Sodium in PDB 5eem: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2, PDB code: 5eem was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	15.91 / 2.00
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	48.485, 55.400, 74.183, 73.58, 89.84, 82.64
*R / R_free (%)*	22.4 / 27.3

Other elements in 5eem:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Zinc	(Zn)	2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (pdb code 5eem). 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 Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2, PDB code: 5eem:

Sodium binding site 1 out of 1 in 5eem

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Sodium Binding Sites List in 5eem

Sodium binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na804 b:31.6 occ:1.00	CZ2	B:TRP794	3.2	16.0	1.0
	O	B:PHE793	3.2	15.5	1.0
	CH2	B:TRP794	3.3	15.9	1.0
	CE2	B:TRP794	3.4	14.4	1.0
	CZ	B:TYR662	3.4	20.3	1.0
	OH	B:TYR662	3.5	24.4	1.0
	CE1	B:TYR662	3.6	20.7	1.0
	CZ3	B:TRP794	3.6	16.4	1.0
	CD2	B:TRP794	3.7	14.7	1.0
	CE3	B:TRP794	3.8	15.7	1.0
	CE2	B:TYR662	4.0	20.0	1.0
	C	B:PHE793	4.1	15.9	1.0
	NE1	B:TRP794	4.1	11.0	1.0
	CB	B:PHE793	4.1	15.2	1.0
	CD1	B:TYR662	4.3	18.4	1.0
	CA	B:PHE793	4.5	16.2	1.0
	CG	B:TRP794	4.5	13.5	1.0
	CD2	B:TYR662	4.7	18.0	1.0
	CD1	B:TRP794	4.7	13.8	1.0
	CG	B:TYR662	4.8	17.7	1.0
	O	B:ARG660	4.8	15.4	1.0
	CA	B:GLY661	4.8	13.6	1.0
	C	B:GLY661	4.9	14.8	1.0
	O	B:GLY661	4.9	14.5	1.0

Reference:

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134

Page generated: Mon Oct 7 20:45:29 2024

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