Sodium in PDB 6ybo: Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip.

Enzymatic activity of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip.

All present enzymatic activity of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip.:
5.3.1.5;

Protein crystallography data

The structure of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip., PDB code: 6ybo was solved by J.A.Gavira, S.Martinez-Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	41.12 / 1.06
*Space group*	I 2 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	93.940, 99.370, 103.040, 90.00, 90.00, 90.00
*R / R_free (%)*	12.3 / 13.1

Other elements in 6ybo:

The structure of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip. also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip. (pdb code 6ybo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip., PDB code: 6ybo:

Sodium binding site 1 out of 1 in 6ybo

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Sodium Binding Sites List in 6ybo

Sodium binding site 1 out of 1 in the Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip.

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rt Structure of Glucose Isomerase Obtained at 1.06 A Resolution From Crystal Grown in A Kapton Microchip. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na403 b:25.9 occ:1.00	OD1	A:ASP163	2.7	16.7	1.0
	O	A:HOH534	2.8	29.7	1.0
	OH	A:TYR212	2.9	18.3	1.0
	N	A:ARG208	3.0	19.2	1.0
	N	A:GLU207	3.4	17.1	0.3
	N	A:GLU207	3.4	17.4	0.7
	CE1	A:TYR212	3.4	16.6	1.0
	CZ	A:TYR212	3.6	16.6	1.0
	CB	A:GLU207	3.6	19.7	0.3
	CA	A:ASP163	3.6	15.2	1.0
	CG	A:ASP163	3.7	16.0	1.0
	CB	A:ARG208	3.7	23.8	1.0
	CA	A:GLU207	3.7	18.6	0.3
	CB	A:GLU207	3.8	22.2	0.7
	CA	A:GLU207	3.8	19.4	0.7
	C	A:GLU207	3.8	19.6	0.7
	C	A:GLU207	3.8	19.9	0.3
	CA	A:ARG208	3.8	20.2	1.0
	CB	A:LEU206	4.0	14.9	1.0
	CG	A:ARG208	4.1	28.9	1.0
	CB	A:ASP163	4.1	15.7	1.0
	C	A:LEU206	4.2	16.8	1.0
	O	A:ARG208	4.2	18.8	1.0
	C	A:ARG208	4.3	18.8	1.0
	O	A:PHE162	4.3	14.8	1.0
	O	A:ASP163	4.4	16.6	1.0
	N	A:ASP163	4.4	14.3	1.0
	C	A:ASP163	4.5	15.5	1.0
	CA	A:LEU206	4.6	15.5	1.0
	CD1	A:TYR212	4.6	16.1	1.0
	C	A:PHE162	4.6	14.0	1.0
	CD	A:ARG208	4.7	35.6	1.0
	OD2	A:ASP163	4.8	17.3	1.0
	CG	A:GLU207	4.8	22.6	0.3
	CG	A:GLU207	4.8	25.3	0.7
	CA	A:GLY166	4.8	17.0	1.0
	CE2	A:TYR212	4.8	16.0	1.0
	O	A:GLU207	4.9	21.2	0.7
	CG	A:LEU206	5.0	15.1	1.0
	O	A:GLU207	5.0	22.7	0.3

Reference:

J.A.Gavira, I.Rodriguez-Ruiz, S.Martinez-Rodriguez, S.Basu, S.Teychene, A.A.Mccarthy, C.Mueller-Dieckman. Attaining Atomic Resolution From in Situ Data Collection at Room Temperature Using Counter-Diffusion-Based Low-Cost Microchips. Acta Crystallogr D Struct V. 76 751 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32744257
DOI: 10.1107/S2059798320008475

Page generated: Tue Oct 8 15:01:25 2024

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