Zinc 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
Potassium	(K)	4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 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 Muation 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 with A Gain-of-Function Muation Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1411 b:25.4 occ:1.00 OD2 A:ASP196 1.9 24.7 1.0 OD2 A:ASP290 2.0 25.4 1.0 ND1 A:HIS198 2.1 22.7 1.0 O3 A:TFG1410 2.2 34.2 1.0 O2 A:TFG1410 2.3 33.7 1.0 C5 A:TFG1410 2.8 33.5 1.0 CG A:ASP196 2.9 24.1 1.0 CE1 A:HIS198 3.0 22.5 1.0 CG A:ASP290 3.1 24.6 1.0 OD1 A:ASP196 3.2 25.2 1.0 CG A:HIS198 3.2 22.9 1.0 OD1 A:ASP290 3.5 22.4 1.0 CB A:HIS198 3.6 24.1 1.0 C1 A:TFG1410 3.7 32.8 1.0 N A:HIS198 3.8 24.5 1.0 S1 A:TFG1410 3.9 32.5 1.0 F2 A:TFG1410 3.9 32.0 1.0 C6 A:TFG1410 4.0 33.2 1.0 NE2 A:HIS198 4.1 22.3 1.0 N A:VAL197 4.2 24.1 1.0 CB A:ASP196 4.2 24.7 1.0 CG1 A:VAL197 4.3 23.3 1.0 CD2 A:HIS198 4.3 22.4 1.0 CB A:ASP290 4.3 24.6 1.0 O A:HOH2125 4.4 21.7 1.0 CA A:HIS198 4.4 24.5 1.0 CA A:GLY330 4.5 26.2 1.0 NE2 A:HIS158 4.6 21.1 1.0 C A:VAL197 4.7 24.4 1.0 F3 A:TFG1410 4.7 33.4 1.0 NE2 A:HIS159 4.8 25.6 1.0 C A:ASP196 4.8 24.5 1.0 CA A:VAL197 4.9 24.2 1.0 CE1 A:HIS158 4.9 21.3 1.0 CA A:ASP196 4.9 24.4 1.0 F1 A:TFG1410 4.9 33.6 1.0 N A:GLY330 5.0 25.8 1.0 C2 A:TFG1410 5.0 32.7 1.0

Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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 B:Zn1410 b:28.3 occ:1.00 OD2 B:ASP290 1.9 23.2 1.0 OD2 B:ASP196 2.0 27.2 1.0 ND1 B:HIS198 2.1 23.4 1.0 O2 B:TFG1409 2.2 32.3 1.0 O3 B:TFG1409 2.3 33.0 1.0 C5 B:TFG1409 2.8 32.8 1.0 CG B:ASP196 2.8 25.4 1.0 CE1 B:HIS198 3.0 24.8 1.0 OD1 B:ASP196 3.0 25.6 1.0 CG B:ASP290 3.1 23.6 1.0 CG B:HIS198 3.1 24.1 1.0 CB B:HIS198 3.5 24.3 1.0 OD1 B:ASP290 3.5 19.8 1.0 C1 B:TFG1409 3.7 32.4 1.0 F2 B:TFG1409 3.8 33.3 1.0 N B:HIS198 3.8 24.3 1.0 S1 B:TFG1409 3.8 33.6 1.0 C6 B:TFG1409 3.9 33.4 1.0 NE2 B:HIS198 4.1 24.1 1.0 O B:HOH2127 4.2 21.5 1.0 CD2 B:HIS198 4.2 23.2 1.0 CG1 B:VAL197 4.2 24.3 1.0 CB B:ASP196 4.3 25.5 1.0 CA B:HIS198 4.3 24.8 1.0 N B:VAL197 4.3 24.1 1.0 CB B:ASP290 4.3 23.7 1.0 NE2 B:HIS158 4.5 26.1 1.0 CA B:GLY330 4.5 24.8 1.0 F1 B:TFG1409 4.7 33.4 1.0 NE2 B:HIS159 4.7 27.3 1.0 C B:VAL197 4.8 24.2 1.0 F3 B:TFG1409 4.8 32.0 1.0 C B:ASP196 4.8 24.7 1.0 CE1 B:HIS158 4.8 25.9 1.0 CA B:VAL197 4.9 24.1 1.0 CA B:ASP196 4.9 25.1 1.0 C2 B:TFG1409 5.0 32.9 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 Zinc-Binding Domain. J.Biol.Chem. V. 283 26694 2008.
ISSN: ISSN 0021-9258
PubMed: 18614528
DOI: 10.1074/JBC.M803514200