Potassium in PDB 2vqo: Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor

The structure of Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqo 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)	40.00 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.092, 70.965, 88.331, 90.00, 108.11, 90.00
R / Rfree (%)	21 / 25

The structure of Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Zinc	(Zn)	2 atoms

The binding sites of Potassium atom in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor (pdb code 2vqo). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqo:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone 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 with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:K1408 b:31.1 occ:1.00 O A:ASP196 2.7 24.1 1.0 O A:HIS198 2.8 24.8 1.0 OG A:SER217 2.8 27.0 1.0 OD1 A:ASP194 2.9 25.6 1.0 O A:ASP194 3.0 25.4 1.0 O A:LEU218 3.0 27.9 1.0 CG A:ASP194 3.5 26.7 1.0 C A:ASP194 3.6 25.6 1.0 C A:HIS198 3.7 24.6 1.0 C A:ASP196 3.7 24.5 1.0 C A:LEU218 3.8 27.7 1.0 N A:ASP196 3.9 24.9 1.0 CB A:ASP194 3.9 26.1 1.0 CB A:HIS219 4.0 27.6 1.0 CB A:SER217 4.1 28.1 1.0 N A:LEU218 4.1 27.5 1.0 CA A:HIS199 4.2 25.4 1.0 N A:TRP195 4.2 25.4 1.0 OD2 A:ASP194 4.2 27.8 1.0 CA A:ASP196 4.3 24.4 1.0 N A:GLY200 4.3 26.2 1.0 N A:HIS199 4.3 25.1 1.0 CB A:ASP196 4.3 24.7 1.0 C A:TRP195 4.4 25.3 1.0 CA A:TRP195 4.4 25.2 1.0 CA A:ASP194 4.4 26.0 1.0 CA A:SER217 4.4 28.1 1.0 N A:HIS198 4.5 24.5 1.0 C A:HIS199 4.6 25.8 1.0 N A:HIS219 4.6 27.4 1.0 C A:SER217 4.6 27.9 1.0 CA A:HIS219 4.6 27.8 1.0 ND1 A:HIS219 4.6 27.3 1.0 CA A:LEU218 4.6 27.5 1.0 CG A:HIS219 4.7 27.6 1.0 CA A:HIS198 4.7 24.5 1.0 O A:HOH2060 4.7 24.1 1.0 C A:VAL197 4.8 24.4 1.0 CE1 A:HIS158 4.8 21.3 1.0 N A:VAL197 4.8 24.1 1.0 OH A:TYR215 4.9 29.0 1.0 ND1 A:HIS158 5.0 22.3 1.0

Potassium binding site 2 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone 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 with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:K1409 b:59.4 occ:1.00 O A:PHE207 2.7 35.1 1.0 O A:HOH2069 2.7 27.9 1.0 O A:VAL213 2.9 32.6 1.0 O A:HOH2070 3.0 27.6 1.0 O A:PHE244 3.0 38.0 1.0 O A:ASP210 3.0 37.5 1.0 C A:PHE207 3.7 35.0 1.0 C A:PHE244 3.8 37.7 1.0 CB A:PHE207 4.0 34.7 1.0 CB A:PHE244 4.1 38.5 1.0 C A:VAL213 4.1 32.5 1.0 C A:ASP210 4.1 37.4 1.0 N A:ASN245 4.4 36.7 1.0 N A:TYR215 4.5 30.5 1.0 CA A:TYR208 4.5 35.8 1.0 N A:ASP210 4.5 37.3 1.0 CA A:PHE244 4.5 38.5 1.0 CA A:PHE207 4.5 34.7 1.0 N A:TYR208 4.6 35.5 1.0 C A:TYR208 4.6 36.2 1.0 O A:TYR208 4.6 36.2 1.0 CB A:ASN245 4.6 35.5 1.0 ND2 A:ASN245 4.7 32.5 1.0 CA A:ASN245 4.7 35.7 1.0 CB A:TYR215 4.7 29.9 1.0 CA A:ASP210 4.8 37.4 1.0 O A:GLY241 4.9 42.8 1.0 CA A:LEU214 4.9 31.4 1.0 N A:LEU214 5.0 31.9 1.0 CA A:VAL213 5.0 33.2 1.0 CB A:VAL213 5.0 33.2 1.0

Potassium binding site 3 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ B:K1407 b:32.0 occ:1.00 O B:ASP196 2.5 24.3 1.0 O B:HIS198 2.8 25.2 1.0 OG B:SER217 2.8 29.0 1.0 OD1 B:ASP194 2.9 26.2 1.0 O B:LEU218 2.9 29.6 1.0 O B:ASP194 2.9 26.0 1.0 CG B:ASP194 3.5 26.7 1.0 C B:ASP194 3.6 26.3 1.0 C B:ASP196 3.6 24.7 1.0 C B:HIS198 3.7 25.1 1.0 C B:LEU218 3.8 29.8 1.0 N B:ASP196 3.9 25.5 1.0 CB B:HIS219 3.9 29.9 1.0 CB B:ASP194 4.0 26.7 1.0 CB B:SER217 4.1 29.8 1.0 N B:LEU218 4.1 29.5 1.0 CA B:ASP196 4.2 25.1 1.0 OD2 B:ASP194 4.2 27.3 1.0 N B:TRP195 4.2 26.0 1.0 CA B:HIS199 4.2 26.1 1.0 C B:TRP195 4.3 25.8 1.0 CB B:ASP196 4.3 25.5 1.0 N B:HIS199 4.3 25.6 1.0 CA B:TRP195 4.3 25.8 1.0 N B:GLY200 4.3 27.5 1.0 N B:HIS198 4.4 24.3 1.0 CA B:ASP194 4.4 26.5 1.0 CA B:SER217 4.5 29.7 1.0 CA B:HIS219 4.5 30.2 1.0 N B:HIS219 4.5 29.9 1.0 ND1 B:HIS219 4.6 28.7 1.0 C B:VAL197 4.6 24.2 1.0 C B:SER217 4.6 29.6 1.0 CA B:LEU218 4.6 29.6 1.0 C B:HIS199 4.6 26.7 1.0 O B:HOH2054 4.7 18.6 1.0 CG B:HIS219 4.7 29.0 1.0 CA B:HIS198 4.7 24.8 1.0 N B:VAL197 4.7 24.1 1.0 CE1 B:HIS158 4.9 25.9 1.0 CA B:VAL197 5.0 24.1 1.0 O B:VAL197 5.0 24.0 1.0

Potassium binding site 4 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of HDAC4 Catalytic Domain with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ B:K1408 b:59.2 occ:1.00 O B:PHE207 2.7 35.2 1.0 O B:HOH2068 2.8 27.5 1.0 O B:VAL213 2.9 33.4 1.0 O B:HOH2069 3.2 35.8 1.0 O B:PHE244 3.2 36.1 1.0 O B:ASP210 3.2 37.0 1.0 C B:PHE207 3.7 34.9 1.0 C B:PHE244 3.8 36.2 1.0 CB B:PHE244 4.0 36.7 1.0 C B:VAL213 4.1 33.2 1.0 CB B:PHE207 4.1 34.5 1.0 C B:ASP210 4.3 37.0 1.0 CA B:TYR208 4.4 35.9 1.0 N B:TYR215 4.5 31.3 1.0 N B:ASN245 4.5 35.5 1.0 C B:TYR208 4.5 36.4 1.0 N B:TYR208 4.5 35.4 1.0 O B:TYR208 4.5 36.6 1.0 CA B:PHE244 4.6 36.9 1.0 CA B:PHE207 4.6 34.7 1.0 N B:ASP210 4.6 37.2 1.0 ND2 B:ASN245 4.7 33.7 1.0 CB B:ASN245 4.7 34.7 1.0 CA B:ASN245 4.7 34.8 1.0 CB B:TYR215 4.8 31.0 1.0 CB B:VAL213 4.9 33.6 1.0 CA B:LEU214 4.9 32.1 1.0 CA B:ASP210 4.9 37.2 1.0 O B:GLY241 4.9 41.6 1.0 N B:LEU214 5.0 32.6 1.0 CA B:VAL213 5.0 33.5 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