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 / R_free (%)*	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

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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

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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

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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: Fri Jul 26 02:54:37 2024

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