Potassium in PDB 6uhu: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid, PDB code: 6uhu 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)	60.61 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.550, 80.550, 244.817, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 25.4

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid 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 5-[(3-Aminopropyl)Amino]Pentylboronic Acid (pdb code 6uhu). 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 5-[(3-Aminopropyl)Amino]Pentylboronic Acid, PDB code: 6uhu:
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 5-[(3-Aminopropyl)Amino]Pentylboronic Acid


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 5-[(3-Aminopropyl)Amino]Pentylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:K706 b:24.1 occ:1.00 O A:ASP174 2.7 20.7 1.0 OG A:SER195 2.7 25.9 1.0 O A:TRP196 2.7 28.1 1.0 O A:HIS176 2.7 23.5 1.0 OD2 A:ASP172 2.8 16.9 1.0 O A:ASP172 2.9 25.3 1.0 CG A:ASP172 3.1 20.9 1.0 C A:ASP172 3.4 25.8 1.0 C A:ASP174 3.6 23.9 1.0 CB A:ASP172 3.6 19.1 1.0 N A:ASP174 3.6 19.0 1.0 CB A:SER195 3.6 25.0 1.0 OD1 A:ASP172 3.7 23.5 1.0 C A:HIS176 3.8 25.2 1.0 C A:TRP196 3.9 24.1 1.0 CA A:ASP174 3.9 22.6 1.0 CB A:ASP174 4.1 19.0 1.0 C A:TRP173 4.1 19.8 1.0 N A:TRP173 4.1 20.1 1.0 CA A:ASP172 4.1 26.8 1.0 CA A:SER195 4.1 26.5 1.0 N A:TRP196 4.1 22.7 1.0 CA A:TRP173 4.3 18.7 1.0 C A:SER195 4.4 25.0 1.0 CB A:HIS197 4.4 22.3 1.0 CA A:HIS177 4.5 22.9 1.0 N A:HIS176 4.5 26.1 1.0 N A:HIS177 4.5 27.1 1.0 N A:GLY178 4.6 21.7 1.0 CD1 A:TRP196 4.6 17.5 1.0 ND1 A:HIS197 4.6 25.8 1.0 N A:VAL175 4.7 23.2 1.0 CA A:TRP196 4.7 25.3 1.0 OH A:TYR193 4.7 17.6 1.0 CE1 A:HIS136 4.8 21.4 1.0 CA A:HIS197 4.8 20.9 1.0 CA A:HIS176 4.8 20.3 1.0 N A:HIS197 4.8 19.0 1.0 C A:VAL175 4.8 26.2 1.0 ND1 A:HIS136 4.9 17.6 1.0 O A:TRP173 4.9 24.4 1.0 C A:HIS177 4.9 23.2 1.0 OD2 A:ASP174 4.9 26.1 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 5-[(3-Aminopropyl)Amino]Pentylboronic Acid


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 5-[(3-Aminopropyl)Amino]Pentylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:K707 b:26.6 occ:1.00 O A:PHE185 2.7 33.2 1.0 O A:VAL191 2.7 30.4 1.0 O A:PHE224 2.9 23.5 1.0 O A:ASP188 2.9 34.8 1.0 O A:HOH832 3.1 26.2 1.0 C A:PHE224 3.5 30.8 1.0 CB A:PHE224 3.6 28.3 1.0 C A:PHE185 3.8 27.0 1.0 C A:VAL191 3.9 28.8 1.0 CB A:PHE185 4.0 22.7 1.0 C A:ASP188 4.1 36.4 1.0 CA A:PHE224 4.2 32.4 1.0 N A:ASN225 4.3 29.1 1.0 O A:GLU186 4.3 33.4 1.0 N A:TYR193 4.4 27.2 1.0 O A:GLY221 4.5 45.2 1.0 CA A:PHE185 4.5 23.0 1.0 N A:ASP188 4.5 31.5 1.0 CA A:LEU192 4.5 26.4 1.0 C A:GLU186 4.6 33.6 1.0 CB A:ASN225 4.6 19.2 1.0 CA A:ASN225 4.7 28.6 1.0 N A:LEU192 4.7 23.1 1.0 N A:GLU186 4.7 26.5 1.0 CA A:ASP188 4.7 33.9 1.0 CA A:GLU186 4.8 35.1 1.0 CB A:TYR193 4.8 20.6 1.0 CG A:PHE224 4.9 36.4 1.0 CB A:ASP188 4.9 31.7 1.0 CA A:VAL191 4.9 26.9 1.0 C A:LEU192 5.0 28.5 1.0

C.J.Herbst-Gervasoni, D.W.Christianson. Binding of N8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies For Blocking Polyamine Deacetylation. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31746596
DOI: 10.1021/ACS.BIOCHEM.9B00906