Iron in PDB 4whp: Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 6.5

All present enzymatic activity of Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 6.5:
1.13.11.3;

The structure of Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 6.5, PDB code: 4whp 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)	39.02 / 1.54
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	127.919, 140.767, 168.191, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 17.2

The binding sites of Iron atom in the Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 6.5 (pdb code 4whp). 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 6.5, PDB code: 4whp:
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 6.5


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 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe601 b:17.5 occ:0.75 OH F:TYR408 1.9 20.8 1.0 O F:HOH872 2.2 22.1 0.8 NE2 F:HIS460 2.2 17.2 1.0 NE2 F:HIS462 2.2 17.3 1.0 OH F:TYR447 2.2 21.0 1.0 CZ F:TYR408 3.0 18.3 1.0 CE1 F:HIS460 3.0 16.2 1.0 CE1 F:HIS462 3.1 16.9 1.0 CD2 F:HIS462 3.2 17.9 1.0 CD2 F:HIS460 3.2 16.1 1.0 CZ F:TYR447 3.4 20.1 1.0 O F:HOH870 3.5 24.9 1.0 CE1 F:TYR408 3.6 18.0 1.0 CE2 F:TYR447 3.8 19.0 1.0 CE2 F:TYR408 4.0 19.5 1.0 O F:HOH764 4.0 15.9 1.0 ND1 F:HIS460 4.2 16.6 1.0 ND1 F:HIS462 4.2 17.5 1.0 O F:HOH871 4.3 23.3 1.0 CG F:HIS460 4.3 15.7 1.0 CG F:HIS462 4.3 16.5 1.0 O E:HOH305 4.4 19.4 1.0 NH1 F:ARG457 4.4 18.2 1.0 CE1 F:TYR447 4.6 20.4 1.0 OE1 F:GLN477 4.9 17.0 1.0 CD1 F:TYR408 4.9 18.4 1.0 CD2 E:TYR16 5.0 24.2 1.0

Iron binding site 2 out of 3 in the Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 6.5


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 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:17.2 occ:0.75 OH D:TYR408 1.8 19.9 1.0 O D:HOH894 2.1 21.4 0.8 NE2 D:HIS462 2.2 16.4 1.0 NE2 D:HIS460 2.2 16.9 1.0 OH D:TYR447 2.2 20.9 1.0 CZ D:TYR408 2.9 17.7 1.0 CE1 D:HIS460 3.0 16.6 1.0 CE1 D:HIS462 3.1 16.2 1.0 CD2 D:HIS462 3.2 17.1 1.0 CD2 D:HIS460 3.3 17.3 1.0 CZ D:TYR447 3.4 19.8 1.0 CE1 D:TYR408 3.6 18.4 1.0 O D:HOH895 3.6 26.3 1.0 CE2 D:TYR447 3.9 19.9 1.0 CE2 D:TYR408 3.9 19.0 1.0 O D:HOH766 4.0 15.4 1.0 ND1 D:HIS460 4.2 15.8 1.0 ND1 D:HIS462 4.2 16.1 1.0 O D:HOH896 4.3 23.5 1.0 CG D:HIS462 4.3 15.4 1.0 CG D:HIS460 4.3 15.6 1.0 O C:HOH522 4.4 17.6 1.0 NH1 D:ARG457 4.5 18.8 1.0 CE1 D:TYR447 4.6 19.0 1.0 OE1 D:GLN477 4.9 17.2 1.0 CD1 D:TYR408 4.9 17.8 1.0

Iron binding site 3 out of 3 in the Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 6.5


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 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:17.4 occ:0.75 OH B:TYR408 1.9 19.2 1.0 O B:HOH887 2.1 20.0 0.8 NE2 B:HIS460 2.2 16.2 1.0 NE2 B:HIS462 2.2 15.8 1.0 OH B:TYR447 2.2 19.9 1.0 CZ B:TYR408 3.0 17.9 1.0 CE1 B:HIS460 3.0 16.2 1.0 CE1 B:HIS462 3.1 16.0 1.0 CD2 B:HIS462 3.2 16.6 1.0 CD2 B:HIS460 3.2 15.5 1.0 CZ B:TYR447 3.4 18.6 1.0 O B:HOH885 3.5 24.9 1.0 CE1 B:TYR408 3.7 18.4 1.0 CE2 B:TYR447 3.8 19.4 1.0 CE2 B:TYR408 3.9 17.8 1.0 O B:HOH797 4.0 16.0 1.0 ND1 B:HIS460 4.2 15.2 1.0 ND1 B:HIS462 4.2 15.3 1.0 O B:HOH886 4.3 24.3 1.0 CG B:HIS460 4.3 15.2 1.0 CG B:HIS462 4.3 15.6 1.0 O A:HOH416 4.4 17.2 1.0 NH1 B:ARG457 4.4 17.6 1.0 CE1 B:TYR447 4.6 18.3 1.0 OE1 B:GLN477 4.9 16.4 1.0 CD1 B:TYR408 4.9 18.4 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