Iron in PDB 4whs: 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5

All present enzymatic activity of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5:
1.13.11.3;

The structure of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5, PDB code: 4whs was solved by C.J.Knoot, V.M.Purpero, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.55 / 1.35
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.013, 140.665, 168.138, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 16.7

The structure of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 also contains other interesting chemical elements:

Fluorine	(F)	13 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Iron atom in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 (pdb code 4whs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5, PDB code: 4whs:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe601 b:14.5 occ:0.75 OH F:TYR408 1.9 19.3 1.0 OH F:TYR447 2.0 17.2 0.2 O7 F:3N8605 2.0 16.2 0.3 O8 F:3N8605 2.1 18.5 0.3 O8 F:3N8605 2.1 16.5 0.3 O7 F:3N8605 2.1 18.7 0.3 NE2 F:HIS460 2.2 14.8 1.0 NE2 F:HIS462 2.2 15.5 1.0 C1 F:3N8605 2.7 17.7 0.3 C2 F:3N8605 2.7 17.0 0.3 C2 F:3N8605 2.8 17.1 0.3 C1 F:3N8605 2.8 15.8 0.3 CE1 F:HIS460 3.0 15.7 1.0 CZ F:TYR408 3.0 18.0 1.0 CE1 F:HIS462 3.1 15.4 1.0 CZ F:TYR447 3.2 17.1 0.2 CD2 F:HIS460 3.2 15.8 1.0 CD2 F:HIS462 3.3 16.2 1.0 CE2 F:TYR447 3.7 16.9 0.2 CE2 F:TYR408 3.8 19.1 1.0 CE1 F:TYR408 3.9 16.9 1.0 C6 F:3N8605 4.0 17.4 0.3 O F:HOH889 4.1 19.1 1.0 C3 F:3N8605 4.1 18.1 0.3 C3 F:3N8605 4.1 18.2 0.3 C6 F:3N8605 4.1 16.6 0.3 NH1 F:ARG457 4.2 15.7 1.0 ND1 F:HIS460 4.2 15.2 1.0 O F:HOH768 4.2 14.5 1.0 O F:HOH763 4.2 22.0 1.0 ND1 F:HIS462 4.2 15.7 1.0 CE1 F:TYR447 4.3 16.0 0.2 CG F:HIS460 4.3 13.8 1.0 CG F:HIS462 4.4 14.7 1.0 OE1 F:GLN477 4.9 15.6 1.0

Iron binding site 2 out of 3 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:13.8 occ:0.75 O7 D:3N8602 1.9 15.3 0.3 OH D:TYR408 1.9 17.2 1.0 O7 D:3N8602 2.0 17.1 0.3 O8 D:3N8602 2.1 16.9 0.3 O8 D:3N8602 2.1 15.2 0.3 OH D:TYR447 2.2 16.0 0.2 NE2 D:HIS460 2.2 13.7 1.0 NE2 D:HIS462 2.2 15.2 1.0 C1 D:3N8602 2.7 16.8 0.3 C2 D:3N8602 2.7 16.3 0.3 C1 D:3N8602 2.8 15.8 0.3 C2 D:3N8602 2.8 16.7 0.3 CE1 D:HIS460 3.0 14.8 1.0 CZ D:TYR408 3.0 15.3 1.0 CE1 D:HIS462 3.1 14.2 1.0 CD2 D:HIS462 3.3 17.0 1.0 CD2 D:HIS460 3.3 14.2 1.0 CZ D:TYR447 3.3 15.8 0.2 CE2 D:TYR408 3.8 17.0 1.0 CE2 D:TYR447 3.8 16.0 0.2 CE1 D:TYR408 3.9 16.1 1.0 C6 D:3N8602 4.0 18.0 0.3 O D:HOH914 4.1 18.9 1.0 C3 D:3N8602 4.1 17.8 0.3 C6 D:3N8602 4.1 17.1 0.3 C3 D:3N8602 4.1 18.3 0.3 NH1 D:ARG457 4.2 15.4 1.0 O D:HOH777 4.2 13.6 1.0 O D:HOH891 4.2 19.6 1.0 ND1 D:HIS460 4.2 14.4 1.0 ND1 D:HIS462 4.2 15.4 1.0 CG D:HIS460 4.3 13.2 1.0 CG D:HIS462 4.4 15.7 1.0 CE1 D:TYR447 4.5 14.0 0.2 OE1 D:GLN477 4.9 14.3 1.0 C5 D:3N8602 5.0 17.6 0.3

Iron binding site 3 out of 3 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:14.2 occ:0.75 OH B:TYR408 2.0 17.8 1.0 O7 B:3N8603 2.0 16.5 0.3 O8 B:3N8603 2.0 15.5 0.3 OH B:TYR447 2.1 13.3 0.2 O8 B:3N8603 2.1 18.2 0.3 O7 B:3N8603 2.1 18.7 0.3 NE2 B:HIS460 2.2 13.8 1.0 NE2 B:HIS462 2.2 15.7 1.0 C1 B:3N8603 2.7 17.9 0.3 C2 B:3N8603 2.8 16.9 0.3 C2 B:3N8603 2.8 16.3 0.3 C1 B:3N8603 2.8 15.5 0.3 CE1 B:HIS460 3.0 15.7 1.0 CZ B:TYR408 3.1 17.9 1.0 CE1 B:HIS462 3.1 15.5 1.0 CD2 B:HIS462 3.2 15.8 1.0 CD2 B:HIS460 3.2 15.1 1.0 CZ B:TYR447 3.3 15.1 0.2 CE2 B:TYR447 3.7 16.0 0.2 CE2 B:TYR408 3.8 17.3 1.0 CE1 B:TYR408 3.9 16.0 1.0 C6 B:3N8603 4.0 18.5 0.3 O B:HOH905 4.1 18.7 1.0 C3 B:3N8603 4.1 17.9 0.3 C3 B:3N8603 4.1 18.2 0.3 NH1 B:ARG457 4.1 15.3 1.0 C6 B:3N8603 4.2 17.1 0.3 ND1 B:HIS460 4.2 14.1 1.0 O B:HOH878 4.2 19.9 1.0 ND1 B:HIS462 4.2 15.2 1.0 O B:HOH803 4.2 13.7 1.0 CG B:HIS460 4.3 13.0 1.0 CG B:HIS462 4.3 14.7 1.0 CE1 B:TYR447 4.4 14.7 0.2 OE1 B:GLN477 4.8 14.5 1.0

C.J.Knoot, V.M.Purpero, J.D.Lipscomb. Crystal Structures of Alkylperoxo and Anhydride Intermediates in An Intradiol Ring-Cleaving Dioxygenase. Proc.Natl.Acad.Sci.Usa V. 112 388 2015.
ISSN: ESSN 1091-6490
PubMed: 25548185
DOI: 10.1073/PNAS.1419118112