Zinc 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:

Potassium

(K)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of HDAC4 Catalytic Domain Bound to A Hydroxamic Acid Inhbitor, PDB code: 2vqm:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn1411 b:20.5 occ:1.00 OD2 A:ASP290 1.9 19.3 1.0 O A:HOH2375 2.0 28.4 1.0 OD2 A:ASP196 2.1 18.7 1.0 ND1 A:HIS198 2.1 19.4 1.0 OAY A:HA31410 2.5 31.7 1.0 CG A:ASP196 2.7 20.0 1.0 OD1 A:ASP196 2.8 19.2 1.0 CG A:ASP290 3.0 20.6 1.0 CE1 A:HIS198 3.0 20.0 1.0 CG A:HIS198 3.2 18.1 1.0 CAW A:HA31410 3.4 33.4 1.0 OD1 A:ASP290 3.4 19.3 1.0 CB A:HIS198 3.6 18.1 1.0 OAZ A:HA31410 4.0 41.2 1.0 N A:HIS198 4.0 18.5 1.0 NAX A:HA31410 4.0 36.3 1.0 NE2 A:HIS198 4.2 19.4 1.0 CB A:ASP196 4.2 19.3 1.0 CA A:GLY330 4.2 22.5 1.0 CD2 A:HIS198 4.3 19.1 1.0 O A:HOH2296 4.3 24.6 1.0 NE2 A:HIS158 4.3 23.1 1.0 CAV A:HA31410 4.3 30.0 1.0 CB A:ASP290 4.3 20.2 1.0 CG1 A:VAL197 4.4 17.9 1.0 CA A:HIS198 4.4 18.4 1.0 N A:VAL197 4.5 18.2 1.0 NE2 A:HIS159 4.7 22.6 1.0 N A:GLY330 4.7 22.0 1.0 CE1 A:HIS158 4.7 21.9 1.0 SAS A:HA31410 4.8 29.2 1.0 C A:ASP196 4.9 18.4 1.0 CA A:ASP196 4.9 18.8 1.0 C A:VAL197 4.9 18.4 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1412 b:54.5 occ:1.00 NE2 A:HIS34 1.9 41.0 1.0 NE2 A:HIS21 2.2 44.3 1.0 SG A:CYS107 2.2 59.8 1.0 SG A:CYS23 2.4 50.5 1.0 CE1 A:HIS34 2.7 44.5 1.0 CB A:CYS23 3.0 48.9 1.0 CD2 A:HIS34 3.0 44.4 1.0 CD2 A:HIS21 3.0 43.9 1.0 CE1 A:HIS21 3.2 45.7 1.0 CB A:CYS107 3.3 59.6 1.0 ND1 A:HIS34 3.9 44.7 1.0 CG A:HIS34 4.1 45.4 1.0 CG A:HIS21 4.2 42.9 1.0 CA A:CYS23 4.2 48.8 1.0 ND1 A:HIS21 4.3 44.4 1.0 CD1 A:LEU105 4.5 61.4 1.0 CA A:CYS107 4.7 59.6 1.0 O A:GLN22 4.9 46.8 1.0 CB A:LEU105 5.0 61.4 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