Fluorine 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:

Potassium	(K)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 6 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 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 Fluorine with other atoms in the F 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:F1410 b:33.6 occ:1.00 F1 A:TFG1410 0.0 33.6 1.0 C6 A:TFG1410 1.3 33.2 1.0 F2 A:TFG1410 2.2 32.0 1.0 F3 A:TFG1410 2.2 33.4 1.0 C5 A:TFG1410 2.3 33.5 1.0 C1 A:TFG1410 2.9 32.8 1.0 O2 A:TFG1410 2.9 33.7 1.0 C2 A:TFG1410 3.1 32.7 1.0 CG A:PRO156 3.5 24.9 1.0 O3 A:TFG1410 3.6 34.2 1.0 O A:HOH2125 3.6 21.7 1.0 CD1 A:PHE168 3.7 30.4 1.0 O A:GLY167 4.0 28.7 1.0 CA A:GLY330 4.3 26.2 1.0 S1 A:TFG1410 4.3 32.5 1.0 C3 A:TFG1410 4.4 32.5 1.0 CB A:PHE168 4.4 28.4 1.0 CB A:PRO156 4.4 24.4 1.0 CG A:PHE168 4.4 29.4 1.0 CE1 A:PHE168 4.5 30.9 1.0 CD A:PRO156 4.6 24.7 1.0 N A:GLY330 4.9 25.8 1.0 ZN A:ZN1411 4.9 25.4 1.0 C A:GLY167 5.0 28.7 1.0 C4 A:TFG1410 5.0 32.4 1.0

Fluorine binding site 2 out of 6 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 Fluorine with other atoms in the F 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 A:F1410 b:32.0 occ:1.00 F2 A:TFG1410 0.0 32.0 1.0 C6 A:TFG1410 1.3 33.2 1.0 F1 A:TFG1410 2.2 33.6 1.0 F3 A:TFG1410 2.2 33.4 1.0 C5 A:TFG1410 2.3 33.5 1.0 O2 A:TFG1410 2.7 33.7 1.0 O3 A:TFG1410 2.8 34.2 1.0 CA A:GLY330 3.0 26.2 1.0 N A:GLY330 3.1 25.8 1.0 CG A:PRO156 3.5 24.9 1.0 OD1 A:ASP196 3.6 25.2 1.0 C A:GLU329 3.6 25.5 1.0 CB A:PRO156 3.6 24.4 1.0 C1 A:TFG1410 3.7 32.8 1.0 ZN A:ZN1411 3.9 25.4 1.0 O A:GLU329 4.0 25.9 1.0 O A:HOH2125 4.1 21.7 1.0 NE2 A:HIS158 4.2 21.1 1.0 C2 A:TFG1410 4.4 32.7 1.0 CG A:ASP196 4.4 24.1 1.0 C A:GLY330 4.4 26.3 1.0 CB A:GLU329 4.5 25.2 1.0 OD2 A:ASP196 4.5 24.7 1.0 CA A:GLU329 4.5 25.3 1.0 CD2 A:HIS158 4.6 21.9 1.0 CD A:PRO156 4.8 24.7 1.0 OD2 A:ASP290 4.9 25.4 1.0 N A:GLY331 4.9 26.7 1.0 NE2 A:HIS159 4.9 25.6 1.0 CD2 A:HIS159 4.9 25.3 1.0

Fluorine binding site 3 out of 6 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 Fluorine with other atoms in the F binding site number 3 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:F1410 b:33.4 occ:1.00 F3 A:TFG1410 0.0 33.4 1.0 C6 A:TFG1410 1.3 33.2 1.0 F2 A:TFG1410 2.2 32.0 1.0 F1 A:TFG1410 2.2 33.6 1.0 C5 A:TFG1410 2.4 33.5 1.0 O3 A:TFG1410 2.7 34.2 1.0 C1 A:TFG1410 3.0 32.8 1.0 C2 A:TFG1410 3.0 32.7 1.0 O A:GLY167 3.1 28.7 1.0 CD2 A:HIS159 3.1 25.3 1.0 NE2 A:HIS159 3.5 25.6 1.0 CG A:PRO156 3.6 24.9 1.0 O2 A:TFG1410 3.6 33.7 1.0 SG A:CYS169 3.9 26.9 1.0 NE2 A:HIS158 4.0 21.1 1.0 CB A:PRO156 4.0 24.4 1.0 CD2 A:HIS158 4.2 21.9 1.0 C A:GLY167 4.3 28.7 1.0 C3 A:TFG1410 4.3 32.5 1.0 CG A:HIS159 4.4 25.2 1.0 S1 A:TFG1410 4.6 32.5 1.0 CD1 A:PHE168 4.7 30.4 1.0 ZN A:ZN1411 4.7 25.4 1.0 CE1 A:HIS159 4.8 25.6 1.0 CB A:PHE168 4.8 28.4 1.0 CA A:GLY167 4.9 29.0 1.0

Fluorine binding site 4 out of 6 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 Fluorine with other atoms in the F binding site number 4 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:F1409 b:33.4 occ:1.00 F1 B:TFG1409 0.0 33.4 1.0 C6 B:TFG1409 1.3 33.4 1.0 F3 B:TFG1409 2.2 32.0 1.0 F2 B:TFG1409 2.2 33.3 1.0 C5 B:TFG1409 2.3 32.8 1.0 O2 B:TFG1409 2.8 32.3 1.0 C1 B:TFG1409 3.0 32.4 1.0 O B:HOH2127 3.3 21.5 1.0 C2 B:TFG1409 3.4 32.9 1.0 CG B:PRO156 3.5 27.5 1.0 O3 B:TFG1409 3.6 33.0 1.0 CA B:GLY330 3.9 24.8 1.0 CD1 B:PHE168 4.1 30.8 1.0 CB B:PRO156 4.2 26.8 1.0 O B:GLY167 4.3 28.4 1.0 S1 B:TFG1409 4.4 33.6 1.0 N B:GLY330 4.5 24.7 1.0 CD B:PRO156 4.6 27.3 1.0 C3 B:TFG1409 4.6 32.3 1.0 ZN B:ZN1410 4.7 28.3 1.0 CB B:PHE168 4.7 28.6 1.0 CE1 B:PHE168 4.8 30.9 1.0 CG B:PHE168 4.8 29.7 1.0

Fluorine binding site 5 out of 6 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 Fluorine with other atoms in the F binding site number 5 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:F1409 b:33.3 occ:1.00 F2 B:TFG1409 0.0 33.3 1.0 C6 B:TFG1409 1.3 33.4 1.0 F3 B:TFG1409 2.2 32.0 1.0 F1 B:TFG1409 2.2 33.4 1.0 C5 B:TFG1409 2.3 32.8 1.0 O3 B:TFG1409 2.6 33.0 1.0 O2 B:TFG1409 2.8 32.3 1.0 CA B:GLY330 3.1 24.8 1.0 N B:GLY330 3.2 24.7 1.0 OD1 B:ASP196 3.4 25.6 1.0 NE2 B:HIS158 3.6 26.1 1.0 CB B:PRO156 3.6 26.8 1.0 CG B:PRO156 3.7 27.5 1.0 C1 B:TFG1409 3.7 32.4 1.0 ZN B:ZN1410 3.8 28.3 1.0 C B:GLU329 3.8 24.2 1.0 CD2 B:HIS158 4.0 27.2 1.0 CG B:ASP196 4.2 25.4 1.0 O B:HOH2127 4.2 21.5 1.0 OD2 B:ASP196 4.3 27.2 1.0 O B:GLU329 4.3 24.4 1.0 C2 B:TFG1409 4.4 32.9 1.0 CB B:GLU329 4.4 23.9 1.0 CA B:GLU329 4.6 24.2 1.0 NE2 B:HIS159 4.6 27.3 1.0 C B:GLY330 4.6 24.8 1.0 CD2 B:HIS159 4.7 27.1 1.0 CE1 B:HIS158 4.8 25.9 1.0 OD2 B:ASP290 4.8 23.2 1.0 OE1 B:GLU329 5.0 22.6 1.0

Fluorine binding site 6 out of 6 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 Fluorine with other atoms in the F binding site number 6 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:F1409 b:32.0 occ:1.00 F3 B:TFG1409 0.0 32.0 1.0 C6 B:TFG1409 1.3 33.4 1.0 F2 B:TFG1409 2.2 33.3 1.0 F1 B:TFG1409 2.2 33.4 1.0 C5 B:TFG1409 2.4 32.8 1.0 O3 B:TFG1409 2.8 33.0 1.0 C2 B:TFG1409 2.9 32.9 1.0 C1 B:TFG1409 2.9 32.4 1.0 O B:GLY167 3.0 28.4 1.0 CD2 B:HIS159 3.2 27.1 1.0 CG B:PRO156 3.5 27.5 1.0 NE2 B:HIS159 3.6 27.3 1.0 O2 B:TFG1409 3.6 32.3 1.0 SG B:CYS169 3.9 27.9 1.0 CB B:PRO156 3.9 26.8 1.0 NE2 B:HIS158 4.1 26.1 1.0 C B:GLY167 4.2 28.9 1.0 C3 B:TFG1409 4.2 32.3 1.0 CD2 B:HIS158 4.3 27.2 1.0 CG B:HIS159 4.4 27.0 1.0 CD1 B:PHE168 4.5 30.8 1.0 S1 B:TFG1409 4.6 33.6 1.0 CB B:PHE168 4.7 28.6 1.0 ZN B:ZN1410 4.8 28.3 1.0 CE1 B:HIS159 4.8 27.1 1.0 CA B:GLY167 4.9 29.2 1.0 CD B:PRO156 4.9 27.3 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