Potassium in PDB 4qa7: Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

The structure of Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa7 was solved by C.Decroos, C.B.Bowman, J.-A.S.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.19 / 2.31
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.406, 80.406, 106.063, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24.1

The structure of Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Potassium atom in the Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 4qa7). 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 H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa7:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of H334R/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 H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K402 b:48.5 occ:1.00 O A:ASP178 2.7 51.1 1.0 O A:LEU200 2.8 54.5 1.0 O A:HIS180 2.8 46.9 1.0 OD1 A:ASP176 2.8 47.5 1.0 O A:ASP176 2.9 45.9 1.0 OG A:SER199 3.0 46.8 1.0 N A:ASP178 3.4 49.0 1.0 CG A:ASP176 3.4 46.1 1.0 C A:ASP176 3.5 52.3 1.0 C A:ASP178 3.5 47.1 1.0 C A:LEU200 3.6 51.3 1.0 CB A:ASP176 3.8 48.1 1.0 CB A:HIS201 3.8 51.8 1.0 CA A:ASP178 3.8 48.1 1.0 C A:HIS180 3.8 49.8 1.0 N A:LEU200 3.9 55.2 1.0 CB A:ASP178 3.9 41.3 1.0 C A:LEU177 4.0 45.8 1.0 N A:LEU177 4.1 48.4 1.0 CB A:SER199 4.2 47.8 1.0 CA A:LEU177 4.3 45.0 1.0 CA A:ASP176 4.3 47.3 1.0 OD2 A:ASP176 4.3 44.6 1.0 N A:GLY182 4.3 45.8 1.0 CA A:HIS201 4.3 53.4 1.0 N A:HIS201 4.4 53.5 1.0 CA A:SER199 4.4 49.3 1.0 CA A:HIS181 4.4 45.8 1.0 C A:SER199 4.4 52.0 1.0 CA A:LEU200 4.4 51.0 1.0 ND1 A:HIS201 4.4 52.5 1.0 N A:HIS181 4.5 50.7 1.0 N A:HIS180 4.6 51.7 1.0 CG A:HIS201 4.6 52.0 1.0 N A:LEU179 4.7 47.4 1.0 CE1 A:HIS142 4.7 43.2 1.0 C A:LEU179 4.7 50.6 1.0 C A:HIS181 4.8 47.7 1.0 O A:LEU177 4.8 50.3 1.0 CA A:HIS180 4.8 44.9 1.0 O A:LEU179 5.0 48.8 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of H334R/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 H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K403 b:59.2 occ:1.00 O A:PHE189 2.7 55.0 1.0 O A:VAL195 2.7 51.4 1.0 O A:HOH523 2.8 50.4 1.0 O A:TYR225 2.8 53.5 1.0 O A:HOH536 2.9 51.5 1.0 O A:THR192 2.9 60.2 1.0 CB A:TYR225 3.5 59.3 1.0 C A:TYR225 3.6 58.5 1.0 OG A:SER226 3.7 54.2 1.0 C A:PHE189 3.7 53.4 1.0 C A:VAL195 3.9 54.1 1.0 C A:THR192 4.1 57.9 1.0 CA A:TYR225 4.2 59.1 1.0 O A:GLY222 4.3 65.8 1.0 CB A:PHE189 4.3 48.0 1.0 CA A:MET196 4.3 52.8 1.0 N A:SER226 4.5 56.4 1.0 CA A:SER190 4.5 52.4 1.0 N A:SER190 4.5 54.9 1.0 N A:MET196 4.6 53.8 1.0 CA A:GLY222 4.6 56.8 1.0 N A:THR197 4.6 51.4 1.0 CG2 A:THR192 4.6 48.9 1.0 C A:SER190 4.6 57.6 1.0 CA A:PHE189 4.6 51.0 1.0 O A:SER190 4.7 55.6 1.0 N A:THR192 4.7 51.9 1.0 CG A:TYR225 4.8 60.9 1.0 OG1 A:THR197 4.9 56.0 1.0 CB A:SER226 4.9 48.0 1.0 CA A:SER226 4.9 53.1 1.0 C A:GLY222 4.9 60.1 1.0 CA A:THR192 4.9 52.3 1.0 C A:MET196 5.0 51.4 1.0 CA A:VAL195 5.0 54.6 1.0

C.Decroos, C.M.Bowman, J.A.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson. Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia De Lange Syndrome Spectrum Disorders. Acs Chem.Biol. V. 9 2157 2014.
ISSN: ISSN 1554-8929
PubMed: 25075551
DOI: 10.1021/CB5003762