Potassium in PDB 7sgk: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728:
3.5.1.48; 3.5.1.62;

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728, PDB code: 7sgk 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)	69.76 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.548, 80.548, 243.35, 90, 90, 120
R / Rfree (%)	19.5 / 24.3

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728 also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Sodium	(Na)	1 atom

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728 (pdb code 7sgk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728, PDB code: 7sgk:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728 within 5.0Å range: probe atom residue distance (Å) B Occ A:K703 b:28.9 occ:1.00 O A:ASP174 2.6 33.9 1.0 O A:HIS176 2.6 31.1 1.0 O A:TRP196 2.7 32.3 1.0 OD2 A:ASP172 2.8 25.4 1.0 O A:ASP172 2.8 33.4 1.0 OG A:SER195 2.9 26.3 1.0 CG A:ASP172 3.1 24.4 1.0 C A:ASP174 3.5 34.3 1.0 C A:ASP172 3.5 36.3 1.0 OD1 A:ASP172 3.6 34.9 1.0 C A:HIS176 3.7 32.8 1.0 N A:ASP174 3.8 26.2 1.0 CB A:ASP172 3.8 22.1 1.0 C A:TRP196 3.9 33.0 1.0 CA A:ASP174 3.9 32.9 1.0 CB A:ASP174 4.0 29.4 1.0 CB A:SER195 4.0 28.8 1.0 N A:TRP196 4.1 32.9 1.0 C A:TRP173 4.3 26.6 1.0 CA A:ASP172 4.3 27.4 1.0 N A:TRP173 4.3 30.6 1.0 CA A:SER195 4.3 25.8 1.0 N A:HIS176 4.4 36.9 1.0 CA A:HIS177 4.4 29.3 1.0 CB A:HIS197 4.4 31.7 1.0 N A:HIS177 4.4 30.1 1.0 CA A:TRP173 4.5 23.5 1.0 N A:VAL175 4.5 31.1 1.0 ND1 A:HIS197 4.5 29.9 1.0 N A:GLY178 4.6 27.1 1.0 C A:SER195 4.6 38.7 1.0 C A:VAL175 4.6 34.2 1.0 CD1 A:TRP196 4.6 29.3 1.0 CA A:HIS176 4.7 30.4 1.0 CA A:TRP196 4.7 28.1 1.0 OH A:TYR193 4.7 30.3 1.0 CE1 A:HIS136 4.7 25.8 1.0 CA A:HIS197 4.8 32.1 1.0 N A:HIS197 4.8 31.2 1.0 ND1 A:HIS136 4.9 27.4 1.0 C A:HIS177 4.9 27.9 1.0 CA A:VAL175 4.9 34.0 1.0 CG A:HIS197 5.0 29.0 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728 within 5.0Å range: probe atom residue distance (Å) B Occ A:K704 b:47.4 occ:1.00 O A:HOH949 2.4 42.3 0.7 O A:VAL191 2.5 38.4 1.0 O A:PHE185 2.5 35.7 1.0 O A:ASP188 2.6 37.3 1.0 O A:HOH804 2.7 37.6 1.0 O A:PHE224 3.4 36.8 1.0 C A:PHE185 3.5 40.0 1.0 CB A:PHE185 3.5 32.0 1.0 O A:HOH934 3.6 35.4 1.0 C A:VAL191 3.7 37.5 1.0 C A:ASP188 3.7 35.8 1.0 CB A:PHE224 3.7 31.3 1.0 C A:PHE224 4.0 37.8 1.0 CA A:PHE185 4.1 25.8 1.0 N A:ASP188 4.2 44.3 1.0 CA A:ASP188 4.3 37.1 1.0 O A:GLU186 4.4 35.4 1.0 CB A:ASP188 4.4 37.2 1.0 N A:GLU186 4.5 33.3 1.0 CA A:PHE224 4.5 40.7 1.0 CA A:VAL191 4.5 38.4 1.0 CB A:VAL191 4.6 42.2 1.0 N A:LEU192 4.6 34.3 1.0 C A:GLU186 4.6 41.2 1.0 CA A:LEU192 4.7 38.8 1.0 N A:TYR193 4.7 32.2 1.0 N A:VAL191 4.7 32.3 1.0 CA A:GLU186 4.7 41.5 1.0 N A:ASN225 4.8 36.1 1.0 N A:PRO189 4.8 39.0 1.0 CG A:PHE185 4.8 38.9 1.0 O A:GLY221 4.9 40.8 1.0 CG1 A:VAL191 4.9 32.2 1.0 CA A:PRO189 5.0 36.3 1.0 CG A:PHE224 5.0 32.5 1.0

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