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

Go back to

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

Go back to

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

Last articles

Mg in 4JI5
Mg in 4JI1
Mg in 4JI0
Mg in 4JI2
Mg in 4JI3
Mg in 4JHD
Mg in 4JH6
Mg in 4JH8
Mg in 4JH7
Mg in 4JH3

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy