Potassium in PDB 5vi6: Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A

All present enzymatic activity of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A:
3.5.1.98;

The structure of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A, PDB code: 5vi6 was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.29 / 1.24
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	50.980, 50.980, 116.517, 90.00, 90.00, 120.00
R / Rfree (%)	12.1 / 14.3

The structure of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Potassium atom in the Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A (pdb code 5vi6). 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 8 in Complex with Trapoxin A, PDB code: 5vi6:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A


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 8 in Complex with Trapoxin A within 5.0Å range: probe atom residue distance (Å) B Occ A:K402 b:8.5 occ:1.00 O A:LEU200 2.7 9.2 1.0 OD1 A:ASP176 2.7 9.0 1.0 O A:ASP178 2.7 8.9 1.0 O A:HIS180 2.8 8.8 1.0 O A:ASP176 2.8 8.9 1.0 HG A:SER199 2.8 10.8 1.0 HB3 A:HIS201 2.9 10.1 1.0 OG A:SER199 2.9 9.0 1.0 HB3 A:ASP178 3.3 10.3 1.0 H A:ASP178 3.4 10.3 1.0 C A:ASP176 3.4 8.7 1.0 CG A:ASP176 3.4 8.4 1.0 HB3 A:ASP176 3.5 11.1 1.0 H A:LEU200 3.5 10.8 1.0 N A:ASP178 3.5 8.6 1.0 C A:ASP178 3.6 8.1 1.0 C A:LEU200 3.6 8.9 1.0 C A:HIS180 3.7 8.3 1.0 HA A:HIS181 3.7 10.9 1.0 CB A:HIS201 3.8 8.4 1.0 H A:GLY182 3.8 10.7 1.0 HA A:LEU177 3.9 9.8 1.0 CB A:ASP176 3.9 9.2 1.0 HA A:SER199 3.9 10.6 1.0 N A:LEU200 3.9 9.0 1.0 CA A:ASP178 3.9 8.2 1.0 C A:LEU177 4.0 8.9 1.0 CB A:ASP178 4.0 8.6 1.0 N A:LEU177 4.0 8.3 1.0 HE1 A:HIS142 4.0 10.8 1.0 CB A:SER199 4.1 9.5 1.0 HA A:HIS201 4.1 11.4 1.0 CA A:LEU177 4.2 8.2 1.0 N A:GLY182 4.3 8.9 1.0 CA A:ASP176 4.3 8.8 1.0 ND1 A:HIS201 4.3 9.9 1.0 CA A:HIS201 4.3 9.5 1.0 CA A:SER199 4.3 8.8 1.0 OD2 A:ASP176 4.3 9.4 1.0 HB2 A:ASP178 4.4 10.3 1.0 HB2 A:HIS201 4.4 10.1 1.0 CA A:HIS181 4.4 9.1 1.0 HB2 A:SER199 4.4 11.4 1.0 N A:HIS181 4.4 8.5 1.0 N A:HIS180 4.4 8.3 1.0 N A:HIS201 4.4 9.2 1.0 H A:HIS180 4.4 9.9 1.0 C A:SER199 4.5 8.7 1.0 CA A:LEU200 4.5 9.1 1.0 CG A:HIS201 4.5 8.9 1.0 O A:HOH621 4.6 10.8 1.0 C A:HIS181 4.6 9.3 1.0 C A:LEU179 4.6 8.6 1.0 H A:LEU177 4.7 10.0 1.0 HD1 A:HIS142 4.7 10.3 1.0 CA A:HIS180 4.7 8.7 1.0 N A:LEU179 4.7 9.0 1.0 O A:LEU177 4.7 9.4 1.0 HB3 A:SER199 4.8 11.4 1.0 HB2 A:ASP176 4.8 11.1 1.0 HA A:ASP176 4.8 10.6 1.0 CE1 A:HIS142 4.8 9.0 1.0 HB2 A:LEU200 4.8 11.8 1.0 HA A:ASP178 4.9 9.9 1.0 HA3 A:GLY182 4.9 10.9 1.0 O A:LEU179 4.9 9.5 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A


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 8 in Complex with Trapoxin A within 5.0Å range: probe atom residue distance (Å) B Occ A:K403 b:12.0 occ:1.00 O A:VAL195 2.6 14.2 1.0 O A:PHE189 2.6 12.5 1.0 O A:HOH590 2.7 13.0 1.0 O A:HOH730 2.8 12.2 1.0 O A:THR192 2.8 15.8 1.0 O A:TYR225 3.0 12.8 1.0 HB3 A:TYR225 3.0 16.8 1.0 HB2 A:TYR225 3.2 16.8 1.0 HB3 A:PHE189 3.4 15.0 1.0 CB A:TYR225 3.5 14.0 1.0 HA A:MET196 3.6 14.3 0.7 C A:PHE189 3.6 11.7 1.0 C A:TYR225 3.6 12.5 1.0 HA A:MET196 3.7 14.4 0.3 HA A:SER190 3.7 17.1 0.3 HG23 A:THR192 3.8 20.3 1.0 C A:VAL195 3.8 13.2 1.0 H A:THR192 3.8 17.1 1.0 HA A:SER190 3.9 15.5 0.7 HB2 A:PHE189 3.9 15.0 1.0 CB A:PHE189 4.0 12.5 1.0 C A:THR192 4.0 14.8 1.0 H A:THR197 4.0 13.0 0.7 H A:THR197 4.1 13.0 0.3 HG1 A:THR197 4.1 14.0 1.0 HG23 A:THR197 4.1 14.9 1.0 OG A:SER226 4.2 13.7 1.0 HG22 A:THR192 4.2 20.3 1.0 CA A:TYR225 4.2 12.8 1.0 O A:SER190 4.3 13.6 0.7 CA A:SER190 4.3 14.2 0.3 HB A:VAL195 4.3 15.3 1.0 H A:VAL195 4.4 15.9 1.0 HA3 A:GLY222 4.4 18.8 1.0 C A:SER190 4.4 13.8 0.7 CA A:SER190 4.4 12.9 0.7 N A:SER190 4.4 13.2 0.3 CA A:MET196 4.4 11.9 0.7 N A:SER190 4.4 13.0 0.7 CA A:PHE189 4.4 11.8 1.0 CG2 A:THR192 4.4 16.9 1.0 N A:SER226 4.5 11.8 1.0 CA A:MET196 4.5 12.0 0.3 N A:THR192 4.5 14.3 1.0 C A:SER190 4.5 14.1 0.3 HA2 A:GLY222 4.5 18.8 1.0 O A:SER190 4.6 13.8 0.3 N A:MET196 4.6 11.9 0.7 N A:MET196 4.6 12.4 0.3 HA A:SER193 4.6 20.7 1.0 O A:GLY222 4.6 14.3 1.0 HG A:SER226 4.7 16.4 1.0 N A:THR197 4.7 10.8 1.0 HG12 A:VAL195 4.7 16.2 1.0 CA A:THR192 4.8 14.4 1.0 HA A:SER226 4.8 14.3 1.0 CG A:TYR225 4.8 14.4 1.0 CA A:VAL195 4.8 13.1 1.0 HA A:TYR225 4.9 15.3 1.0 CA A:GLY222 4.9 15.6 1.0 HA A:PHE189 4.9 14.2 1.0 OG1 A:THR197 4.9 11.7 1.0 C A:MET196 5.0 10.6 0.3 H A:SER226 5.0 14.2 1.0 N A:VAL195 5.0 13.2 1.0 H A:TYR225 5.0 15.5 1.0

N.J.Porter, D.W.Christianson. Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8. Acs Chem. Biol. V. 12 2281 2017.
ISSN: ESSN 1554-8937
PubMed: 28846375
DOI: 10.1021/ACSCHEMBIO.7B00330