Potassium in PDB 5dc6: Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

The structure of Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc6 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)	49.10 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.332, 98.206, 104.281, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.6

The structure of Crystal Structure of D176N-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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 5dc6). 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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc6:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of D176N-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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K402 b:18.9 occ:1.00 O A:VAL195 2.6 20.6 1.0 O A:PHE189 2.6 21.1 1.0 O A:HOH582 2.7 20.7 1.0 O A:THR192 2.8 22.9 1.0 O A:HOH690 2.9 23.1 1.0 O A:TYR225 3.0 20.2 1.0 C A:PHE189 3.6 21.4 1.0 CB A:TYR225 3.6 18.7 1.0 C A:TYR225 3.7 20.1 1.0 C A:VAL195 3.8 18.1 1.0 C A:THR192 4.0 22.4 1.0 CB A:PHE189 4.0 19.8 1.0 OG A:SER226 4.1 24.0 1.0 CA A:TYR225 4.3 19.6 1.0 CA A:SER190 4.4 21.0 0.3 CG2 A:THR192 4.4 26.2 1.0 O A:SER190 4.4 21.5 0.7 N A:SER190 4.4 20.1 0.3 CA A:PHE189 4.4 18.3 1.0 N A:SER190 4.4 19.5 0.7 CA A:MET196 4.5 16.4 0.8 CA A:SER190 4.5 20.5 0.7 C A:SER190 4.5 21.9 0.7 N A:THR192 4.5 22.7 1.0 CA A:MET196 4.5 17.1 0.2 N A:SER226 4.5 16.9 1.0 C A:SER190 4.5 21.7 0.3 O A:SER190 4.6 22.6 0.3 N A:MET196 4.6 17.2 0.8 N A:MET196 4.6 17.1 0.2 O A:GLY222 4.7 22.3 1.0 N A:THR197 4.7 17.2 1.0 CA A:THR192 4.7 23.1 1.0 CA A:VAL195 4.8 18.2 1.0 CG A:TYR225 4.9 20.4 1.0 CB A:VAL195 4.9 17.2 1.0 N A:VAL195 4.9 16.3 1.0 N A:SER193 4.9 22.9 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of D176N-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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:K402 b:20.2 occ:1.00 O B:VAL195 2.6 22.9 1.0 O B:PHE189 2.6 19.8 1.0 O B:HOH569 2.7 21.3 1.0 O B:THR192 2.8 21.7 1.0 O B:HOH663 2.8 23.1 1.0 O B:TYR225 3.0 22.9 1.0 C B:PHE189 3.6 20.7 1.0 CB B:TYR225 3.7 20.4 1.0 C B:TYR225 3.7 22.2 1.0 C B:VAL195 3.8 20.7 1.0 C B:THR192 4.0 19.5 1.0 OG B:SER226 4.0 22.8 1.0 CB B:PHE189 4.1 20.2 1.0 CA B:SER190 4.3 20.8 0.3 CA B:TYR225 4.3 20.4 1.0 N B:SER190 4.4 20.2 0.3 CA B:MET196 4.4 20.1 1.0 N B:SER190 4.4 19.8 0.7 CA B:SER190 4.4 20.7 0.7 CG2 B:THR192 4.4 19.5 1.0 CA B:PHE189 4.5 20.2 1.0 O B:SER190 4.5 21.6 0.7 N B:THR192 4.5 21.7 1.0 C B:SER190 4.5 20.9 0.7 C B:SER190 4.5 20.9 0.3 N B:SER226 4.5 19.7 1.0 O B:SER190 4.6 21.9 0.3 N B:MET196 4.6 19.2 1.0 O B:GLY222 4.6 23.5 1.0 N B:THR197 4.6 17.8 1.0 CA B:THR192 4.8 20.6 1.0 CA B:VAL195 4.8 19.7 1.0 CA B:GLY222 4.9 23.5 1.0 C B:MET196 4.9 19.6 1.0 CG B:TYR225 5.0 22.1 1.0 N B:VAL195 5.0 19.2 1.0 CB B:VAL195 5.0 18.9 1.0 OG1 B:THR197 5.0 25.6 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