Potassium in PDB 5dc7: Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

The structure of Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc7 was solved by C.Decroos, M.S.Lee, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.20 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.845, 97.748, 103.616, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.6

The structure of Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Potassium atom in the Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 5dc7). 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 D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc7:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K402 b:30.5 occ:1.00 O A:PHE189 2.6 30.4 1.0 O A:VAL195 2.6 31.0 1.0 O A:HOH510 2.8 25.3 1.0 O A:HOH561 2.8 28.7 1.0 O A:THR192 2.9 33.1 1.0 O A:TYR225 2.9 28.5 1.0 C A:TYR225 3.6 30.4 1.0 CB A:TYR225 3.6 24.7 1.0 C A:PHE189 3.6 29.4 1.0 OG A:SER226 3.8 28.6 1.0 C A:VAL195 3.8 25.3 1.0 C A:THR192 4.0 30.9 1.0 CB A:PHE189 4.1 26.5 1.0 CA A:TYR225 4.2 29.9 1.0 N A:SER226 4.4 27.6 1.0 CA A:MET196 4.4 27.1 1.0 O A:GLY222 4.4 40.9 1.0 N A:SER190 4.4 25.7 1.0 O A:SER190 4.4 32.3 1.0 CA A:SER190 4.4 27.5 1.0 C A:SER190 4.5 33.4 1.0 CG2 A:THR192 4.5 28.3 1.0 CA A:PHE189 4.5 29.7 1.0 N A:MET196 4.6 23.5 1.0 N A:THR192 4.6 33.8 1.0 N A:THR197 4.6 28.6 1.0 CA A:SER226 4.8 28.2 1.0 CA A:THR192 4.9 31.9 1.0 CA A:VAL195 4.9 29.3 1.0 CB A:SER226 4.9 24.9 1.0 CG A:TYR225 4.9 28.5 1.0 CA A:GLY222 4.9 31.9 1.0 OG1 A:THR197 4.9 31.8 1.0 C A:MET196 5.0 28.9 1.0 N A:SER193 5.0 27.3 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:K402 b:33.6 occ:1.00 O B:PHE189 2.6 31.8 1.0 O B:VAL195 2.7 32.5 1.0 O B:HOH521 2.7 30.7 1.0 O B:HOH538 2.9 27.8 1.0 O B:THR192 2.9 34.1 1.0 O B:TYR225 3.0 31.6 1.0 C B:TYR225 3.6 35.3 1.0 C B:PHE189 3.7 31.0 1.0 CB B:TYR225 3.7 31.2 1.0 C B:VAL195 3.9 27.9 1.0 OG B:SER226 3.9 32.0 1.0 C B:THR192 4.1 40.3 1.0 CB B:PHE189 4.1 24.9 1.0 CA B:TYR225 4.3 34.0 1.0 CA B:MET196 4.4 27.1 1.0 N B:SER226 4.4 29.4 1.0 O B:GLY222 4.4 38.5 1.0 N B:SER190 4.5 31.7 1.0 CA B:SER190 4.5 28.8 1.0 CA B:PHE189 4.6 30.4 1.0 C B:SER190 4.6 39.2 1.0 N B:THR197 4.6 30.6 1.0 O B:SER190 4.6 32.7 1.0 N B:MET196 4.6 27.1 1.0 N B:THR192 4.6 32.5 1.0 CG2 B:THR192 4.7 29.2 1.0 CA B:SER226 4.8 31.8 1.0 OG1 B:THR197 4.9 34.6 1.0 CA B:GLY222 4.9 36.6 1.0 C B:MET196 4.9 29.5 1.0 CA B:VAL195 4.9 35.6 1.0 CA B:THR192 4.9 32.3 1.0 CG B:TYR225 5.0 39.8 1.0 CG2 B:THR197 5.0 31.5 1.0 CB B:SER226 5.0 28.8 1.0

S.M.Gantt, C.Decroos, M.S.Lee, L.E.Gullett, C.M.Bowman, D.W.Christianson, C.A.Fierke. General Base-General Acid Catalysis in Human Histone Deacetylase 8. Biochemistry V. 55 820 2016.
ISSN: ISSN 0006-2960
PubMed: 26806311
DOI: 10.1021/ACS.BIOCHEM.5B01327