Fluorine in PDB 6gwg: Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile

Enzymatic activity of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile

All present enzymatic activity of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile:
3.2.1.22;

Protein crystallography data

The structure of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile, PDB code: 6gwg was solved by T.M.Gloster, V.Oehler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	24.36 / 1.77
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	66.730, 95.870, 97.440, 90.00, 90.00, 90.00
*R / R_free (%)*	16.7 / 21.5

Other elements in 6gwg:

The structure of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile (pdb code 6gwg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile, PDB code: 6gwg:

Fluorine binding site 1 out of 1 in 6gwg

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Fluorine Binding Sites List in 6gwg

Fluorine binding site 1 out of 1 in the Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F609 b:20.6 occ:1.00	FAH	A:FEK609	0.0	20.6	1.0
	CAE	A:FEK609	1.5	19.7	1.0
	CAD	A:FEK609	2.4	18.9	1.0
	CAA	A:FEK609	2.5	23.2	1.0
	SG	A:CYS368	2.7	23.0	0.5
	OAG	A:FEK609	3.0	18.4	1.0
	OD1	A:ASP387	3.1	18.7	1.0
	NE1	A:TRP65	3.2	33.8	1.0
	NH1	A:ARG383	3.3	17.0	1.0
	OD2	A:ASP327	3.3	20.5	1.0
	OD1	A:ASP327	3.4	19.4	1.0
	O	A:HOH966	3.5	25.2	1.0
	CAB	A:FEK609	3.6	18.8	1.0
	CZ2	A:TRP65	3.6	26.0	1.0
	CG	A:ASP327	3.7	20.3	1.0
	CE2	A:TRP65	3.7	29.1	1.0
	CAC	A:FEK609	3.8	19.0	1.0
	NH2	A:ARG383	3.9	16.4	1.0
	CZ	A:ARG383	4.0	17.6	1.0
	CG	A:ASP387	4.0	22.2	1.0
	CB	A:CYS368	4.1	14.9	0.5
	OD2	A:ASP387	4.2	20.0	1.0
	CAI	A:FEK609	4.2	19.5	1.0
	SG	A:CYS368	4.3	14.7	0.5
	CB	A:CYS368	4.3	21.2	0.5
	OAF	A:FEK609	4.3	18.4	1.0
	CD1	A:TRP65	4.4	30.8	1.0
	OH	A:TYR191	4.8	19.6	1.0
	CE	A:LYS325	4.8	19.0	1.0
	N	A:GLY369	4.9	18.1	1.0
	CH2	A:TRP65	4.9	24.4	1.0
	NZ	A:LYS325	5.0	19.2	1.0

Reference:

W.Ren, R.Pengelly, M.Farren-Dai, S.Shamsi Kazem Abadi, V.Oehler, O.Akintola, J.Draper, M.Meanwell, S.Chakladar, K.Swiderek, V.Moliner, R.Britton, T.M.Gloster, A.J.Bennet. Revealing the Mechanism For Covalent Inhibition of Glycoside Hydrolases By Carbasugars at An Atomic Level. Nat Commun V. 9 3243 2018.
ISSN: ESSN 2041-1723
PubMed: 30104598
DOI: 10.1038/S41467-018-05702-7

Page generated: Thu Aug 1 20:49:32 2024

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