Potassium in PDB 5fcw: HDAC8 Complexed with A Hydroxamic Acid

All present enzymatic activity of HDAC8 Complexed with A Hydroxamic Acid:
3.5.1.98;

The structure of HDAC8 Complexed with A Hydroxamic Acid, PDB code: 5fcw was solved by K.E.Cole, K.Perry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.66 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.443, 84.548, 94.307, 90.00, 100.08, 90.00
R / Rfree (%)	17.2 / 21.6

The structure of HDAC8 Complexed with A Hydroxamic Acid also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Potassium atom in the HDAC8 Complexed with A Hydroxamic Acid (pdb code 5fcw). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the HDAC8 Complexed with A Hydroxamic Acid, PDB code: 5fcw:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the HDAC8 Complexed with A Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of HDAC8 Complexed with A Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:K403 b:14.0 occ:1.00 O A:LEU200 2.6 14.5 1.0 OD1 A:ASP176 2.7 14.0 1.0 O A:ASP178 2.7 15.7 1.0 O A:ASP176 2.7 11.8 1.0 O A:HIS180 2.8 12.6 1.0 OG A:SER199 2.9 16.6 1.0 C A:ASP176 3.4 15.6 1.0 CG A:ASP176 3.4 17.8 1.0 N A:ASP178 3.5 14.9 1.0 C A:ASP178 3.6 14.7 1.0 C A:LEU200 3.6 16.6 1.0 CB A:ASP176 3.7 14.9 1.0 CB A:HIS201 3.8 12.5 1.0 C A:HIS180 3.8 12.7 1.0 CA A:ASP178 3.9 14.9 1.0 N A:LEU200 3.9 15.7 1.0 C A:LEU177 3.9 14.6 1.0 N A:LEU177 4.0 14.3 1.0 CB A:ASP178 4.0 14.3 1.0 CB A:SER199 4.1 13.4 1.0 CA A:LEU177 4.2 13.7 1.0 CA A:ASP176 4.2 15.3 1.0 CA A:SER199 4.3 16.1 1.0 CA A:HIS201 4.3 16.5 1.0 OD2 A:ASP176 4.3 19.2 1.0 N A:HIS201 4.4 15.4 1.0 N A:GLY182 4.4 13.6 1.0 C A:SER199 4.4 17.1 1.0 CA A:HIS181 4.5 14.1 1.0 CA A:LEU200 4.5 16.4 1.0 N A:HIS180 4.5 14.5 1.0 ND1 A:HIS201 4.5 14.3 1.0 O A:HOH529 4.5 15.9 1.0 N A:HIS181 4.5 12.1 1.0 CG A:HIS201 4.6 14.5 1.0 O A:LEU177 4.7 13.3 1.0 C A:LEU179 4.7 15.7 1.0 N A:LEU179 4.7 13.8 1.0 CA A:HIS180 4.8 11.4 1.0 C A:HIS181 4.8 17.3 1.0 CE1 A:HIS142 4.9 14.9 1.0

Potassium binding site 2 out of 2 in the HDAC8 Complexed with A Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of HDAC8 Complexed with A Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:K403 b:16.2 occ:1.00 O B:ASP178 2.5 14.5 1.0 O B:LEU200 2.6 16.8 1.0 OD1 B:ASP176 2.7 21.0 1.0 O B:HIS180 2.7 13.6 1.0 O B:ASP176 2.7 21.5 1.0 OG B:SER199 2.9 19.5 1.0 CG B:ASP176 3.4 19.9 1.0 C B:ASP176 3.5 19.9 1.0 C B:ASP178 3.5 19.9 1.0 N B:ASP178 3.5 19.3 1.0 C B:LEU200 3.6 21.4 1.0 C B:HIS180 3.7 15.3 1.0 CB B:HIS201 3.8 14.2 1.0 CB B:ASP176 3.8 15.0 1.0 N B:LEU200 3.9 19.0 1.0 CA B:ASP178 3.9 17.4 1.0 C B:LEU177 4.0 18.9 1.0 CB B:ASP178 4.1 20.2 1.0 CB B:SER199 4.1 19.2 1.0 N B:LEU177 4.1 16.4 1.0 CA B:LEU177 4.3 14.9 1.0 CA B:ASP176 4.3 19.0 1.0 CA B:HIS201 4.3 17.1 1.0 ND1 B:HIS201 4.3 17.1 1.0 CA B:SER199 4.3 23.7 1.0 OD2 B:ASP176 4.3 20.7 1.0 N B:HIS180 4.4 18.0 1.0 N B:GLY182 4.4 17.2 1.0 N B:HIS201 4.4 19.0 1.0 C B:SER199 4.4 22.6 1.0 CA B:LEU200 4.4 18.1 1.0 CA B:HIS181 4.5 15.1 1.0 N B:HIS181 4.5 13.3 1.0 O B:HOH528 4.5 12.2 1.0 CG B:HIS201 4.5 13.4 1.0 C B:LEU179 4.6 18.9 1.0 N B:LEU179 4.6 17.8 1.0 CA B:HIS180 4.7 16.5 1.0 O B:LEU177 4.8 16.5 1.0 C B:HIS181 4.8 16.3 1.0 CE1 B:HIS142 4.9 20.7 1.0 O B:LEU179 4.9 16.6 1.0

A.A.Tabackman, R.Frankson, E.S.Marsan, K.Perry, K.E.Cole. Structure of 'Linkerless' Hydroxamic Acid Inhibitor-HDAC8 Complex Confirms the Formation of An Isoform-Specific Subpocket. J.Struct.Biol. V. 195 373 2016.
ISSN: ESSN 1095-8657
PubMed: 27374062
DOI: 10.1016/J.JSB.2016.06.023