Zinc in PDB 2vqq: Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor

The structure of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqq 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)	60.00 / 1.9
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.605, 70.673, 88.201, 90.00, 108.08, 90.00
R / Rfree (%)	19.4 / 22.1

The structure of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) 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 (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor (pdb code 2vqq). 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 (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) 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 (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1411 b:13.6 occ:1.00 OD2 A:ASP290 1.9 10.9 1.0 O2 A:TFG1410 2.0 17.0 1.0 OD2 A:ASP196 2.0 11.0 1.0 ND1 A:HIS198 2.2 12.8 1.0 O3 A:TFG1410 2.3 20.0 1.0 C5 A:TFG1410 2.7 18.7 1.0 CG A:ASP196 2.8 10.9 1.0 OD1 A:ASP196 2.9 9.8 1.0 CG A:ASP290 3.0 12.0 1.0 CE1 A:HIS198 3.1 13.1 1.0 CG A:HIS198 3.3 11.7 1.0 OD1 A:ASP290 3.4 11.3 1.0 C1 A:TFG1410 3.6 17.9 1.0 F1 A:TFG1410 3.6 17.1 1.0 CB A:HIS198 3.7 11.5 1.0 S1 A:TFG1410 3.8 17.9 1.0 C6 A:TFG1410 3.9 18.8 1.0 N A:HIS198 3.9 11.4 1.0 O A:HOH2270 4.0 13.8 1.0 NE2 A:HIS198 4.2 12.8 1.0 CB A:ASP196 4.3 11.6 1.0 CB A:ASP290 4.3 11.8 1.0 CG1 A:VAL197 4.3 12.0 1.0 N A:VAL197 4.3 11.7 1.0 O A:HOH2195 4.3 23.9 1.0 CD2 A:HIS198 4.4 11.2 1.0 CA A:GLY330 4.4 14.5 1.0 CA A:HIS198 4.4 11.8 1.0 NE2 A:HIS158 4.5 14.5 1.0 F3 A:TFG1410 4.6 20.0 1.0 C A:VAL197 4.8 11.7 1.0 F2 A:TFG1410 4.8 19.2 1.0 NE2 A:HIS159 4.8 12.7 1.0 CE1 A:HIS158 4.9 13.4 1.0 N A:GLY330 4.9 13.7 1.0 C A:ASP196 4.9 11.4 1.0 C2 A:TFG1410 4.9 18.5 1.0 CA A:ASP196 4.9 11.6 1.0 N A:GLY331 4.9 15.5 1.0 CA A:VAL197 5.0 11.6 1.0

Zinc binding site 2 out of 2 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) 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 (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1410 b:14.6 occ:1.00 OD2 B:ASP290 2.0 12.4 1.0 OD2 B:ASP196 2.0 12.8 1.0 O2 B:TFG1409 2.2 15.5 1.0 ND1 B:HIS198 2.2 13.0 1.0 O3 B:TFG1409 2.3 20.7 1.0 CG B:ASP196 2.8 11.2 1.0 C5 B:TFG1409 2.8 18.2 1.0 OD1 B:ASP196 2.8 9.6 1.0 CE1 B:HIS198 3.0 13.8 1.0 CG B:ASP290 3.0 13.4 1.0 CG B:HIS198 3.2 13.2 1.0 OD1 B:ASP290 3.4 12.1 1.0 CB B:HIS198 3.6 13.0 1.0 C1 B:TFG1409 3.7 16.6 1.0 F1 B:TFG1409 3.7 19.4 1.0 N B:HIS198 3.8 12.8 1.0 S1 B:TFG1409 3.9 16.2 1.0 C6 B:TFG1409 3.9 19.7 1.0 O B:HOH2338 4.2 15.6 1.0 NE2 B:HIS198 4.2 13.0 1.0 CB B:ASP196 4.2 12.2 1.0 CG1 B:VAL197 4.2 12.3 1.0 CD2 B:HIS198 4.3 12.8 1.0 CB B:ASP290 4.3 13.4 1.0 N B:VAL197 4.3 11.9 1.0 CA B:HIS198 4.3 13.4 1.0 CA B:GLY330 4.4 13.4 1.0 O B:HOH2254 4.4 28.1 1.0 NE2 B:HIS158 4.5 13.1 1.0 F3 B:TFG1409 4.7 21.9 1.0 C B:VAL197 4.8 12.6 1.0 F2 B:TFG1409 4.8 18.4 1.0 N B:GLY330 4.8 12.9 1.0 C B:ASP196 4.8 11.7 1.0 CE1 B:HIS158 4.9 13.7 1.0 NE2 B:HIS159 4.9 13.1 1.0 CA B:ASP196 4.9 11.8 1.0 CA B:VAL197 4.9 12.2 1.0 N B:GLY331 5.0 14.2 1.0 C2 B:TFG1409 5.0 17.6 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