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Chlorine in PDB 4whs: 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5

Enzymatic activity of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5

All present enzymatic activity of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5:
1.13.11.3;

Protein crystallography data

The structure of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5, PDB code: 4whs 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) 29.55 / 1.35
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.013, 140.665, 168.138, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 16.7

Other elements in 4whs:

The structure of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 also contains other interesting chemical elements:

Fluorine (F) 13 atoms
Iron (Fe) 3 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 3 in 4whs

Go back to Chlorine Binding Sites List in 4whs
Chlorine binding site 1 out of 3 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl606

b:43.5
occ:1.00
N F:LEU419 3.1 18.2 1.0
O F:HOH904 3.1 53.1 1.0
CA F:PRO418 3.7 18.0 1.0
CB F:LEU419 3.7 19.1 1.0
NH1 F:ARG407 3.8 24.2 1.0
C F:PRO418 3.9 18.9 1.0
CA F:LEU419 3.9 18.6 1.0
CG F:LEU419 4.0 21.4 1.0
CB F:PRO418 4.0 19.0 1.0
CD1 F:LEU419 4.2 23.5 1.0
O F:LEU419 4.4 20.6 1.0
C F:LEU419 4.7 18.8 1.0
CZ F:ARG407 4.7 24.0 1.0
NH2 F:ARG407 4.8 26.7 1.0
N F:PRO418 5.0 19.3 1.0

Chlorine binding site 2 out of 3 in 4whs

Go back to Chlorine Binding Sites List in 4whs
Chlorine binding site 2 out of 3 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:49.2
occ:1.00
N B:HIS410 3.4 18.1 1.0
C B:ARG409 3.6 17.6 1.0
CA B:ARG409 3.7 17.2 1.0
O B:HIS410 3.8 20.3 1.0
C B:HIS410 3.8 20.0 1.0
CG B:ARG409 3.9 17.9 1.0
CD1 B:LEU419 3.9 23.6 1.0
CA B:HIS410 4.1 19.3 1.0
CD2 B:LEU419 4.3 21.0 1.0
N B:LYS411 4.3 21.2 1.0
O B:HOH854 4.3 60.5 1.0
CB B:ARG409 4.4 18.0 1.0
O B:TYR408 4.4 16.8 1.0
O B:ARG409 4.4 19.8 1.0
CA B:LYS411 4.6 24.5 1.0
CG B:LEU419 4.7 20.7 1.0
NH2 B:ARG407 4.7 28.5 1.0
N B:ARG409 4.9 16.0 1.0
NH1 B:ARG409 4.9 20.5 1.0
OD1 A:ASN28 4.9 29.0 1.0

Chlorine binding site 3 out of 3 in 4whs

Go back to Chlorine Binding Sites List in 4whs
Chlorine binding site 3 out of 3 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl606

b:35.7
occ:1.00
O B:HOH881 2.8 23.1 1.0
O B:HOH915 3.0 38.5 1.0
N B:ARG450 3.0 14.5 1.0
CA B:TRP449 3.5 13.2 1.0
CB B:TRP449 3.7 13.2 1.0
CB B:ARG450 3.7 16.8 1.0
CG B:ARG450 3.7 18.7 1.0
C B:TRP449 3.8 12.9 1.0
CA B:ARG450 3.9 14.6 1.0
O A:HOH556 4.1 35.2 1.0
NH2 B:ARG450 4.1 43.5 1.0
O B:HOH906 4.2 35.5 1.0
F9 B:3N8603 4.3 23.6 0.3
F9 B:3N8603 4.4 19.6 0.3
CD B:ARG450 4.5 22.7 1.0
OH B:TYR447 4.7 17.3 0.8
O B:PRO448 4.7 13.8 1.0
C B:ARG450 4.8 14.7 1.0
N B:TRP449 4.8 13.4 1.0
O A:HOH544 4.9 36.5 1.0
CE2 B:TYR447 4.9 17.4 0.8
O B:TRP449 5.0 13.8 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: Sat Dec 12 11:18:02 2020

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