Potassium in PDB 6uo5: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Ar-42

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Ar-42, PDB code: 6uo5 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)	60.99 / 1.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.569, 60.546, 121.972, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.7

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Ar-42 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) Y363F Mutant Complexed with Ar-42 (pdb code 6uo5). 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) Y363F Mutant Complexed with Ar-42, PDB code: 6uo5:
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) Y363F Mutant Complexed with Ar-42


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) Y363F Mutant Complexed with Ar-42 within 5.0Å range: probe atom residue distance (Å) B Occ A:K504 b:11.0 occ:0.85 O A:ASP230 2.5 11.6 1.0 O A:HIS232 2.7 11.1 1.0 OD1 A:ASP228 2.7 11.9 1.0 OG A:SER251 2.8 11.7 1.0 O A:VAL252 2.8 12.9 1.0 O A:ASP228 2.9 11.6 1.0 CG A:ASP228 3.2 13.4 1.0 C A:ASP228 3.5 11.3 1.0 C A:ASP230 3.6 11.7 1.0 C A:VAL252 3.7 13.5 1.0 C A:HIS232 3.7 11.9 1.0 OD2 A:ASP228 3.8 13.2 1.0 N A:ASP230 3.8 10.4 1.0 CB A:ASP228 3.8 10.6 1.0 N A:VAL252 3.9 11.7 1.0 CB A:SER251 3.9 10.9 1.0 CB A:HIS253 3.9 12.5 1.0 CA A:ASP230 4.1 10.7 1.0 C A:TRP229 4.2 12.5 1.0 N A:TRP229 4.2 10.9 1.0 CA A:SER251 4.2 10.9 1.0 CB A:ASP230 4.2 12.1 1.0 ND1 A:HIS253 4.3 12.8 1.0 CA A:ASP228 4.3 11.1 1.0 CA A:HIS233 4.3 12.7 1.0 CA A:TRP229 4.3 11.8 1.0 C A:SER251 4.4 13.6 1.0 N A:HIS233 4.4 11.2 1.0 CA A:HIS253 4.4 12.2 1.0 N A:HIS232 4.5 11.6 1.0 N A:HIS253 4.5 12.5 1.0 CA A:VAL252 4.5 11.3 1.0 N A:GLY234 4.5 12.6 1.0 CG A:HIS253 4.6 12.5 1.0 O A:HOH646 4.7 14.5 1.0 N A:VAL231 4.7 11.6 1.0 C A:VAL231 4.7 13.3 1.0 CA A:HIS232 4.7 10.6 1.0 OH A:TYR249 4.8 12.4 1.0 C A:HIS233 4.9 12.2 1.0 O A:TRP229 4.9 13.1 1.0 CE1 A:HIS192 4.9 13.1 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Ar-42


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) Y363F Mutant Complexed with Ar-42 within 5.0Å range: probe atom residue distance (Å) B Occ A:K505 b:18.6 occ:0.84 O A:VAL247 2.6 19.9 1.0 O A:HOH658 2.6 21.4 1.0 O A:PHE241 2.7 18.2 1.0 O A:TYR280 2.9 16.1 1.0 O A:ASP244 2.9 20.2 1.0 O A:HOH649 3.1 19.3 1.0 C A:TYR280 3.6 16.2 1.0 CB A:PHE241 3.6 17.4 1.0 C A:PHE241 3.6 18.6 1.0 CB A:TYR280 3.7 17.6 1.0 C A:VAL247 3.8 15.7 1.0 C A:ASP244 4.0 21.4 1.0 CA A:PHE241 4.2 13.7 1.0 CA A:TYR280 4.3 14.7 1.0 N A:ASN281 4.4 15.4 1.0 N A:ASP244 4.5 20.5 1.0 N A:TYR249 4.5 12.7 1.0 CA A:LEU248 4.5 13.3 1.0 N A:GLU242 4.6 18.3 0.9 CA A:ASP244 4.6 20.1 1.0 N A:LEU248 4.6 13.9 1.0 CB A:ASP244 4.7 19.8 1.0 O A:GLU242 4.7 18.2 0.9 CB A:ASN281 4.8 13.7 1.0 CA A:ASN281 4.8 12.9 1.0 C A:GLU242 4.8 18.1 0.9 CA A:VAL247 4.8 15.4 1.0 CG A:PHE241 4.9 15.0 1.0 O A:GLY277 4.9 21.1 1.0 CA A:GLU242 4.9 19.4 0.9 C A:LEU248 4.9 13.6 1.0 CB A:VAL247 5.0 15.6 1.0 CB A:TYR249 5.0 13.0 1.0 N A:VAL247 5.0 17.6 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