Potassium in PDB 7sgg: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Saha

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

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Saha, PDB code: 7sgg 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)	69.58 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.338, 80.338, 247.241, 90, 90, 120
R / Rfree (%)	18.3 / 20.6

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


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 Saha within 5.0Å range: probe atom residue distance (Å) B Occ A:K704 b:28.7 occ:1.00 O A:HIS176 2.6 30.3 1.0 O A:TRP196 2.7 29.9 1.0 O A:ASP174 2.7 30.6 1.0 OG A:SER195 2.8 25.4 1.0 OD2 A:ASP172 2.8 28.2 1.0 O A:ASP172 2.9 29.6 1.0 CG A:ASP172 3.1 29.1 1.0 C A:ASP172 3.5 36.3 1.0 C A:ASP174 3.6 35.5 1.0 OD1 A:ASP172 3.7 34.4 1.0 C A:HIS176 3.7 28.3 1.0 CB A:ASP172 3.7 29.3 1.0 C A:TRP196 3.8 30.6 1.0 N A:ASP174 3.9 26.3 1.0 CB A:SER195 3.9 27.3 1.0 N A:TRP196 4.0 28.6 1.0 CA A:ASP174 4.1 28.3 1.0 CB A:ASP174 4.1 23.7 1.0 CA A:SER195 4.2 24.6 1.0 CA A:ASP172 4.2 24.5 1.0 N A:TRP173 4.3 32.5 1.0 C A:TRP173 4.3 29.4 1.0 CB A:HIS197 4.3 25.3 1.0 CA A:HIS177 4.3 27.8 1.0 N A:HIS176 4.4 34.0 1.0 N A:HIS177 4.4 26.4 1.0 ND1 A:HIS197 4.4 26.1 1.0 C A:SER195 4.5 34.8 1.0 CA A:TRP173 4.5 26.1 1.0 N A:GLY178 4.5 27.3 1.0 CA A:TRP196 4.6 25.7 1.0 CD1 A:TRP196 4.6 28.7 1.0 N A:VAL175 4.6 28.8 1.0 C A:VAL175 4.7 35.4 1.0 CA A:HIS176 4.7 28.4 1.0 CE1 A:HIS136 4.7 25.2 1.0 CA A:HIS197 4.7 24.9 1.0 OH A:TYR193 4.7 31.9 1.0 N A:HIS197 4.8 24.4 1.0 C A:HIS177 4.8 26.7 1.0 ND1 A:HIS136 4.9 26.4 1.0 CG A:HIS197 4.9 29.8 1.0 CA A:VAL175 5.0 31.6 1.0

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


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 Saha within 5.0Å range: probe atom residue distance (Å) B Occ A:K705 b:51.8 occ:1.00 O A:HOH946 2.4 35.8 1.0 O A:ASP188 2.4 35.2 1.0 O A:VAL191 2.4 33.5 1.0 O A:PHE185 2.5 30.2 1.0 O A:HOH859 2.6 31.7 1.0 C A:ASP188 3.4 40.2 1.0 C A:PHE185 3.6 30.9 1.0 C A:VAL191 3.6 37.5 1.0 O A:PHE224 3.6 31.5 1.0 CB A:PHE224 3.7 31.3 1.0 CB A:PHE185 3.7 28.1 1.0 N A:ASP188 3.9 39.9 1.0 CA A:ASP188 4.1 36.0 1.0 O A:HOH843 4.1 33.2 1.0 C A:PHE224 4.2 35.9 1.0 CA A:PHE185 4.2 29.9 1.0 CB A:ASP188 4.3 40.1 1.0 CA A:VAL191 4.3 38.8 1.0 N A:VAL191 4.4 34.1 1.0 CB A:VAL191 4.4 35.8 1.0 N A:PRO189 4.4 36.0 1.0 O A:GLU186 4.5 36.3 1.0 C A:GLU186 4.5 39.0 1.0 N A:GLU186 4.6 30.2 1.0 CA A:PHE224 4.6 35.4 1.0 CA A:GLU186 4.6 33.8 1.0 CA A:PRO189 4.6 33.0 1.0 N A:LEU192 4.7 34.8 1.0 O A:GLY221 4.8 35.7 1.0 CG A:PHE224 4.8 33.9 1.0 CA A:LEU192 4.8 33.5 0.7 CA A:LEU192 4.8 33.5 0.3 CG1 A:VAL191 4.9 28.9 1.0 CG A:PHE185 4.9 30.2 1.0 C A:PRO189 5.0 36.6 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