Zinc in PDB 2vqj: Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor

The structure of Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqj 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)	84.00 / 2.1
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	106.770, 137.562, 68.993, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 27.6

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

Fluorine	(F)	3 atoms
Potassium	(K)	2 atoms

The binding sites of Zinc atom in the Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor (pdb code 2vqj). 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 Trifluoromethylketone Inhbitor, PDB code: 2vqj:
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 Trifluoromethylketone 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 Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1415 b:30.7 occ:1.00 OD2 A:ASP290 1.9 28.8 1.0 ND1 A:HIS198 2.0 27.5 1.0 OD2 A:ASP196 2.0 29.0 1.0 O2 A:TFG1414 2.1 39.3 1.0 O3 A:TFG1414 2.4 38.3 1.0 C5 A:TFG1414 2.8 39.1 1.0 CG A:ASP196 2.8 27.1 1.0 CE1 A:HIS198 2.9 29.0 1.0 OD1 A:ASP196 2.9 27.6 1.0 CG A:ASP290 3.0 29.2 1.0 CG A:HIS198 3.1 27.7 1.0 OD1 A:ASP290 3.5 26.3 1.0 CB A:HIS198 3.6 27.7 1.0 C1 A:TFG1414 3.7 41.6 1.0 F3 A:TFG1414 3.8 34.6 1.0 N A:HIS198 3.8 27.5 1.0 S1 A:TFG1414 3.9 44.8 1.0 C6 A:TFG1414 3.9 35.9 1.0 NE2 A:HIS198 4.0 27.9 1.0 O A:HOH2226 4.2 32.6 1.0 CD2 A:HIS198 4.2 26.8 1.0 CB A:ASP196 4.2 26.8 1.0 N A:VAL197 4.3 26.8 1.0 CG1 A:VAL197 4.3 26.2 1.0 CB A:ASP290 4.3 29.2 1.0 CA A:GLY330 4.3 32.0 1.0 CA A:HIS198 4.3 27.4 1.0 NE2 A:HIS158 4.5 27.4 1.0 NE2 A:HIS159 4.7 30.2 1.0 F2 A:TFG1414 4.8 36.4 1.0 F1 A:TFG1414 4.8 32.0 1.0 C A:VAL197 4.8 27.0 1.0 C A:ASP196 4.8 27.1 1.0 N A:GLY330 4.8 31.8 1.0 CE1 A:HIS158 4.9 27.6 1.0 CA A:ASP196 4.9 26.7 1.0 CA A:VAL197 4.9 26.8 1.0 C2 A:TFG1414 5.0 42.9 1.0

Zinc binding site 2 out of 2 in the Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone 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 Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1416 b:76.1 occ:1.00 SG A:CYS23 1.9 69.3 1.0 NE2 A:HIS34 2.3 74.1 1.0 CE1 A:HIS34 2.5 73.8 1.0 NE2 A:HIS21 2.6 63.2 1.0 SG A:CYS107 2.6 85.3 1.0 CB A:CYS23 2.8 69.0 1.0 CD2 A:HIS21 3.0 62.2 1.0 CD2 A:HIS34 3.6 73.9 1.0 ND1 A:HIS34 3.8 73.7 1.0 CE1 A:HIS21 3.8 63.7 1.0 CB A:CYS107 3.9 85.1 1.0 CA A:CYS23 4.2 68.9 1.0 CG A:HIS21 4.3 61.9 1.0 CG A:HIS34 4.4 73.4 1.0 ND1 A:HIS21 4.7 62.8 1.0 N A:CYS23 4.8 67.7 1.0 CD1 A:LEU105 4.8 87.2 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 Zinc-Binding Domain. J.Biol.Chem. V. 283 26694 2008.
ISSN: ISSN 0021-9258
PubMed: 18614528
DOI: 10.1074/JBC.M803514200