Potassium in PDB 6uoc: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat, PDB code: 6uoc was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.95 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.160, 60.400, 122.160, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 16.8

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat 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 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat (pdb code 6uoc). 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 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat, PDB code: 6uoc:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat


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 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat within 5.0Å range: probe atom residue distance (Å) B Occ A:K605 b:7.2 occ:0.91 O A:ASP230 2.6 7.7 1.0 O A:HIS232 2.7 8.3 1.0 OD1 A:ASP228 2.7 8.2 1.0 OG A:SER251 2.8 8.2 1.0 O A:VAL252 2.8 7.6 1.0 O A:ASP228 2.9 8.0 1.0 CG A:ASP228 3.2 8.9 1.0 C A:ASP228 3.5 7.9 1.0 C A:ASP230 3.6 7.1 1.0 C A:VAL252 3.7 8.5 1.0 C A:HIS232 3.7 7.5 1.0 OD2 A:ASP228 3.8 8.4 1.0 N A:ASP230 3.8 7.0 1.0 CB A:ASP228 3.8 7.7 1.0 N A:VAL252 3.9 7.0 1.0 CB A:SER251 3.9 8.6 1.0 CB A:HIS253 4.0 8.2 1.0 CA A:ASP230 4.1 6.7 1.0 C A:TRP229 4.2 8.2 1.0 N A:TRP229 4.2 7.2 1.0 CA A:SER251 4.2 7.9 1.0 CB A:ASP230 4.3 7.8 1.0 CA A:ASP228 4.3 6.7 1.0 ND1 A:HIS253 4.3 8.2 1.0 CA A:HIS233 4.3 7.4 1.0 CA A:TRP229 4.4 7.2 1.0 C A:SER251 4.4 8.2 1.0 N A:HIS233 4.4 6.8 1.0 N A:HIS232 4.4 6.8 1.0 CA A:HIS253 4.5 7.6 1.0 CA A:VAL252 4.5 8.1 1.0 N A:HIS253 4.5 7.8 1.0 N A:GLY234 4.6 6.8 1.0 CG A:HIS253 4.6 7.7 1.0 O A:HOH748 4.7 8.7 1.0 C A:VAL231 4.7 7.8 1.0 N A:VAL231 4.7 7.1 1.0 CA A:HIS232 4.7 6.5 1.0 OH A:TYR249 4.8 8.3 1.0 O A:TRP229 4.9 7.9 1.0 C A:HIS233 4.9 7.8 1.0 CE1 A:HIS192 4.9 9.7 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat


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 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat within 5.0Å range: probe atom residue distance (Å) B Occ A:K606 b:10.8 occ:0.87 O A:VAL247 2.6 12.0 1.0 O A:HOH829 2.6 12.8 1.0 O A:PHE241 2.7 11.8 1.0 O A:TYR280 2.9 10.7 1.0 O A:ASP244 2.9 13.5 1.0 O A:HOH825 3.0 11.3 1.0 C A:PHE241 3.6 10.4 1.0 C A:TYR280 3.7 11.1 1.0 CB A:PHE241 3.7 11.4 1.0 CB A:TYR280 3.8 12.4 1.0 C A:VAL247 3.9 9.0 1.0 C A:ASP244 4.0 15.8 1.0 CA A:PHE241 4.3 9.9 1.0 CA A:TYR280 4.3 10.2 1.0 N A:TYR249 4.4 8.4 1.0 N A:ASP244 4.5 14.7 1.0 N A:ASN281 4.5 10.6 1.0 CA A:LEU248 4.5 9.2 0.3 CA A:LEU248 4.6 9.1 0.7 N A:GLU242 4.6 11.5 1.0 CA A:ASP244 4.6 13.6 1.0 N A:LEU248 4.6 8.5 0.3 N A:LEU248 4.7 8.5 0.7 CB A:ASP244 4.7 14.2 1.0 O A:GLU242 4.7 12.3 1.0 C A:GLU242 4.8 11.4 1.0 CB A:ASN281 4.8 9.9 1.0 CA A:ASN281 4.8 8.4 1.0 CA A:GLU242 4.8 12.0 1.0 CA A:VAL247 4.9 9.5 1.0 C A:LEU248 4.9 8.9 0.3 CB A:TYR249 4.9 9.5 1.0 CG A:PHE241 4.9 8.7 1.0 C A:LEU248 4.9 8.9 0.7 O A:GLY277 4.9 15.2 1.0

J.D.Osko, D.W.Christianson. Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31755702
DOI: 10.1021/ACS.BIOCHEM.9B00934