Potassium in PDB 6vnq: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor

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

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor, PDB code: 6vnq 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 / 2.05
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.549, 80.549, 245.370, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 23.1

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor 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 Bishydroxamic Acid Based Inhibitor (pdb code 6vnq). 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 Bishydroxamic Acid Based Inhibitor, PDB code: 6vnq:
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 Bishydroxamic Acid Based Inhibitor


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 Bishydroxamic Acid Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:K705 b:24.8 occ:1.00 O A:TRP196 2.6 26.8 1.0 O A:HIS176 2.6 26.5 1.0 O A:ASP174 2.7 25.5 1.0 OD2 A:ASP172 2.7 22.3 1.0 OG A:SER195 2.8 20.4 1.0 O A:ASP172 2.9 30.3 1.0 CG A:ASP172 3.1 27.6 1.0 C A:ASP174 3.5 34.0 1.0 C A:ASP172 3.6 32.3 1.0 OD1 A:ASP172 3.7 29.4 1.0 C A:HIS176 3.7 28.5 1.0 N A:ASP174 3.7 25.1 1.0 CB A:ASP172 3.8 24.2 1.0 C A:TRP196 3.8 32.3 1.0 CB A:SER195 3.9 23.8 1.0 CA A:ASP174 4.0 25.2 1.0 CB A:ASP174 4.1 24.6 1.0 N A:TRP196 4.1 28.3 1.0 C A:TRP173 4.2 22.7 1.0 CA A:SER195 4.2 22.4 1.0 N A:TRP173 4.2 27.6 1.0 CA A:ASP172 4.3 25.6 1.0 N A:HIS176 4.4 30.4 1.0 CA A:HIS177 4.4 23.8 1.0 CB A:HIS197 4.4 24.0 1.0 CA A:TRP173 4.4 25.3 1.0 N A:HIS177 4.5 27.9 1.0 C A:SER195 4.5 32.4 1.0 N A:GLY178 4.6 25.8 1.0 ND1 A:HIS197 4.6 23.1 1.0 N A:VAL175 4.6 28.6 1.0 CD1 A:TRP196 4.6 29.2 1.0 CA A:TRP196 4.6 26.5 1.0 CE1 A:HIS136 4.6 24.2 1.0 C A:VAL175 4.7 35.2 1.0 CA A:HIS176 4.7 30.9 1.0 CA A:HIS197 4.7 23.7 1.0 N A:HIS197 4.8 26.3 1.0 OH A:TYR193 4.8 27.6 1.0 C A:HIS177 4.9 23.7 1.0 ND1 A:HIS136 4.9 27.2 1.0 CA A:VAL175 5.0 30.4 1.0 CG A:HIS197 5.0 25.9 1.0 O A:TRP173 5.0 28.2 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor


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 Bishydroxamic Acid Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:K706 b:31.8 occ:1.00 O A:VAL191 2.6 29.1 1.0 O A:PHE185 2.7 30.8 1.0 O A:HOH860 2.7 28.4 1.0 O A:HOH977 2.8 31.6 1.0 O A:PHE224 2.9 31.5 1.0 O A:ASP188 3.0 33.7 1.0 C A:PHE185 3.6 29.5 1.0 C A:PHE224 3.6 35.9 1.0 CB A:PHE185 3.6 26.2 1.0 CB A:PHE224 3.8 29.1 1.0 C A:VAL191 3.8 33.7 1.0 C A:ASP188 4.1 30.6 1.0 CA A:PHE185 4.2 27.6 1.0 CA A:PHE224 4.3 32.8 1.0 N A:TYR193 4.4 25.8 1.0 N A:ASN225 4.4 29.2 1.0 N A:ASP188 4.5 37.2 1.0 N A:GLU186 4.5 29.6 1.0 O A:GLU186 4.6 33.6 1.0 CA A:LEU192 4.6 35.8 1.0 N A:LEU192 4.7 30.8 1.0 CA A:ASP188 4.7 32.0 1.0 CB A:ASN225 4.7 26.9 1.0 CA A:ASN225 4.7 29.0 1.0 C A:GLU186 4.8 39.8 1.0 CB A:TYR193 4.8 23.9 1.0 CA A:GLU186 4.8 39.9 1.0 CB A:ASP188 4.8 34.2 1.0 CA A:VAL191 4.8 33.0 1.0 C A:LEU192 4.9 31.2 1.0 O A:GLY221 4.9 27.9 1.0 CG A:PHE185 4.9 25.5 1.0 CB A:VAL191 4.9 29.3 1.0 OD1 A:ASN225 5.0 30.9 1.0

A.K.Miller, M.Morgen, R.R.Steimbach, M.Geraldy, L.Hellweg, P.Sehr, J.Ridinger, O.Witt, I.Oehme, C.J.Herbst-Gervasoni, J.D.Osko, N.J.Porter, D.W.Christianson, N.Gunkel. Design and Synthesis of Dihydroxamic Acids As HDAC6/8/10 Inhibitors. Chemmedchem 2020.
ISSN: ESSN 1860-7187
PubMed: 32348628
DOI: 10.1002/CMDC.202000149