Potassium in PDB 6uo3: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Ar-42

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Ar-42, PDB code: 6uo3 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)	43.09 / 1.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.750, 61.060, 121.650, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 19

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) 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) Complexed with Ar-42 (pdb code 6uo3). 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) Complexed with Ar-42, PDB code: 6uo3:
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) 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) Complexed with Ar-42 within 5.0Å range: probe atom residue distance (Å) B Occ A:K502 b:4.5 occ:0.70 O A:ASP230 2.6 6.6 1.0 O A:HIS232 2.7 6.8 1.0 O A:VAL252 2.7 6.8 1.0 OD1 A:ASP228 2.8 7.6 1.0 OG A:SER251 2.8 7.2 1.0 O A:ASP228 2.9 6.3 1.0 CG A:ASP228 3.2 7.9 1.0 C A:ASP228 3.5 6.4 1.0 C A:ASP230 3.6 6.5 1.0 C A:VAL252 3.7 6.7 1.0 C A:HIS232 3.7 6.3 1.0 OD2 A:ASP228 3.8 8.9 1.0 N A:ASP230 3.8 7.0 1.0 CB A:ASP228 3.8 7.3 1.0 N A:VAL252 3.9 6.5 1.0 CB A:HIS253 3.9 7.0 1.0 CB A:SER251 3.9 6.3 1.0 CA A:ASP230 4.1 6.8 1.0 C A:TRP229 4.2 6.4 1.0 N A:TRP229 4.2 6.1 1.0 CA A:SER251 4.2 6.5 1.0 CB A:ASP230 4.3 7.5 1.0 ND1 A:HIS253 4.3 7.9 1.0 CA A:ASP228 4.3 6.4 1.0 CA A:TRP229 4.3 7.9 1.0 CA A:HIS233 4.4 6.7 1.0 C A:SER251 4.4 6.1 1.0 CA A:HIS253 4.4 7.1 1.0 N A:HIS233 4.4 6.7 1.0 N A:HIS232 4.5 6.1 1.0 CA A:VAL252 4.5 6.6 1.0 N A:HIS253 4.5 6.8 1.0 N A:GLY234 4.6 7.1 1.0 CG A:HIS253 4.6 7.1 1.0 O A:HOH634 4.7 8.3 1.0 N A:VAL231 4.7 6.8 1.0 C A:VAL231 4.7 5.9 1.0 CA A:HIS232 4.8 7.1 1.0 OH A:TYR249 4.8 7.9 1.0 O A:TRP229 4.9 7.0 1.0 CE1 A:HIS192 4.9 9.2 1.0 C A:HIS233 4.9 7.3 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) 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) Complexed with Ar-42 within 5.0Å range: probe atom residue distance (Å) B Occ A:K503 b:12.5 occ:0.75 O A:HOH674 2.5 13.4 1.0 O A:VAL247 2.6 14.4 1.0 O A:PHE241 2.6 10.2 1.0 O A:TYR280 2.9 8.1 1.0 O A:ASP244 3.0 11.9 1.0 O A:HOH715 3.1 13.5 1.0 C A:PHE241 3.6 10.6 1.0 C A:TYR280 3.6 7.5 1.0 CB A:PHE241 3.7 9.1 1.0 CB A:TYR280 3.7 8.5 1.0 C A:VAL247 3.8 9.4 1.0 C A:ASP244 4.1 12.1 1.0 CA A:PHE241 4.2 9.0 1.0 CA A:TYR280 4.3 8.8 1.0 N A:ASN281 4.4 8.1 1.0 N A:ASP244 4.4 12.0 1.0 N A:TYR249 4.5 7.8 1.0 N A:GLU242 4.5 10.4 1.0 CA A:LEU248 4.6 8.1 1.0 CA A:ASP244 4.6 11.8 1.0 N A:LEU248 4.7 8.3 1.0 O A:GLU242 4.7 12.1 1.0 CB A:ASP244 4.7 13.6 1.0 C A:GLU242 4.7 11.2 1.0 CA A:GLU242 4.7 11.6 1.0 CA A:ASN281 4.8 7.3 1.0 CA A:VAL247 4.8 9.0 1.0 CB A:ASN281 4.8 9.1 1.0 O A:GLY277 4.9 11.5 1.0 CB A:VAL247 4.9 10.2 1.0 CG A:PHE241 4.9 8.7 1.0 C A:LEU248 5.0 7.7 1.0 CB A:TYR249 5.0 9.1 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