Sodium in PDB 7sgi: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Inhibitor 14

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Inhibitor 14

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Inhibitor 14:
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Inhibitor 14, PDB code: 7sgi 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) 69.71 / 2.15
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.5, 80.5, 246.632, 90, 90, 120
R / Rfree (%) 19 / 22.2

Other elements in 7sgi:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Inhibitor 14 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 in Complex with Inhibitor 14 (pdb code 7sgi). 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 in Complex with Inhibitor 14, PDB code: 7sgi:

Sodium binding site 1 out of 1 in 7sgi

Go back to Sodium Binding Sites List in 7sgi
Sodium binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Inhibitor 14


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 in Complex with Inhibitor 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:63.6
occ:1.00
 O A:HOH968 2.6 45.7 1.0
O A:HOH1000 2.6 55.0 1.0
O A:HOH965 2.6 55.6 1.0
O A:HOH1019 2.9 51.5 1.0
O A:HOH906 3.0 30.7 1.0
O A:TYR92 4.1 31.5 1.0
OE2 A:GLU24 4.4 65.3 1.0
O A:HOH915 4.5 41.2 1.0
N A:ALA94 4.5 28.9 1.0
OD2 A:ASP22 4.5 50.2 1.0
CA A:LYS90 4.8 39.5 1.0
CG A:LYS90 4.8 39.8 1.0
O A:SER89 4.9 34.5 1.0

Reference:

R.R.Steimbach, C.J.Herbst-Gervasoni, S.Lechner, T.M.Stewart, G.Klinke, J.Ridinger, M.N.E.Geraldy, G.Tihanyi, J.R.Foley, U.Uhrig, B.Kuster, G.Poschet, R.A.Casero Jr., G.Medard, I.Oehme, D.W.Christianson, N.Gunkel, A.K.Miller. Aza-Saha Derivatives Are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation and Phenocopy HDAC10 Knockout. J.Am.Chem.Soc. V. 144 18861 2022.
ISSN: ESSN 1520-5126
PubMed: 36200994
DOI: 10.1021/JACS.2C05030
Page generated: Fri Apr 7 16:16:58 2023

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