Potassium in PDB 2vqv: Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor

The structure of Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor, PDB code: 2vqv 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)	30.00 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.524, 70.766, 89.011, 90.00, 108.57, 90.00
R / Rfree (%)	23.4 / 26.5

The structure of Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Potassium atom in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor (pdb code 2vqv). 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 Mutation Bound to A Hydroxamic Acid Inhibitor, PDB code: 2vqv:
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 Mutation Bound to A Hydroxamic Acid Inhibitor


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 Mutation Bound to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:K1407 b:53.6 occ:1.00 O A:ASP194 2.6 30.9 1.0 O A:HIS198 2.6 32.4 1.0 O A:ASP196 2.8 31.7 1.0 OD1 A:ASP194 2.9 28.6 1.0 O A:LEU218 3.0 33.5 1.0 OG A:SER217 3.1 32.2 1.0 C A:ASP194 3.6 30.8 1.0 CG A:ASP194 3.7 30.1 1.0 C A:HIS198 3.7 32.5 1.0 C A:LEU218 3.8 33.4 1.0 C A:ASP196 3.8 31.7 1.0 CB A:HIS219 3.9 34.2 1.0 N A:ASP196 4.0 31.4 1.0 CB A:SER217 4.0 32.4 1.0 N A:LEU218 4.1 32.8 1.0 CB A:ASP194 4.1 30.5 1.0 CA A:SER217 4.3 32.4 1.0 CA A:HIS199 4.3 33.0 1.0 CA A:ASP196 4.3 31.6 1.0 C A:SER217 4.3 32.6 1.0 C A:TRP195 4.4 31.2 1.0 N A:TRP195 4.4 30.9 1.0 N A:HIS219 4.4 33.8 1.0 CB A:ASP196 4.4 31.7 1.0 N A:GLY200 4.4 33.1 1.0 CA A:HIS219 4.4 34.2 1.0 ND1 A:HIS219 4.4 34.8 1.0 CA A:TRP195 4.4 31.0 1.0 N A:HIS199 4.4 32.8 1.0 CA A:ASP194 4.5 30.5 1.0 N A:HIS198 4.5 32.2 1.0 O A:HOH2002 4.5 34.4 1.0 C A:VAL197 4.6 32.1 1.0 CA A:LEU218 4.6 33.1 1.0 CG A:HIS219 4.6 34.5 1.0 C A:HIS199 4.7 33.0 1.0 OD2 A:ASP194 4.7 30.0 1.0 CE1 A:HIS158 4.7 35.4 1.0 O A:VAL197 4.7 32.2 1.0 CA A:HIS198 4.7 32.3 1.0 N A:VAL197 4.9 31.8 1.0 OH A:TYR215 4.9 29.7 1.0 ND1 A:HIS158 5.0 34.9 1.0

Potassium binding site 2 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor


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 Mutation Bound to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:K1408 b:69.2 occ:1.00 O A:PHE207 2.7 34.9 1.0 O A:PHE244 3.2 35.7 1.0 O A:ASP210 3.5 36.6 1.0 O A:VAL213 3.6 35.8 1.0 C A:PHE244 3.7 35.6 1.0 C A:PHE207 3.8 34.9 1.0 CB A:PHE244 4.0 36.5 1.0 O A:GLY241 4.0 39.7 1.0 N A:ASN245 4.1 34.7 1.0 CB A:ASN245 4.2 33.8 1.0 CA A:TYR208 4.3 36.0 1.0 C A:ASP210 4.3 36.5 1.0 CB A:PHE207 4.4 34.3 1.0 CA A:PHE244 4.4 36.4 1.0 C A:TYR208 4.4 36.3 1.0 CA A:ASN245 4.5 33.9 1.0 N A:TYR208 4.5 35.5 1.0 N A:ASP210 4.6 36.4 1.0 C A:VAL213 4.7 35.6 1.0 ND2 A:ASN245 4.7 32.9 1.0 O A:TYR208 4.7 36.6 1.0 CA A:PHE207 4.7 34.5 1.0 N A:SER209 4.8 36.4 1.0 N A:TYR215 4.9 33.2 1.0 CA A:GLY241 4.9 39.8 1.0 C A:GLY241 4.9 39.5 1.0

Potassium binding site 3 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor


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 Mutation Bound to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:K1409 b:40.4 occ:1.00 O B:HIS198 2.5 32.5 1.0 O B:ASP194 2.6 30.9 1.0 O B:ASP196 2.9 31.6 1.0 OD1 B:ASP194 2.9 28.5 1.0 OG B:SER217 3.0 32.1 1.0 O B:LEU218 3.2 33.3 1.0 C B:HIS198 3.6 32.5 1.0 C B:ASP194 3.7 30.7 1.0 CG B:ASP194 3.7 30.0 1.0 C B:ASP196 3.8 31.6 1.0 C B:LEU218 3.9 33.4 1.0 CB B:HIS219 3.9 34.3 1.0 CB B:SER217 4.0 32.3 1.0 N B:ASP196 4.0 31.4 1.0 CB B:ASP194 4.1 30.5 1.0 N B:LEU218 4.1 32.8 1.0 CA B:HIS199 4.2 33.0 1.0 N B:GLY200 4.3 33.1 1.0 CA B:SER217 4.3 32.3 1.0 N B:HIS199 4.3 32.8 1.0 CA B:ASP196 4.3 31.7 1.0 C B:SER217 4.4 32.5 1.0 ND1 B:HIS219 4.4 34.8 1.0 CB B:ASP196 4.4 31.8 1.0 CA B:HIS219 4.4 34.2 1.0 N B:HIS219 4.4 33.8 1.0 C B:TRP195 4.5 31.2 1.0 N B:HIS198 4.5 32.2 1.0 N B:TRP195 4.5 30.9 1.0 CA B:ASP194 4.5 30.5 1.0 C B:HIS199 4.5 32.9 1.0 CA B:TRP195 4.6 30.9 1.0 C B:VAL197 4.6 32.1 1.0 CG B:HIS219 4.6 34.5 1.0 CE1 B:HIS158 4.6 35.6 1.0 OD2 B:ASP194 4.7 29.9 1.0 CA B:LEU218 4.7 33.1 1.0 CA B:HIS198 4.7 32.2 1.0 O B:VAL197 4.7 32.2 1.0 OH B:TYR215 4.9 29.7 1.0 N B:VAL197 4.9 31.7 1.0 ND1 B:HIS158 4.9 35.0 1.0

Potassium binding site 4 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor


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 Mutation Bound to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:K1410 b:64.4 occ:1.00 O B:PHE207 2.6 34.9 1.0 O B:PHE244 3.4 35.5 1.0 O B:ASP210 3.4 36.7 1.0 O B:VAL213 3.6 35.8 1.0 C B:PHE207 3.7 34.9 1.0 C B:PHE244 3.8 35.6 1.0 O B:GLY241 4.0 39.5 1.0 CB B:PHE244 4.0 36.6 1.0 C B:ASP210 4.2 36.5 1.0 N B:ASN245 4.2 34.7 1.0 CA B:TYR208 4.3 36.0 1.0 CB B:PHE207 4.3 34.3 1.0 CB B:ASN245 4.3 33.8 1.0 C B:TYR208 4.4 36.2 1.0 N B:ASP210 4.4 36.4 1.0 N B:TYR208 4.5 35.5 1.0 CA B:PHE244 4.5 36.4 1.0 CA B:ASN245 4.6 33.8 1.0 CA B:PHE207 4.7 34.5 1.0 C B:VAL213 4.7 35.5 1.0 N B:SER209 4.7 36.4 1.0 O B:TYR208 4.8 36.5 1.0 CA B:GLY241 4.8 39.7 1.0 C B:GLY241 4.8 39.5 1.0 ND2 B:ASN245 4.9 32.9 1.0 CA B:ASP210 4.9 36.3 1.0 N B:PRO211 5.0 36.7 1.0 N B:TYR215 5.0 33.2 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 Structural Zinc-Binding Domain. J.Biol.Chem. V. 283 26694 2008.
ISSN: ISSN 0021-9258
PubMed: 18614528
DOI: 10.1074/JBC.M803514200