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Chlorine 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
Sodium (Na) 1 atom

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 3 in 4whq

Go back to Chlorine Binding Sites List in 4whq
Chlorine 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 Chlorine with other atoms in the Cl 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
A:Cl301

b:57.2
occ:1.00
 NE2 A:HIS107 3.5 36.1 1.0
OG1 A:THR105 3.5 29.1 1.0
ND2 A:ASN37 3.6 24.7 1.0
CD2 A:HIS107 4.3 32.8 1.0
CE1 A:HIS107 4.4 33.6 1.0
NH2 A:ARG38 4.6 50.6 1.0
CG A:ASN37 4.6 25.8 1.0
OD1 A:ASN37 4.7 25.4 1.0
CB A:THR105 4.7 26.5 1.0

Chlorine binding site 2 out of 3 in 4whq

Go back to Chlorine Binding Sites List in 4whq
Chlorine 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 Chlorine with other atoms in the Cl 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
A:Cl303

b:49.8
occ:1.00
 N A:LEU62 3.2 24.6 1.0
CA A:HIS61 3.6 25.3 1.0
NH1 A:ARG64 3.7 44.4 1.0
CB A:HIS61 3.9 28.1 1.0
CG A:LEU62 3.9 27.0 1.0
C A:HIS61 3.9 24.0 1.0
O A:HOH478 4.0 31.2 1.0
CB A:LEU62 4.0 26.5 1.0
CD2 A:HIS61 4.0 33.3 1.0
CD1 A:LEU62 4.1 30.1 1.0
CA A:LEU62 4.2 23.3 1.0
CG A:HIS61 4.3 30.9 1.0
OE1 C:GLN163 4.5 35.1 1.0
O A:GLY60 4.6 24.0 1.0
CZ A:ARG64 4.7 41.0 1.0
N A:HIS61 4.9 22.4 1.0
NE A:ARG64 5.0 39.6 1.0
NE2 C:GLN163 5.0 32.2 1.0

Chlorine binding site 3 out of 3 in 4whq

Go back to Chlorine Binding Sites List in 4whq
Chlorine 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 Chlorine with other atoms in the Cl 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
C:Cl303

b:64.6
occ:1.00
 NE2 C:HIS107 3.4 32.2 1.0
OG1 C:THR105 3.5 28.3 1.0
ND2 C:ASN37 3.6 22.8 1.0
O C:HOH484 3.8 39.9 1.0
NH1 C:ARG38 4.3 49.5 1.0
CD2 C:HIS107 4.3 30.2 1.0
CE1 C:HIS107 4.4 30.8 1.0
CG C:ASN37 4.5 22.1 1.0
OD1 C:ASN37 4.5 22.3 1.0
CB C:THR105 4.7 25.9 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: Fri Jul 26 02:54:17 2024

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