1.0 CB B:ALA216 4.7 5.7 1.0 CZ B:TYR257 4.8 6.6 1.0 CG B:ASN157 5.0 6.3 1.0

Iron binding site 3 out of 4 in the Structure of H200Q Variant of Homoprotocatechuate 2,3-Dioxygenase From B.Fuscum at 1.35 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 at 1.35 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:8.7 occ:1.00 OE1 C:GLU267 2.0 9.1 1.0 O C:HOH521 2.1 8.3 1.0 O C:HOH726 2.2 9.7 1.0 NE2 C:HIS214 2.2 7.5 1.0 O C:HOH508 2.2 11.1 1.0 NE2 C:HIS155 2.2 7.7 1.0 CE1 C:HIS214 3.1 7.4 1.0 CD C:GLU267 3.1 8.2 1.0 CE1 C:HIS155 3.1 7.8 1.0 CD2 C:HIS214 3.2 7.8 1.0 CD2 C:HIS155 3.2 8.1 1.0 OE2 C:GLU267 3.5 9.3 1.0 OE1 C:GLN200 4.0 11.2 1.0 NE2 C:GLN200 4.1 10.7 1.0 OH C:TYR257 4.1 10.2 1.0 ND1 C:HIS214 4.2 8.1 1.0 ND1 C:HIS155 4.3 8.0 1.0 CG C:HIS214 4.3 7.4 1.0 ND2 C:ASN157 4.3 10.1 1.0 CG C:HIS155 4.4 7.3 1.0 O C:HOH830 4.4 18.0 1.0 CG C:GLU267 4.4 7.3 1.0 CD C:GLN200 4.4 9.8 1.0 CB C:ASN157 4.6 8.6 1.0 CE1 C:TYR257 4.6 7.6 1.0 CB C:GLU267 4.6 7.1 1.0 CB C:ALA216 4.7 7.6 1.0 CZ C:TYR257 4.8 8.0 1.0 CG C:ASN157 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 at 1.35 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 at 1.35 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:8.7 occ:1.00 OE1 D:GLU267 2.0 8.4 1.0 O D:HOH710 2.2 9.0 1.0 O D:HOH526 2.2 7.5 1.0 NE2 D:HIS155 2.2 7.6 1.0 NE2 D:HIS214 2.2 7.8 1.0 O D:HOH506 2.2 10.0 1.0 CE1 D:HIS214 3.1 8.3 1.0 CE1 D:HIS155 3.1 7.4 1.0 CD D:GLU267 3.1 8.2 1.0 CD2 D:HIS155 3.2 7.3 1.0 CD2 D:HIS214 3.3 8.3 1.0 OE2 D:GLU267 3.5 8.0 1.0 OE1 D:GLN200 4.0 11.3 1.0 OH D:TYR257 4.1 8.9 1.0 NE2 D:GLN200 4.2 11.4 1.0 ND1 D:HIS214 4.2 8.0 1.0 ND1 D:HIS155 4.2 7.6 1.0 CG D:HIS214 4.3 7.8 1.0 CG D:HIS155 4.3 7.7 1.0 ND2 D:ASN157 4.4 10.2 1.0 CG D:GLU267 4.4 7.6 1.0 CD D:GLN200 4.4 10.1 1.0 O D:HOH830 4.4 17.8 1.0 CE1 D:TYR257 4.6 7.2 1.0 CB D:GLU267 4.6 7.5 1.0 CB D:ASN157 4.6 8.7 1.0 CB D:ALA216 4.7 8.0 1.0 CZ D:TYR257 4.8 7.8 1.0 CG D:ASN157 5.0 8.5 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