Iron in PDB 4who: Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5

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

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

Resolution Low / High (Å)	32.45 / 1.83
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.092, 140.636, 168.660, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.6

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

Iron binding site 1 out of 3 in the Resting 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 Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:17.4 occ:0.75 OH B:TYR408 1.9 18.1 1.0 OH B:TYR447 2.2 20.2 1.0 NE2 B:HIS462 2.2 15.3 1.0 O B:HOH868 2.2 15.1 0.8 NE2 B:HIS460 2.2 16.3 1.0 CZ B:TYR408 3.0 16.0 1.0 CE1 B:HIS460 3.1 16.2 1.0 CE1 B:HIS462 3.1 15.8 1.0 O B:HOH869 3.3 24.8 1.0 CD2 B:HIS462 3.3 18.1 1.0 CD2 B:HIS460 3.3 16.4 1.0 CZ B:TYR447 3.4 19.8 1.0 CE1 B:TYR408 3.6 16.5 1.0 CE2 B:TYR447 3.8 19.8 1.0 CE2 B:TYR408 3.9 16.6 1.0 O B:HOH783 4.0 15.7 1.0 ND1 B:HIS460 4.2 15.4 1.0 ND1 B:HIS462 4.3 15.4 1.0 O B:HOH870 4.3 19.9 1.0 CG B:HIS462 4.4 15.5 1.0 CG B:HIS460 4.4 15.4 1.0 O A:HOH508 4.4 16.9 1.0 NH1 B:ARG457 4.5 16.9 1.0 CE1 B:TYR447 4.5 20.9 1.0 CD1 B:TYR408 4.9 16.3 1.0 OE1 B:GLN477 5.0 15.7 1.0

Iron binding site 2 out of 3 in the Resting 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 Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe600 b:18.3 occ:0.75 OH D:TYR408 1.8 20.8 1.0 O D:HOH889 2.1 18.5 0.8 NE2 D:HIS460 2.2 16.9 1.0 NE2 D:HIS462 2.2 18.7 1.0 OH D:TYR447 2.2 26.1 1.0 CZ D:TYR408 2.9 18.7 1.0 CE1 D:HIS460 3.0 17.0 1.0 CE1 D:HIS462 3.2 17.9 1.0 O D:HOH888 3.2 31.4 1.0 CD2 D:HIS462 3.2 17.5 1.0 CD2 D:HIS460 3.3 16.8 1.0 CZ D:TYR447 3.4 23.8 1.0 CE2 D:TYR408 3.6 18.4 1.0 CE2 D:TYR447 3.8 23.3 1.0 CE1 D:TYR408 3.8 17.7 1.0 O D:HOH758 4.0 16.0 1.0 ND1 D:HIS460 4.2 15.3 1.0 O D:HOH887 4.3 21.1 1.0 ND1 D:HIS462 4.3 17.9 1.0 CG D:HIS460 4.3 15.1 1.0 CG D:HIS462 4.3 17.0 1.0 O C:HOH421 4.4 15.8 1.0 NH1 D:ARG457 4.4 17.7 1.0 CE1 D:TYR447 4.6 24.6 1.0 CD2 D:TYR408 4.9 18.8 1.0 OE1 D:GLN477 5.0 16.8 1.0

Iron binding site 3 out of 3 in the Resting 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 Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe602 b:19.7 occ:0.75 OH F:TYR408 1.8 20.4 1.0 NE2 F:HIS460 2.1 14.5 1.0 OH F:TYR447 2.2 21.9 1.0 NE2 F:HIS462 2.3 18.6 1.0 O F:HOH859 2.3 18.1 0.8 CZ F:TYR408 2.9 19.8 1.0 CE1 F:HIS460 3.0 15.3 1.0 CE1 F:HIS462 3.2 16.4 1.0 CD2 F:HIS460 3.2 14.4 1.0 CD2 F:HIS462 3.3 16.4 1.0 O F:HOH858 3.3 28.2 1.0 CZ F:TYR447 3.3 21.9 1.0 CE1 F:TYR408 3.7 19.1 1.0 CE2 F:TYR447 3.7 22.6 1.0 CE2 F:TYR408 3.8 20.5 1.0 O F:HOH754 4.0 16.2 1.0 ND1 F:HIS460 4.1 15.2 1.0 CG F:HIS460 4.3 13.4 1.0 ND1 F:HIS462 4.3 18.1 1.0 O F:HOH860 4.3 16.8 1.0 CG F:HIS462 4.4 16.6 1.0 NH1 F:ARG457 4.4 17.6 1.0 O E:HOH305 4.4 20.8 1.0 CE1 F:TYR447 4.5 23.4 1.0 OE1 F:GLN477 4.9 18.5 1.0 CD1 F:TYR408 5.0 19.8 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