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Iron in PDB 4whr: Anhydride Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 8.5

Enzymatic activity of Anhydride Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 8.5

All present enzymatic activity of Anhydride Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 8.5:
1.13.11.3;

Protein crystallography data

The structure of Anhydride Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 8.5, PDB code: 4whr 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) 31.47 / 1.58
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.437, 140.644, 168.291, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 19.2

Other elements in 4whr:

The structure of Anhydride Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 8.5 also contains other interesting chemical elements:

Fluorine (F) 15 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

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

Iron binding site 1 out of 3 in 4whr

Go back to Iron Binding Sites List in 4whr
Iron binding site 1 out of 3 in the Anhydride Reaction Intermediate Trapped in 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 Anhydride Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe601

b:18.1
occ:0.75
 OH D:TYR408 1.9 23.0 1.0
O D:HOH895 1.9 19.4 0.8
OH D:TYR447 2.1 28.8 1.0
NE2 D:HIS460 2.2 17.8 1.0
NE2 D:HIS462 2.3 20.3 1.0
CZ D:TYR408 3.0 21.5 1.0
CE1 D:HIS460 3.0 17.4 1.0
CE1 D:HIS462 3.1 19.2 1.0
CD2 D:HIS460 3.3 18.6 1.0
CZ D:TYR447 3.4 30.6 1.0
CD2 D:HIS462 3.4 18.9 1.0
CE2 D:TYR408 3.7 21.3 1.0
CE2 D:TYR447 3.8 29.9 1.0
CE1 D:TYR408 4.0 21.1 1.0
O C:HOH517 4.1 29.9 1.0
O D:HOH760 4.2 18.4 1.0
ND1 D:HIS460 4.2 17.4 1.0
NH1 D:ARG457 4.2 21.3 1.0
ND1 D:HIS462 4.3 20.6 1.0
CG D:HIS460 4.3 15.2 1.0
CG D:HIS462 4.4 16.4 1.0
CE1 D:TYR447 4.5 27.0 1.0
CD2 D:TYR408 5.0 20.1 1.0
OE1 D:GLN477 5.0 22.2 1.0

Iron binding site 2 out of 3 in 4whr

Go back to Iron Binding Sites List in 4whr
Iron binding site 2 out of 3 in the Anhydride Reaction Intermediate Trapped in 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 Anhydride Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:19.2
occ:0.75
 OH B:TYR408 1.9 23.4 1.0
O2 B:3NJ607 2.0 27.9 0.7
O B:HOH882 2.1 20.2 0.7
NE2 B:HIS460 2.2 17.5 1.0
OH B:TYR447 2.2 30.5 1.0
NE2 B:HIS462 2.3 19.6 1.0
C2 B:3NJ607 2.4 15.6 0.7
O3 B:3NJ607 2.9 29.2 0.7
CE1 B:HIS460 3.0 18.2 1.0
CZ B:TYR408 3.1 21.0 1.0
CE1 B:HIS462 3.1 17.9 1.0
CD2 B:HIS460 3.2 18.3 1.0
CZ B:TYR447 3.3 28.5 1.0
C3 B:3NJ607 3.4 27.1 0.7
CD2 B:HIS462 3.4 19.8 1.0
CE2 B:TYR408 3.7 23.9 1.0
CE2 B:TYR447 3.7 30.1 1.0
CE1 B:TYR408 4.0 20.1 1.0
C1 B:3NJ607 4.1 26.7 0.7
O B:HOH785 4.1 17.1 1.0
ND1 B:HIS460 4.2 16.7 1.0
O A:HOH510 4.2 30.2 1.0
NH1 B:ARG457 4.2 22.4 1.0
ND1 B:HIS462 4.3 19.9 1.0
CG B:HIS460 4.3 15.8 1.0
CG B:HIS462 4.4 21.1 1.0
O1 B:3NJ607 4.5 36.6 0.7
CE1 B:TYR447 4.5 29.1 1.0
C4 B:3NJ607 4.6 26.9 0.7
CD2 B:TYR408 5.0 22.4 1.0

Iron binding site 3 out of 3 in 4whr

Go back to Iron Binding Sites List in 4whr
Iron binding site 3 out of 3 in the Anhydride Reaction Intermediate Trapped in 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 Anhydride Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe607

b:18.6
occ:0.75
 OH F:TYR408 1.9 24.4 1.0
O F:HOH866 2.1 22.1 0.8
OH F:TYR447 2.1 27.6 1.0
NE2 F:HIS460 2.2 18.4 1.0
NE2 F:HIS462 2.2 22.5 1.0
CZ F:TYR408 3.0 20.8 1.0
CE1 F:HIS462 3.0 22.7 1.0
CE1 F:HIS460 3.1 17.8 1.0
CD2 F:HIS460 3.2 18.5 1.0
CD2 F:HIS462 3.3 19.4 1.0
CZ F:TYR447 3.3 28.5 1.0
CE2 F:TYR408 3.7 21.6 1.0
CE2 F:TYR447 3.8 28.4 1.0
CE1 F:TYR408 4.0 22.1 1.0
O E:HOH409 4.1 33.5 1.0
O F:HOH759 4.2 18.0 1.0
ND1 F:HIS462 4.2 22.7 1.0
ND1 F:HIS460 4.2 18.3 1.0
NH1 F:ARG457 4.3 21.4 1.0
CG F:HIS460 4.3 15.9 1.0
CG F:HIS462 4.4 18.4 1.0
CE1 F:TYR447 4.5 29.5 1.0
OE1 F:GLN477 5.0 23.3 1.0
CD2 F:TYR408 5.0 22.9 1.0

Reference:

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
Page generated: Tue Aug 5 16:44:39 2025

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