Sodium in PDB 7kuq: Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine:
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 N8-Acetylspermidine, PDB code: 7kuq 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) 60.85 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.509, 80.509, 249.38, 90, 90, 120
R / Rfree (%) 20.5 / 24.7

Other elements in 7kuq:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine (pdb code 7kuq). 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 N8-Acetylspermidine, PDB code: 7kuq:

Sodium binding site 1 out of 1 in 7kuq

Go back to Sodium Binding Sites List in 7kuq
Sodium binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine


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 N8-Acetylspermidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:54.8
occ:1.00
 O A:HOH965 2.5 52.4 1.0
O A:HOH871 2.6 34.2 1.0
O A:HOH833 2.6 39.8 1.0
O A:HOH811 2.7 46.6 1.0
O A:HOH976 2.8 45.2 1.0
O A:TYR92 3.9 32.1 1.0
N A:ALA94 4.2 24.8 1.0
O A:HOH877 4.4 40.4 1.0
OD2 A:ASP22 4.5 44.1 1.0
CA A:ALA94 4.6 31.0 1.0
CA A:LYS90 4.7 37.6 1.0
N A:VAL95 4.8 30.1 1.0
O A:VAL95 4.9 32.9 1.0
O A:SER89 4.9 28.1 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: Wed Mar 3 15:35:23 2021

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