Potassium in PDB 6pzs: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005:
3.5.1.98;

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005, PDB code: 6pzs 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)	47.39 / 1.79
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.650, 83.670, 94.779, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005 (pdb code 6pzs). 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 2 Complexed with JR005, PDB code: 6pzs:
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 2 Complexed with JR005


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 2 Complexed with JR005 within 5.0Å range: probe atom residue distance (Å) B Occ A:K802 b:9.8 occ:1.00 O A:ASP612 2.5 7.7 1.0 O A:LEU634 2.7 10.3 1.0 O A:HIS614 2.7 8.3 1.0 OD1 A:ASP610 2.7 7.7 1.0 OG A:SER633 2.8 8.2 1.0 O A:ASP610 2.8 7.1 1.0 CG A:ASP610 3.3 7.8 1.0 C A:ASP610 3.5 9.2 1.0 C A:ASP612 3.6 7.9 1.0 C A:LEU634 3.7 8.5 1.0 C A:HIS614 3.7 7.4 1.0 CB A:ASP610 3.8 8.7 1.0 N A:ASP612 3.9 9.1 1.0 N A:LEU634 3.9 8.6 1.0 CB A:SER633 3.9 8.8 1.0 OD2 A:ASP610 4.0 11.3 1.0 CB A:HIS635 4.0 6.9 1.0 CA A:ASP612 4.1 7.9 1.0 CB A:ASP612 4.2 7.6 1.0 N A:TRP611 4.2 8.0 1.0 C A:TRP611 4.2 9.7 1.0 CA A:ASP610 4.2 7.0 1.0 CA A:SER633 4.3 6.1 1.0 CA A:HIS615 4.3 7.8 1.0 ND1 A:HIS635 4.4 6.9 1.0 CA A:TRP611 4.4 9.1 1.0 N A:HIS615 4.4 10.5 1.0 C A:SER633 4.4 9.7 1.0 N A:HIS614 4.4 9.5 1.0 N A:GLY616 4.5 8.5 1.0 CA A:HIS635 4.5 7.6 1.0 CA A:LEU634 4.5 4.3 1.0 O A:HOH934 4.5 10.7 1.0 N A:HIS635 4.5 7.6 1.0 CG A:HIS635 4.6 8.0 1.0 OH A:TYR631 4.7 7.2 1.0 C A:VAL613 4.7 8.9 1.0 N A:VAL613 4.7 5.6 1.0 CA A:HIS614 4.7 7.9 1.0 C A:HIS615 4.7 6.1 1.0 CE1 A:HIS573 4.8 7.9 1.0 ND1 A:HIS573 4.9 6.9 1.0 O A:TRP611 4.9 8.0 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005


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 2 Complexed with JR005 within 5.0Å range: probe atom residue distance (Å) B Occ A:K803 b:11.7 occ:1.00 O A:VAL629 2.7 11.8 1.0 O A:PHE623 2.7 10.6 1.0 O A:HOH984 2.7 9.7 1.0 O A:TYR662 2.8 8.4 1.0 O A:HOH1080 2.9 7.4 1.0 O A:ASP626 3.0 14.1 1.0 C A:TYR662 3.6 9.2 1.0 CB A:TYR662 3.6 9.5 1.0 C A:PHE623 3.7 11.7 1.0 CB A:PHE623 3.7 8.7 1.0 C A:VAL629 3.9 10.3 1.0 C A:ASP626 4.1 13.1 1.0 CA A:TYR662 4.3 7.7 1.0 N A:TYR631 4.3 8.5 1.0 CA A:PHE623 4.3 11.7 1.0 CB A:ASP626 4.3 14.5 1.0 N A:ASP626 4.4 14.3 1.0 N A:ASN663 4.4 8.3 1.0 CA A:ASP626 4.5 13.9 1.0 CA A:LEU630 4.6 7.9 1.0 N A:GLU624 4.6 10.9 1.0 CA A:GLU624 4.6 9.0 1.0 C A:GLU624 4.7 11.7 1.0 CB A:TYR631 4.7 9.6 1.0 O A:GLU624 4.7 14.2 1.0 N A:LEU630 4.7 7.7 1.0 CA A:ASN663 4.8 7.2 1.0 CB A:ASN663 4.8 7.9 1.0 O A:GLY659 4.9 12.7 1.0 C A:LEU630 4.9 8.9 1.0 CA A:VAL629 4.9 9.5 1.0 CG A:PHE623 5.0 7.9 1.0 CG A:TYR662 5.0 9.5 1.0

J.D.Osko, N.J.Porter, P.A.Narayana Reddy, Y.C.Xiao, J.Rokka, M.Jung, J.M.Hooker, J.M.Salvino, D.W.Christianson. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J.Med.Chem. V. 63 295 2020.
ISSN: ISSN 0022-2623
PubMed: 31793776
DOI: 10.1021/ACS.JMEDCHEM.9B01540