Potassium in PDB 2vqm: Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor

The structure of Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor, PDB code: 2vqm was solved by M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.8
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	108.866, 138.208, 69.603, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25.6

The structure of Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Potassium atom in the Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor (pdb code 2vqm). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor, PDB code: 2vqm:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:K1408 b:29.1 occ:1.00 O A:ASP196 2.6 17.6 1.0 O A:HIS198 2.7 18.8 1.0 O A:LEU218 2.8 19.5 1.0 OD1 A:ASP194 2.8 21.5 1.0 OG A:SER217 2.9 20.9 1.0 O A:ASP194 2.9 18.3 1.0 CG A:ASP194 3.4 18.6 1.0 C A:ASP194 3.6 18.3 1.0 C A:HIS198 3.6 18.4 1.0 C A:ASP196 3.7 18.4 1.0 C A:LEU218 3.8 19.9 1.0 N A:ASP196 3.9 19.1 1.0 CB A:HIS219 3.9 19.9 1.0 OD2 A:ASP194 4.0 22.2 1.0 CB A:ASP194 4.0 19.0 1.0 N A:LEU218 4.1 20.0 1.0 CB A:SER217 4.1 20.8 1.0 CA A:HIS199 4.2 19.6 1.0 N A:HIS199 4.2 19.4 1.0 CA A:ASP196 4.2 18.8 1.0 N A:TRP195 4.2 18.4 1.0 N A:GLY200 4.3 20.6 1.0 CB A:ASP196 4.3 19.3 1.0 C A:TRP195 4.3 19.1 1.0 CA A:TRP195 4.4 19.3 1.0 CA A:ASP194 4.4 18.7 1.0 N A:HIS198 4.4 18.5 1.0 CA A:SER217 4.5 20.8 1.0 CA A:HIS219 4.5 20.0 1.0 ND1 A:HIS219 4.5 20.6 1.0 N A:HIS219 4.5 20.1 1.0 C A:HIS199 4.5 19.8 1.0 C A:SER217 4.6 20.4 1.0 CA A:LEU218 4.6 19.9 1.0 CG A:HIS219 4.7 20.3 1.0 CA A:HIS198 4.7 18.4 1.0 C A:VAL197 4.7 18.4 1.0 N A:VAL197 4.8 18.2 1.0 CE1 A:HIS158 4.8 21.9 1.0 O A:HOH2249 4.8 19.9 1.0 OH A:TYR215 4.9 21.1 1.0 ND1 A:HIS158 4.9 20.1 1.0

Potassium binding site 2 out of 2 in the Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:K1409 b:45.0 occ:1.00 O A:PHE207 2.7 29.5 1.0 O A:HOH2235 2.8 33.6 1.0 O A:VAL213 2.8 29.2 1.0 O A:PHE244 3.0 28.2 1.0 O A:ASP210 3.0 34.3 1.0 O A:HOH2236 3.1 27.3 1.0 C A:PHE207 3.6 29.3 1.0 C A:PHE244 3.7 28.3 1.0 CB A:PHE244 3.9 29.6 1.0 CB A:PHE207 4.0 28.6 1.0 C A:VAL213 4.0 28.4 1.0 C A:ASP210 4.1 34.4 1.0 N A:ASN245 4.4 27.5 1.0 CA A:PHE244 4.4 29.4 1.0 CA A:TYR208 4.5 31.5 1.0 N A:TYR208 4.5 30.2 1.0 CA A:PHE207 4.5 28.6 1.0 N A:TYR215 4.5 24.2 1.0 N A:ASP210 4.5 34.2 1.0 C A:TYR208 4.6 32.6 1.0 O A:TYR208 4.6 33.4 1.0 CA A:ASN245 4.7 26.9 1.0 CB A:ASN245 4.7 27.0 1.0 CA A:ASP210 4.8 34.2 1.0 CA A:LEU214 4.8 26.2 1.0 O A:GLY241 4.8 36.8 1.0 CB A:TYR215 4.9 23.4 1.0 ND2 A:ASN245 4.9 23.5 1.0 N A:LEU214 4.9 27.4 1.0 CB A:ASP210 5.0 34.3 1.0

M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi. Structural and Functional Analysis of the Human HDAC4 Catalytic Domain Reveals A Regulatory Zinc-Binding Domain. J.Biol.Chem. V. 283 26694 2008.
ISSN: ISSN 0021-9258
PubMed: 18614528
DOI: 10.1074/JBC.M803514200