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Sodium 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
Iron (Fe) 3 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5, PDB code: 4whq:

Sodium binding site 1 out of 1 in 4whq

Go back to Sodium Binding Sites List in 4whq
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
D:Na607

b:37.2
occ:1.00
 O D:HOH835 3.1 25.9 1.0
N D:ASP323 3.2 21.6 1.0
C D:THR321 3.3 21.0 1.0
N D:PRO322 3.4 21.0 1.0
CB D:ASP323 3.5 22.8 1.0
CA D:THR321 3.6 20.9 1.0
O D:THR321 3.7 19.5 1.0
CG D:ASP323 3.7 25.0 1.0
CB D:THR321 3.8 21.2 1.0
CD D:PRO322 3.8 21.9 1.0
OD2 D:ASP323 3.9 28.9 1.0
CA D:ASP323 3.9 20.6 1.0
C D:PRO322 4.2 21.1 1.0
OD1 D:ASP323 4.3 28.6 1.0
O D:HOH880 4.3 35.3 1.0
CA D:PRO322 4.3 21.5 1.0
N D:TYR324 4.6 18.8 1.0
CG2 D:THR321 4.7 21.2 1.0
C D:ASP323 4.8 19.7 1.0
OG1 D:THR321 4.8 20.3 1.0
CB D:PRO322 5.0 23.2 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: Sun Aug 17 22:06:25 2025

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