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

Go back to

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF

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