Sodium in PDB 7kur: Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine:
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine, PDB code: 7kur was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	69.77 / 2.10
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	80.56, 80.56, 245.71, 90, 90, 120
*R / R_free (%)*	19.1 / 21.7

Other elements in 7kur:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Potassium	(K)	2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine (pdb code 7kur). 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 10 Y307F Mutant in Complex with N-Acetylputrescine, PDB code: 7kur:

Sodium binding site 1 out of 1 in 7kur

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Sodium Binding Sites List in 7kur

Sodium binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine

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 10 Y307F Mutant in Complex with N-Acetylputrescine within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na709 b:62.4 occ:1.00	O	A:HOH1048	2.4	62.1	1.0
	O	A:HOH1023	2.5	54.5	1.0
	O	A:HOH865	2.7	49.6	1.0
	O	A:HOH976	2.7	45.3	1.0
	O	A:HOH935	2.8	33.1	1.0
	O	A:HOH1036	2.9	57.4	1.0
	OD2	A:ASP22	4.2	45.0	1.0
	O	A:TYR92	4.3	33.0	1.0
	O	A:HOH848	4.3	36.6	1.0
	N	A:ALA94	4.5	27.9	1.0
	CG	A:LYS90	4.8	43.6	1.0
	CA	A:LYS90	4.8	40.7	1.0
	OE2	A:GLU24	4.9	53.2	1.0
	CA	A:ALA94	4.9	32.0	1.0

Reference:

C.J.Herbst-Gervasoni, D.W.Christianson. X-Ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33449614
DOI: 10.1021/ACS.BIOCHEM.0C00936

Page generated: Tue Oct 8 17:30:10 2024

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