Fluorine in PDB 7dkt: Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Alpha-Glucosyl Fluoride

Enzymatic activity of Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Alpha-Glucosyl Fluoride

All present enzymatic activity of Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Alpha-Glucosyl Fluoride:
3.2.1.21;

Protein crystallography data

The structure of Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Alpha-Glucosyl Fluoride, PDB code: 7dkt was solved by S.Pengthaisong, J.R.Ketudat Cairns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	88.52 / 1.65
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	177.049, 54.689, 83.24, 90, 90, 90
*R / R_free (%)*	16 / 18.7

Other elements in 7dkt:

The structure of Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Alpha-Glucosyl Fluoride also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Alpha-Glucosyl Fluoride (pdb code 7dkt). 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 Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Alpha-Glucosyl Fluoride, PDB code: 7dkt:

Fluorine binding site 1 out of 1 in 7dkt

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Fluorine Binding Sites List in 7dkt

Fluorine binding site 1 out of 1 in the Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Alpha-Glucosyl Fluoride

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Alpha-Glucosyl Fluoride within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F1001 b:11.8 occ:1.00	F1	A:GLF1001	0.0	11.8	1.0
	C1	A:GLF1001	1.4	11.8	1.0
	O5	A:GLF1001	2.3	11.1	1.0
	C2	A:GLF1001	2.4	11.4	1.0
	OH	A:TYR790	2.8	11.3	1.0
	O2	A:GLF1001	2.8	11.5	1.0
	C3	A:GLF1001	2.9	11.5	1.0
	C5	A:GLF1001	2.9	11.4	1.0
	O	A:HOH1120	3.0	25.2	1.0
	CD2	A:TYR445	3.2	12.0	1.0
	C4	A:GLF1001	3.5	11.4	1.0
	CZ	A:TYR790	3.8	10.2	1.0
	CG	A:TYR445	3.8	11.6	1.0
	CB	A:TYR445	3.8	11.4	1.0
	CE1	A:TYR790	3.9	9.9	1.0
	CE2	A:TYR445	3.9	12.1	1.0
	O	A:HOH1158	4.1	20.6	1.0
	O3	A:GLF1001	4.2	12.0	1.0
	C6	A:GLF1001	4.3	11.4	1.0
	CB	A:ALA441	4.4	10.3	1.0
	O4	A:GLF1001	4.5	11.6	1.0
	O6	A:GLF1001	4.5	12.1	1.0
	CG2	A:VAL453	4.8	9.3	1.0
	CD1	A:TYR445	5.0	12.4	1.0
	C1	A:GOL1002	5.0	28.1	1.0

Reference:

S.Pengthaisong, Y.Hua, J.R.Ketudat Cairns. Structural Basis For Transglycosylation in Glycoside Hydrolase Family GH116 Glycosynthases. Arch.Biochem.Biophys. V. 706 08924 2021.
ISSN: ESSN 1096-0384
PubMed: 34019851
DOI: 10.1016/J.ABB.2021.108924

Page generated: Fri Aug 2 06:29:13 2024

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