Zinc 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:

Potassium

(K)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn1410 b:26.3 occ:1.00 OD2 A:ASP290 1.9 30.5 1.0 ND1 A:HIS198 2.2 31.5 1.0 OAY A:HA31409 2.3 35.3 1.0 OD2 A:ASP196 2.5 33.2 1.0 CE1 A:HIS198 2.8 31.8 1.0 OD1 A:ASP196 2.9 32.3 1.0 CG A:ASP290 3.0 31.4 1.0 CAW A:HA31409 3.0 35.5 1.0 CG A:ASP196 3.0 32.1 1.0 OAZ A:HA31409 3.2 37.4 1.0 CG A:HIS198 3.3 31.9 1.0 NAX A:HA31409 3.4 36.0 1.0 OD1 A:ASP290 3.5 30.7 1.0 CB A:HIS198 3.9 32.2 1.0 NE2 A:HIS198 4.0 31.9 1.0 CAV A:HA31409 4.0 35.4 1.0 CA A:GLY330 4.0 33.2 1.0 CB A:ASP290 4.1 31.8 1.0 CG1 A:VAL197 4.2 31.9 1.0 N A:HIS198 4.3 32.2 1.0 CD2 A:HIS198 4.3 31.6 1.0 CB A:ASP196 4.5 31.7 1.0 SAS A:HA31409 4.6 35.0 1.0 N A:VAL197 4.6 31.8 1.0 N A:GLY330 4.7 32.7 1.0 CE2 A:TYR332 4.7 38.1 1.0 OH A:TYR332 4.7 37.9 1.0 CA A:HIS198 4.8 32.3 1.0 NE2 A:HIS159 4.8 33.8 1.0 NE2 A:HIS158 4.9 35.5 1.0 N A:GLY331 4.9 34.0 1.0 C A:GLY330 5.0 33.6 1.0

Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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 B:Zn1412 b:22.0 occ:1.00 ND1 B:HIS198 2.1 31.5 1.0 OD2 B:ASP290 2.1 30.5 1.0 OD2 B:ASP196 2.4 33.2 1.0 OAY B:HA31411 2.5 35.4 1.0 CE1 B:HIS198 2.8 31.7 1.0 OD1 B:ASP196 3.0 32.3 1.0 CG B:ASP196 3.0 32.2 1.0 CAW B:HA31411 3.1 36.9 1.0 CG B:ASP290 3.1 31.3 1.0 CG B:HIS198 3.2 31.9 1.0 OAZ B:HA31411 3.5 39.7 1.0 NAX B:HA31411 3.5 38.0 1.0 OD1 B:ASP290 3.6 30.6 1.0 CB B:HIS198 3.7 32.1 1.0 NE2 B:HIS198 3.9 31.9 1.0 CAV B:HA31411 4.0 37.2 1.0 CD2 B:HIS198 4.1 31.7 1.0 N B:HIS198 4.2 32.2 1.0 CA B:GLY330 4.2 33.1 1.0 CG1 B:VAL197 4.2 32.0 1.0 CB B:ASP290 4.3 31.7 1.0 SAS B:HA31411 4.4 38.0 1.0 CB B:ASP196 4.5 31.8 1.0 NE2 B:HIS159 4.6 33.6 1.0 CA B:HIS198 4.6 32.2 1.0 N B:VAL197 4.7 31.7 1.0 NE2 B:HIS158 4.7 35.5 1.0 N B:GLY330 4.8 32.7 1.0 OH B:TYR332 4.8 38.0 1.0 CE2 B:TYR332 4.8 37.9 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