Potassium in PDB 6wbq: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Tubastatin A

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

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Tubastatin A, PDB code: 6wbq 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)	53.24 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.630, 80.630, 246.811, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.5

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

Zinc

(Zn)

1 atom

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Tubastatin A (pdb code 6wbq). 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 Tubastatin A, PDB code: 6wbq:
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 Tubastatin A


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 Tubastatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:K707 b:26.2 occ:1.00 O A:TRP196 2.6 23.6 1.0 O A:HIS176 2.7 27.0 1.0 O A:ASP174 2.7 24.1 1.0 OD2 A:ASP172 2.7 24.2 1.0 OG A:SER195 2.8 20.7 1.0 O A:ASP172 3.0 27.2 1.0 CG A:ASP172 3.1 26.5 1.0 C A:ASP174 3.6 27.7 1.0 C A:ASP172 3.6 33.8 1.0 OD1 A:ASP172 3.7 29.9 1.0 C A:HIS176 3.7 26.5 1.0 CB A:ASP172 3.7 21.4 1.0 N A:ASP174 3.8 23.3 1.0 C A:TRP196 3.8 29.3 1.0 CB A:SER195 3.9 20.4 1.0 N A:TRP196 4.0 29.1 1.0 CA A:ASP174 4.1 30.0 1.0 CB A:ASP174 4.1 25.5 1.0 CA A:SER195 4.2 21.2 1.0 N A:TRP173 4.3 29.5 1.0 CA A:ASP172 4.3 22.1 1.0 C A:TRP173 4.3 24.5 1.0 CB A:HIS197 4.4 22.8 1.0 CA A:HIS177 4.4 26.8 1.0 N A:HIS176 4.4 27.2 1.0 CA A:TRP173 4.5 26.1 1.0 C A:SER195 4.5 29.8 1.0 N A:HIS177 4.5 26.8 1.0 ND1 A:HIS197 4.5 23.2 1.0 N A:GLY178 4.6 27.2 1.0 CD1 A:TRP196 4.6 24.7 1.0 N A:VAL175 4.6 27.9 1.0 CA A:TRP196 4.6 27.6 1.0 CE1 A:HIS136 4.7 24.9 1.0 C A:VAL175 4.7 30.5 1.0 OH A:TYR193 4.7 29.5 1.0 CA A:HIS176 4.7 28.4 1.0 CA A:HIS197 4.8 22.4 1.0 N A:HIS197 4.8 21.3 1.0 ND1 A:HIS136 4.9 24.8 1.0 C A:HIS177 4.9 28.2 1.0 CA A:VAL175 4.9 29.5 1.0 CG A:HIS197 5.0 28.6 1.0

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


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 Tubastatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:K708 b:44.0 occ:1.00 O A:HOH971 2.4 29.9 0.3 O A:VAL191 2.5 34.2 1.0 O A:HOH887 2.5 29.4 1.0 O A:PHE185 2.6 27.4 1.0 O A:ASP188 2.7 35.8 1.0 O A:PHE224 3.1 31.5 1.0 O A:HOH862 3.5 30.0 1.0 C A:PHE185 3.6 28.5 1.0 CB A:PHE224 3.7 29.6 1.0 CB A:PHE185 3.7 31.3 1.0 C A:VAL191 3.7 34.6 1.0 C A:ASP188 3.8 32.2 1.0 C A:PHE224 3.8 29.7 1.0 CA A:PHE185 4.2 26.7 1.0 N A:ASP188 4.3 34.8 1.0 CA A:PHE224 4.4 31.7 1.0 CA A:ASP188 4.4 33.9 1.0 N A:GLU186 4.5 27.9 1.0 CA A:GLU186 4.5 33.8 1.0 CB A:ASP188 4.6 33.6 1.0 CA A:VAL191 4.6 31.6 1.0 N A:LEU192 4.6 32.9 1.0 CB A:VAL191 4.6 28.6 1.0 CA A:LEU192 4.6 30.8 1.0 N A:TYR193 4.6 25.7 1.0 C A:GLU186 4.7 37.2 1.0 N A:ASN225 4.7 29.0 1.0 O A:GLU186 4.7 34.2 1.0 N A:VAL191 4.7 29.9 1.0 N A:PRO189 4.8 32.6 1.0 O A:GLY221 4.8 30.2 1.0 CG A:PHE224 4.9 32.6 1.0 CG A:PHE185 4.9 30.4 1.0

C.J.Herbst-Gervasoni, R.R.Steimbach, M.Morgen, A.K.Miller, D.W.Christianson. Structural Basis For the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase. Acs Chem.Biol. V. 15 2154 2020.
ISSN: ESSN 1554-8937
PubMed: 32659072
DOI: 10.1021/ACSCHEMBIO.0C00362