Potassium in PDB 5zoo: Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment

All present enzymatic activity of Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment:
3.5.1.98;

The structure of Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment, PDB code: 5zoo was solved by S.Y.Park, H.J.Hwang, J.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.99 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.424, 131.424, 67.770, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 17.5

The structure of Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Potassium atom in the Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment (pdb code 5zoo). 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 Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment, PDB code: 5zoo:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment


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 Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ G:K1101 b:23.9 occ:1.00 O G:ASP840 2.6 18.2 1.0 OG G:SER861 2.7 22.6 1.0 OD1 G:ASP838 2.7 20.7 1.0 O G:LEU862 2.7 20.0 1.0 O G:ASP838 2.7 19.0 1.0 O G:HIS842 2.7 20.5 1.0 CG G:ASP838 3.3 24.2 1.0 C G:ASP838 3.4 21.4 1.0 C G:ASP840 3.6 20.9 1.0 C G:HIS842 3.7 19.0 1.0 C G:LEU862 3.7 18.9 1.0 CB G:ASP838 3.8 18.3 1.0 CB G:SER861 3.9 22.2 1.0 N G:ASP840 3.9 19.7 1.0 CB G:HIS863 3.9 20.9 1.0 N G:LEU862 4.0 19.5 1.0 OD2 G:ASP838 4.0 23.2 1.0 CA G:ASP840 4.1 18.5 1.0 N G:TRP839 4.1 19.4 1.0 C G:TRP839 4.2 20.9 1.0 CA G:ASP838 4.2 18.5 1.0 CA G:SER861 4.3 19.4 1.0 CA G:TRP839 4.3 18.7 1.0 CA G:HIS843 4.3 23.4 1.0 CB G:ASP840 4.3 17.3 1.0 N G:HIS843 4.3 18.9 1.0 N G:HIS842 4.4 18.8 1.0 C G:SER861 4.5 23.5 1.0 ND1 G:HIS863 4.5 23.1 1.0 N G:GLY844 4.5 20.3 1.0 CA G:HIS863 4.5 22.0 1.0 N G:HIS863 4.5 18.5 1.0 CA G:LEU862 4.5 21.5 1.0 O G:HOH1232 4.6 22.5 1.0 C G:VAL841 4.7 22.9 1.0 CG G:HIS863 4.7 20.1 1.0 CA G:HIS842 4.7 21.1 1.0 N G:VAL841 4.7 19.6 1.0 OH G:TYR859 4.7 22.1 1.0 C G:HIS843 4.7 21.9 1.0 CE1 G:HIS802 4.8 20.8 1.0 O G:TRP839 5.0 19.2 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment


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 Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ G:K1102 b:35.2 occ:1.00 O G:PHE851 2.5 22.1 1.0 O G:HOH1234 2.6 27.6 1.0 O G:VAL857 2.6 26.4 1.0 O G:ASP854 2.8 24.7 1.0 O G:PHE888 3.1 22.8 1.0 O G:HOH1258 3.5 25.4 1.0 C G:PHE851 3.6 22.5 1.0 C G:VAL857 3.8 27.1 1.0 CB G:PHE851 3.8 19.8 1.0 CB G:PHE888 3.8 24.0 1.0 C G:PHE888 3.8 24.2 1.0 C G:ASP854 3.9 24.7 1.0 N G:ASP854 4.3 24.9 1.0 CA G:PHE851 4.3 19.0 1.0 CA G:PHE888 4.5 21.0 1.0 N G:TYR852 4.5 22.2 1.0 CA G:ASP854 4.5 24.1 1.0 N G:TYR859 4.5 21.0 1.0 CA G:TYR852 4.5 24.8 1.0 C G:TYR852 4.6 25.2 1.0 O G:TYR852 4.6 25.3 1.0 CB G:ASP854 4.6 20.6 1.0 CA G:LEU858 4.6 20.5 1.0 N G:LEU858 4.7 21.7 1.0 N G:ASN889 4.7 24.2 1.0 CA G:VAL857 4.7 20.5 1.0 CB G:VAL857 4.7 23.7 1.0 N G:VAL857 4.8 19.4 1.0 O G:GLY885 4.9 27.0 1.0 N G:PRO855 4.9 27.2 1.0 CB G:ASN889 5.0 23.1 1.0

S.Y.Park, G.S.Kim, H.J.Hwang, T.H.Nam, H.S.Park, J.Song, T.H.Jang, Y.C.Lee, J.S.Kim. Structural Basis of the Specific Interaction of Smrt Corepressor with Histone Deacetylase 4. Nucleic Acids Res. V. 46 11776 2018.
ISSN: ESSN 1362-4962
PubMed: 30321390
DOI: 10.1093/NAR/GKY926