Potassium in PDB 5icn: HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4

All present enzymatic activity of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4:
3.5.1.98;

The structure of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4, PDB code: 5icn was solved by C.J.Millard, N.S.Robertson, P.J.Watson, A.G.Jameson, J.W.R.Schwabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.40 / 3.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.815, 107.815, 134.161, 90.00, 90.00, 120.00
R / Rfree (%)	25.5 / 29.9

The structure of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Potassium atom in the HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4 (pdb code 5icn). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4, PDB code: 5icn:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ B:K402 b:28.0 occ:1.00 O B:ASP176 2.4 26.3 1.0 OD1 B:ASP174 2.6 27.6 1.0 OG B:SER197 2.9 31.0 1.0 O B:ASP174 3.0 29.4 1.0 O B:PHE198 3.1 31.1 1.0 O B:HIS178 3.2 28.5 1.0 CG B:ASP174 3.5 27.9 1.0 C B:ASP176 3.5 26.8 1.0 C B:ASP174 3.6 29.0 1.0 C B:PHE198 3.7 30.1 1.0 N B:ASP176 3.7 28.1 1.0 N B:PHE198 3.7 30.9 1.0 C B:ILE175 3.9 29.2 1.0 C B:HIS178 3.9 28.1 1.0 CB B:ASP174 4.0 27.9 1.0 CB B:HIS199 4.0 27.2 1.0 CA B:ASP176 4.0 27.4 1.0 CB B:SER197 4.1 30.6 1.0 CB B:ASP176 4.1 26.9 1.0 O B:ILE175 4.2 27.9 1.0 N B:ILE175 4.2 30.3 1.0 ND1 B:HIS199 4.3 26.2 1.0 CA B:HIS179 4.3 28.0 1.0 CA B:SER197 4.3 30.7 1.0 C B:SER197 4.3 30.9 1.0 CA B:PHE198 4.4 30.7 1.0 N B:GLY180 4.4 29.2 1.0 CA B:ILE175 4.4 30.9 1.0 CA B:ASP174 4.4 27.7 1.0 OD2 B:ASP174 4.4 27.7 1.0 N B:HIS179 4.4 28.1 1.0 N B:HIS199 4.5 28.6 1.0 CA B:HIS199 4.5 27.6 1.0 C B:ILE177 4.6 26.4 1.0 CG B:HIS199 4.6 26.8 1.0 N B:HIS178 4.6 27.4 1.0 N B:ILE177 4.6 26.2 1.0 O B:ILE177 4.7 26.7 1.0 C B:HIS179 4.8 28.3 1.0 CA B:HIS178 4.9 27.9 1.0 CA B:ILE177 4.9 25.7 1.0 CE1 B:HIS140 5.0 38.4 1.0

Potassium binding site 2 out of 2 in the HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ B:K403 b:41.9 occ:1.00 O B:PHE187 2.8 37.8 1.0 O B:VAL193 3.2 32.5 1.0 O B:THR190 3.3 39.2 1.0 O B:TYR222 3.5 34.8 1.0 C B:PHE187 3.8 39.4 1.0 CB B:TYR222 3.9 33.4 1.0 C B:TYR222 3.9 33.3 1.0 O B:GLY219 4.0 46.1 1.0 O B:TYR188 4.1 40.5 1.0 CA B:TYR188 4.2 41.8 1.0 C B:TYR188 4.2 40.5 1.0 CA B:GLY219 4.3 46.0 1.0 C B:VAL193 4.4 32.8 1.0 N B:ALA223 4.4 31.7 1.0 N B:TYR188 4.4 40.7 1.0 C B:THR190 4.4 37.8 1.0 CA B:TYR222 4.5 34.0 1.0 CB B:PHE187 4.5 42.6 1.0 N B:THR190 4.6 37.4 1.0 C B:GLY219 4.6 44.6 1.0 CB B:ALA223 4.6 31.7 1.0 CG2 B:THR195 4.7 26.9 1.0 CA B:ALA223 4.8 31.3 1.0 CA B:PHE187 4.8 39.9 1.0 CG2 B:THR190 4.8 36.1 1.0 CA B:MET194 4.9 29.1 1.0 N B:THR195 4.9 27.9 1.0 N B:THR189 4.9 39.8 1.0

P.J.Watson, C.J.Millard, A.M.Riley, N.S.Robertson, L.C.Wright, H.Y.Godage, S.M.Cowley, A.G.Jamieson, B.V.Potter, J.W.Schwabe. Insights Into the Activation Mechanism of Class I Hdac Complexes By Inositol Phosphates. Nat Commun V. 7 11262 2016.
ISSN: ESSN 2041-1723
PubMed: 27109927
DOI: 10.1038/NCOMMS11262