Calcium in PDB 7dkw: Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside.

Enzymatic activity of Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside.

All present enzymatic activity of Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside.:
3.2.1.21;

Protein crystallography data

The structure of Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside., PDB code: 7dkw 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)*	35.00 / 1.78
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	179.214, 54.602, 164.55, 90, 90, 90
*R / R_free (%)*	15.8 / 18.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside. (pdb code 7dkw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside., PDB code: 7dkw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7dkw

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Calcium Binding Sites List in 7dkw

Calcium binding site 1 out of 2 in the Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside.

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca1004 b:36.6 occ:1.00	OD1	A:ASP583	2.3	32.9	1.0
	OD1	A:ASP579	2.3	41.1	1.0
	O	A:ILE581	2.4	33.0	1.0
	OD1	A:ASP577	2.4	46.1	1.0
	O	A:HOH1132	2.5	34.3	1.0
	OD1	A:ASP575	2.5	35.3	1.0
	O	A:HOH1414	2.8	50.7	1.0
	CG	A:ASP579	3.1	40.5	1.0
	CG	A:ASP583	3.3	34.4	1.0
	CG	A:ASP575	3.5	34.9	1.0
	OD2	A:ASP579	3.6	38.3	1.0
	C	A:ILE581	3.6	33.6	1.0
	CG	A:ASP577	3.6	48.8	1.0
	OD2	A:ASP583	3.8	39.6	1.0
	CA	A:ASP575	4.2	38.2	1.0
	N	A:LYS576	4.2	45.3	1.0
	N	A:ILE581	4.2	33.6	1.0
	OD2	A:ASP577	4.2	52.5	1.0
	CB	A:ASP575	4.2	37.0	1.0
	OD2	A:ASP575	4.2	33.5	1.0
	N	A:ASP577	4.3	46.9	1.0
	CB	A:ASP579	4.3	41.7	1.0
	CA	A:ILE581	4.3	33.6	1.0
	N	A:ASP579	4.3	45.2	1.0
	C	A:PRO582	4.3	31.9	1.0
	N	A:ASP583	4.3	30.8	1.0
	OG1	A:THR600	4.4	31.4	1.0
	CB	A:ILE581	4.4	32.9	1.0
	O	A:PRO582	4.5	33.1	1.0
	CB	A:ASP583	4.5	33.0	1.0
	C	A:ASP575	4.6	41.9	1.0
	CA	A:ASP583	4.6	31.6	1.0
	N	A:PRO582	4.6	32.4	1.0
	CA	A:ASP579	4.7	41.8	1.0
	N	A:ASN578	4.8	44.9	1.0
	CB	A:ASP577	4.8	48.0	1.0
	CA	A:PRO582	4.8	32.1	1.0
	CA	A:ASP577	4.9	46.7	1.0
	C	A:ASP577	4.9	46.3	1.0
	N	A:GLY580	4.9	35.9	1.0

Calcium binding site 2 out of 2 in 7dkw

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Calcium Binding Sites List in 7dkw

Calcium binding site 2 out of 2 in the Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside.

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ca905 b:27.6 occ:1.00	OD1	B:ASP579	2.2	24.1	1.0
	OD1	B:ASP583	2.3	26.4	1.0
	O	B:ILE581	2.3	25.1	1.0
	OD1	B:ASP575	2.4	27.2	1.0
	OD1	B:ASP577	2.4	34.3	1.0
	O	B:HOH1032	2.5	23.0	1.0
	CG	B:ASP579	3.2	25.9	1.0
	CG	B:ASP583	3.2	27.6	1.0
	O	B:HOH1225	3.3	42.2	1.0
	CG	B:ASP575	3.4	26.2	1.0
	C	B:ILE581	3.5	23.1	1.0
	CG	B:ASP577	3.6	38.7	1.0
	OD2	B:ASP579	3.6	27.1	1.0
	OD2	B:ASP583	3.7	31.9	1.0
	N	B:ILE581	4.1	23.4	1.0
	CA	B:ASP575	4.1	27.8	1.0
	OD2	B:ASP577	4.1	41.4	1.0
	CA	B:ILE581	4.2	23.1	1.0
	CB	B:ASP575	4.2	26.9	1.0
	N	B:LYS576	4.2	33.0	1.0
	N	B:ASP577	4.2	35.6	1.0
	OD2	B:ASP575	4.3	25.9	1.0
	C	B:PRO582	4.3	22.7	1.0
	N	B:ASP579	4.3	28.5	1.0
	N	B:ASP583	4.3	22.7	1.0
	CB	B:ASP579	4.3	26.8	1.0
	CB	B:ILE581	4.3	22.1	1.0
	CB	B:ASP583	4.4	26.1	1.0
	O	B:PRO582	4.5	24.5	1.0
	OG1	B:THR600	4.5	22.9	1.0
	N	B:PRO582	4.5	23.1	1.0
	CA	B:ASP583	4.5	24.0	1.0
	C	B:ASP575	4.5	30.6	1.0
	CA	B:PRO582	4.7	22.8	1.0
	CA	B:ASP579	4.7	27.2	1.0
	CB	B:ASP577	4.8	36.2	1.0
	N	B:ASN578	4.8	32.8	1.0
	N	B:GLY580	4.8	24.7	1.0
	CA	B:ASP577	4.9	35.7	1.0
	C	B:ASP579	4.9	26.0	1.0
	C	B:ASP577	5.0	35.3	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: Wed Jul 9 21:37:20 2025

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