Potassium in PDB 8qh9: X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A S-29B

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A S-29B, PDB code: 8qh9 was solved by C.Barinka, L.Motlova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.13 / 1.59
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.39, 94.26, 51.65, 90, 90, 90
R / Rfree (%)	19.7 / 22.6

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A S-29B also contains other interesting chemical elements:

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 A S-29B (pdb code 8qh9). 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 A S-29B, PDB code: 8qh9:
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 A S-29B


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 A S-29B within 5.0Å range: probe atom residue distance (Å) B Occ A:K2002 b:19.7 occ:1.00 O A:LEU634 2.5 15.8 1.0 O A:ASP612 2.6 13.5 1.0 O A:HIS614 2.7 13.2 1.0 OG A:SER633 2.7 15.6 1.0 OD1 A:ASP610 2.7 15.9 1.0 O A:ASP610 2.9 15.4 1.0 CG A:ASP610 3.3 15.9 1.0 C A:ASP610 3.5 16.3 1.0 C A:ASP612 3.6 15.2 1.0 C A:LEU634 3.6 14.4 1.0 C A:HIS614 3.7 14.0 1.0 N A:ASP612 3.9 13.2 1.0 N A:LEU634 3.9 13.8 1.0 CB A:ASP610 3.9 15.2 1.0 CB A:HIS635 3.9 12.6 1.0 CB A:SER633 3.9 17.8 1.0 OD2 A:ASP610 4.0 14.3 1.0 CA A:ASP612 4.2 14.3 1.0 C A:TRP611 4.2 14.3 1.0 N A:TRP611 4.2 14.0 1.0 CB A:ASP612 4.3 14.4 1.0 ND1 A:HIS635 4.3 12.8 1.0 CA A:ASP610 4.3 15.7 1.0 CA A:HIS615 4.3 13.5 1.0 CA A:SER633 4.3 17.3 1.0 CA A:TRP611 4.3 14.0 1.0 N A:HIS615 4.4 13.7 1.0 O A:HOH2164 4.4 15.6 1.0 N A:HIS614 4.4 13.6 1.0 CA A:HIS635 4.4 12.8 1.0 N A:HIS635 4.5 13.8 1.0 CA A:LEU634 4.5 14.9 1.0 C A:SER633 4.5 16.2 1.0 CG A:HIS635 4.6 12.8 1.0 N A:GLY616 4.6 15.5 1.0 C A:VAL613 4.6 15.6 1.0 CA A:HIS614 4.7 14.0 1.0 N A:VAL613 4.7 15.8 1.0 OH A:TYR631 4.8 13.9 1.0 C A:HIS615 4.8 14.7 1.0 O A:TRP611 4.8 14.2 1.0 CE1 A:HIS573 4.9 14.6 1.0 ND1 A:HIS573 5.0 13.8 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 A S-29B


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 A S-29B within 5.0Å range: probe atom residue distance (Å) B Occ A:K2003 b:16.2 occ:1.00 O A:PHE623 2.5 14.6 1.0 O A:HOH2150 2.7 15.8 1.0 O A:VAL629 2.8 16.7 1.0 O A:TYR662 3.0 17.8 1.0 O A:HOH2211 3.0 15.0 1.0 O A:ASP626 3.0 20.1 1.0 C A:PHE623 3.6 16.4 1.0 CB A:PHE623 3.7 14.0 1.0 C A:TYR662 3.7 18.1 1.0 CB A:TYR662 3.7 19.6 1.0 C A:VAL629 4.0 17.3 1.0 C A:ASP626 4.1 21.8 1.0 CA A:PHE623 4.3 16.4 1.0 CA A:TYR662 4.4 17.8 1.0 N A:ASP626 4.4 19.8 1.0 N A:TYR631 4.4 13.6 1.0 N A:GLU624 4.4 16.6 1.0 N A:ASN663 4.5 16.7 1.0 CA A:GLU624 4.6 19.9 1.0 CB A:ASP626 4.6 25.7 1.0 CA A:ASP626 4.6 19.8 1.0 O A:GLU624 4.6 18.3 1.0 C A:GLU624 4.7 19.9 1.0 CA A:LEU630 4.7 14.8 1.0 CB A:TYR631 4.8 13.5 1.0 N A:LEU630 4.8 15.8 1.0 CB A:ASN663 4.8 17.6 1.0 CA A:ASN663 4.8 17.4 1.0 O A:GLY659 4.9 22.9 1.0 CA A:VAL629 4.9 17.8 1.0 OD1 A:ASN663 4.9 16.9 1.0 CG A:PHE623 5.0 15.0 1.0 C A:LEU630 5.0 14.1 1.0

S.Scheuerer, L.Motlova, L.Schaker-Hubner, A.Sellmer, F.Feller, F.J.Ertl, P.Koch, F.K.Hansen, C.Barinka, S.Mahboobi. Biological and Structural Investigation of Tetrahydro-Beta-Carboline-Based Selective HDAC6 Inhibitors with Improved Stability. Eur.J.Med.Chem. V. 276 16676 2024.
ISSN: ISSN 0223-5234
PubMed: 39067437
DOI: 10.1016/J.EJMECH.2024.116676