Potassium in PDB 8bjk: X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352, PDB code: 8bjk was solved by C.Barinka, L.Motlova, J.Pavlicek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.64 / 1.35
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.49, 83.78, 94.33, 90, 90, 90
R / Rfree (%)	16.8 / 20.7

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352 also contains other interesting chemical elements:

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

The binding sites of Potassium atom in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352 (pdb code 8bjk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352, PDB code: 8bjk:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352 within 5.0Å range: probe atom residue distance (Å) B Occ A:K802 b:9.9 occ:1.00 O A:ASP612 2.5 8.6 1.0 O A:LEU634 2.6 8.7 1.0 O A:HIS614 2.6 8.8 1.0 OD1 A:ASP610 2.7 8.2 1.0 OG A:SER633 2.7 8.3 1.0 O A:ASP610 2.8 7.8 1.0 CG A:ASP610 3.3 7.8 1.0 C A:ASP610 3.5 8.4 1.0 C A:ASP612 3.6 7.8 1.0 C A:LEU634 3.6 8.0 1.0 C A:HIS614 3.7 8.9 1.0 CB A:ASP610 3.8 8.8 1.0 N A:ASP612 3.9 7.9 1.0 CB A:SER633 3.9 8.9 1.0 N A:LEU634 3.9 7.6 1.0 CB A:HIS635 4.0 8.7 1.0 OD2 A:ASP610 4.0 8.3 1.0 CA A:ASP612 4.1 8.4 1.0 N A:TRP611 4.2 8.1 1.0 C A:TRP611 4.2 7.9 1.0 CB A:ASP612 4.2 7.6 1.0 CA A:ASP610 4.3 8.2 1.0 ND1 A:HIS635 4.3 8.3 1.0 CA A:SER633 4.3 8.0 1.0 CA A:TRP611 4.3 8.9 1.0 CA A:HIS615 4.3 8.7 1.0 N A:HIS615 4.4 8.7 1.0 N A:HIS614 4.4 8.4 1.0 C A:SER633 4.4 8.2 1.0 O A:HOH928 4.5 8.3 1.0 CA A:HIS635 4.5 8.1 1.0 CA A:LEU634 4.5 8.0 1.0 N A:HIS635 4.5 8.3 1.0 N A:GLY616 4.6 7.6 1.0 CG A:HIS635 4.6 8.2 1.0 C A:VAL613 4.6 8.8 1.0 N A:VAL613 4.7 8.3 1.0 CA A:HIS614 4.7 9.1 1.0 OH A:TYR631 4.7 7.9 1.0 CE1 A:HIS573 4.7 8.4 1.0 C A:HIS615 4.8 8.5 1.0 ND1 A:HIS573 4.9 8.0 1.0 O A:TRP611 4.9 9.0 1.0 CA A:VAL613 5.0 8.8 1.0

Potassium binding site 2 out of 2 in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352 within 5.0Å range: probe atom residue distance (Å) B Occ A:K803 b:9.6 occ:1.00 O A:HOH976 2.7 11.6 1.0 O A:VAL629 2.7 11.2 1.0 O A:PHE623 2.7 10.8 1.0 O A:TYR662 2.8 9.5 1.0 O A:HOH1060 2.9 10.0 1.0 O A:ASP626 2.9 11.5 0.6 O A:ASP626 3.0 12.2 0.4 C A:TYR662 3.6 9.5 1.0 C A:PHE623 3.7 11.1 1.0 CB A:TYR662 3.7 11.2 1.0 CB A:PHE623 3.7 10.1 1.0 C A:VAL629 3.9 10.4 1.0 C A:ASP626 4.1 11.7 0.6 C A:ASP626 4.1 12.6 0.4 CA A:TYR662 4.2 10.9 1.0 CA A:PHE623 4.3 11.2 1.0 N A:TYR631 4.3 9.2 1.0 N A:ASN663 4.4 9.2 1.0 CB A:ASP626 4.4 13.5 0.4 N A:ASP626 4.5 12.3 0.6 N A:ASP626 4.5 13.1 0.4 N A:GLU624 4.6 11.3 1.0 CB A:ASP626 4.6 14.2 0.6 CA A:LEU630 4.6 8.5 1.0 CA A:GLU624 4.6 11.9 1.0 CA A:ASP626 4.6 13.3 0.4 CA A:ASP626 4.6 12.7 0.6 C A:GLU624 4.7 12.2 1.0 N A:LEU630 4.7 9.5 1.0 O A:GLU624 4.7 12.2 1.0 CB A:TYR631 4.8 8.2 1.0 CA A:ASN663 4.8 9.7 1.0 CB A:ASN663 4.8 9.0 1.0 O A:GLY659 4.9 12.7 1.0 C A:LEU630 4.9 8.8 1.0 CA A:VAL629 4.9 10.4 1.0 CG A:PHE623 5.0 9.6 1.0 CG A:TYR662 5.0 12.4 1.0

L.Motlova, I.Snajdr, Z.Kutil, E.Andris, J.Ptacek, A.Novotna, Z.Novakova, B.Havlinova, W.Tueckmantel, H.Draberova, P.Majer, M.Schutkowski, A.Kozikowski, L.Rulisek, C.Barinka. Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors By Histone Deacetylase 6 (HDAC6). Acs Chem.Biol. V. 18 1594 2023.
ISSN: ESSN 1554-8937
PubMed: 37392419
DOI: 10.1021/ACSCHEMBIO.3C00212