Potassium in PDB 7sgj: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-711

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-711:
3.5.1.48; 3.5.1.62;

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-711, PDB code: 7sgj 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)	69.64 / 2.15
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.408, 80.408, 248.27, 90, 90, 120
R / Rfree (%)	18.2 / 21.6

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-711 also contains other interesting chemical elements:

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

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-711 (pdb code 7sgj). 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-711, PDB code: 7sgj:
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-711


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-711 within 5.0Å range: probe atom residue distance (Å) B Occ A:K705 b:31.6 occ:1.00 O A:TRP196 2.7 31.7 1.0 O A:HIS176 2.7 32.7 1.0 O A:ASP174 2.7 28.8 1.0 OG A:SER195 2.8 27.4 1.0 OD2 A:ASP172 2.8 31.4 1.0 O A:ASP172 2.9 32.4 1.0 CG A:ASP172 3.1 28.8 1.0 C A:ASP172 3.6 37.5 1.0 C A:ASP174 3.6 36.3 1.0 OD1 A:ASP172 3.6 37.1 1.0 C A:HIS176 3.7 29.8 1.0 CB A:ASP172 3.8 28.4 1.0 C A:TRP196 3.8 32.5 1.0 CB A:SER195 3.9 29.0 1.0 N A:ASP174 3.9 26.5 1.0 N A:TRP196 4.0 30.3 1.0 CA A:ASP174 4.1 32.5 1.0 CA A:SER195 4.2 27.1 1.0 CB A:ASP174 4.2 27.2 1.0 CA A:ASP172 4.3 27.2 1.0 CA A:HIS177 4.3 32.3 1.0 N A:HIS176 4.3 32.9 1.0 C A:TRP173 4.3 30.0 1.0 N A:TRP173 4.4 33.1 1.0 N A:GLY178 4.4 29.2 1.0 CB A:HIS197 4.4 26.0 1.0 N A:HIS177 4.4 29.1 1.0 C A:SER195 4.4 37.1 1.0 ND1 A:HIS197 4.5 25.5 1.0 CA A:TRP173 4.5 29.1 1.0 CA A:TRP196 4.6 29.9 1.0 CD1 A:TRP196 4.6 28.9 1.0 N A:VAL175 4.6 32.6 1.0 C A:VAL175 4.7 33.1 1.0 CA A:HIS176 4.7 29.9 1.0 CE1 A:HIS136 4.7 30.6 1.0 OH A:TYR193 4.7 34.1 1.0 C A:HIS177 4.8 28.8 1.0 CA A:HIS197 4.8 26.3 1.0 N A:HIS197 4.8 25.9 1.0 ND1 A:HIS136 4.8 28.7 1.0 CG A:HIS197 4.9 29.2 1.0 CA A:VAL175 5.0 32.1 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-711


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-711 within 5.0Å range: probe atom residue distance (Å) B Occ A:K706 b:52.5 occ:1.00 O A:HOH949 2.4 35.3 1.0 O A:ASP188 2.4 36.9 1.0 O A:VAL191 2.5 38.7 1.0 O A:PHE185 2.5 35.1 1.0 O A:HOH869 2.6 34.8 1.0 C A:ASP188 3.5 36.4 1.0 O A:PHE224 3.5 35.8 1.0 CB A:PHE224 3.6 31.5 1.0 C A:PHE185 3.6 34.8 1.0 C A:VAL191 3.7 38.1 1.0 CB A:PHE185 3.7 29.1 1.0 N A:ASP188 4.0 43.7 1.0 O A:HOH847 4.0 30.2 1.0 C A:PHE224 4.1 33.8 1.0 CA A:ASP188 4.1 40.4 1.0 CA A:PHE185 4.2 29.4 1.0 CB A:ASP188 4.3 40.9 1.0 CA A:VAL191 4.4 37.2 1.0 N A:VAL191 4.4 36.5 1.0 CB A:VAL191 4.4 36.6 1.0 CA A:PHE224 4.5 34.4 1.0 N A:PRO189 4.5 41.3 1.0 O A:GLU186 4.5 38.9 1.0 N A:GLU186 4.6 34.9 1.0 C A:GLU186 4.6 40.0 1.0 CA A:PRO189 4.7 36.4 1.0 N A:LEU192 4.7 36.5 1.0 CG A:PHE224 4.7 35.1 1.0 O A:GLY221 4.7 38.3 1.0 CA A:LEU192 4.8 38.3 1.0 CA A:GLU186 4.9 35.8 1.0 N A:ASN225 4.9 31.7 1.0 CG A:PHE185 4.9 35.1 1.0 CG1 A:VAL191 5.0 33.0 1.0 C A:PRO189 5.0 38.9 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