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Iron in PDB 4whq: Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5

Enzymatic activity of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5

All present enzymatic activity of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5:
1.13.11.3;

Protein crystallography data

The structure of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5, PDB code: 4whq 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) 39.01 / 1.78
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.259, 140.724, 167.824, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.5

Other elements in 4whq:

The structure of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 also contains other interesting chemical elements:

Fluorine (F) 18 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 (pdb code 4whq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5, PDB code: 4whq:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 4whq

Go back to Iron Binding Sites List in 4whq
Iron binding site 1 out of 3 in the Alkylperoxo Reaction Intermediate Trapped in 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 Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe601

b:22.7
occ:0.75
 OH F:TYR408 1.9 27.6 1.0
O F:HOH865 2.0 23.0 0.7
OH F:TYR447 2.1 28.6 0.5
NE2 F:HIS460 2.2 18.7 1.0
NE2 F:HIS462 2.2 23.3 1.0
CE1 F:HIS462 3.0 21.2 1.0
CE1 F:HIS460 3.0 19.1 1.0
CZ F:TYR408 3.0 25.9 1.0
CZ F:TYR447 3.2 25.7 0.5
CD2 F:HIS460 3.3 19.4 1.0
CD2 F:HIS462 3.3 20.7 1.0
CE2 F:TYR447 3.5 25.7 0.5
CE2 F:TYR408 3.8 25.8 1.0
CE1 F:TYR408 3.9 24.8 1.0
O E:HOH406 4.0 33.9 1.0
O F:HOH753 4.2 19.8 1.0
NH1 F:ARG457 4.2 21.3 1.0
ND1 F:HIS462 4.2 22.6 1.0
ND1 F:HIS460 4.2 19.0 1.0
CG F:HIS460 4.3 17.5 1.0
CG F:HIS462 4.4 21.8 1.0
CE1 F:TYR447 4.4 25.3 0.5
CD2 F:TYR447 4.9 24.4 0.5
OE1 F:GLN477 4.9 23.9 1.0

Iron binding site 2 out of 3 in 4whq

Go back to Iron Binding Sites List in 4whq
Iron binding site 2 out of 3 in the Alkylperoxo Reaction Intermediate Trapped in 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 Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe601

b:21.6
occ:0.75
 OH D:TYR408 1.8 25.7 1.0
O D:HOH882 2.0 19.9 0.7
NE2 D:HIS460 2.2 19.0 1.0
OH D:TYR447 2.2 25.8 0.5
NE2 D:HIS462 2.3 22.6 1.0
CZ D:TYR408 2.9 23.7 1.0
CE1 D:HIS460 3.0 19.3 1.0
CE1 D:HIS462 3.1 20.7 1.0
CD2 D:HIS460 3.3 19.3 1.0
CD2 D:HIS462 3.4 20.1 1.0
CZ D:TYR447 3.4 24.1 0.5
CE2 D:TYR408 3.6 23.5 1.0
CE2 D:TYR447 3.8 24.8 0.5
CE1 D:TYR408 3.9 21.9 1.0
O C:HOH541 4.1 29.3 1.0
O D:HOH753 4.2 19.7 1.0
ND1 D:HIS460 4.2 17.3 1.0
NH1 D:ARG457 4.2 21.8 1.0
ND1 D:HIS462 4.3 21.8 1.0
CG D:HIS460 4.3 17.2 1.0
CG D:HIS462 4.4 20.5 1.0
CE1 D:TYR447 4.6 24.3 0.5
CD2 D:TYR408 4.9 23.6 1.0

Iron binding site 3 out of 3 in 4whq

Go back to Iron Binding Sites List in 4whq
Iron binding site 3 out of 3 in the Alkylperoxo Reaction Intermediate Trapped in 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 Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:21.1
occ:0.75
 O4 B:3N9612 1.8 28.0 0.7
OH B:TYR408 1.9 25.0 1.0
O2 B:3N9612 1.9 29.8 0.7
NE2 B:HIS460 2.1 20.1 1.0
OH B:TYR447 2.2 26.0 0.5
NE2 B:HIS462 2.2 21.2 1.0
O3 B:3N9612 2.5 29.5 0.7
C2 B:3N9612 2.6 33.2 0.7
CE1 B:HIS462 3.0 19.3 1.0
CZ B:TYR408 3.0 23.8 1.0
CE1 B:HIS460 3.0 19.0 1.0
CD2 B:HIS460 3.2 18.6 1.0
C3 B:3N9612 3.3 32.1 0.7
CD2 B:HIS462 3.4 20.7 1.0
CZ B:TYR447 3.4 24.6 0.5
C1 B:3N9612 3.7 34.0 0.7
CE2 B:TYR408 3.7 24.5 1.0
CE2 B:TYR447 3.8 24.3 0.5
O1 B:3N9612 3.8 37.1 0.7
CE1 B:TYR408 3.9 22.3 1.0
O A:HOH511 4.1 30.2 1.0
ND1 B:HIS460 4.2 18.7 1.0
NH1 B:ARG457 4.2 20.9 1.0
O B:HOH779 4.2 19.3 1.0
ND1 B:HIS462 4.2 21.1 1.0
CG B:HIS460 4.3 18.6 1.0
CG B:HIS462 4.4 20.4 1.0
CE1 B:TYR447 4.5 25.5 0.5
C4 B:3N9612 4.6 33.2 0.7
C6 B:3N9612 4.9 36.7 0.7
OE1 B:GLN477 4.9 21.4 1.0
CD2 B:TYR408 5.0 24.4 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: Mon Aug 5 14:49:05 2024

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