Fluorine in PDB 6dvo: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat, PDB code: 6dvo was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.10 / 1.98
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 97.230, 97.230, 78.900, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 21.6

Other elements in 6dvo:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat also contains other interesting chemical elements:

Potassium (K) 2 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat (pdb code 6dvo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat, PDB code: 6dvo:

Fluorine binding site 1 out of 1 in 6dvo

Go back to Fluorine Binding Sites List in 6dvo
Fluorine binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F805

b:24.6
occ:1.00
F01 A:HBV805 0.0 24.6 1.0
C04 A:HBV805 1.3 24.9 1.0
C03 A:HBV805 2.3 24.5 1.0
C05 A:HBV805 2.4 25.2 1.0
C02 A:HBV805 2.7 24.5 1.0
CA A:GLY582 3.1 11.8 1.0
CZ A:PHE643 3.1 11.6 1.0
CE2 A:PHE643 3.2 11.6 1.0
CB A:SER531 3.3 12.1 1.0
C09 A:HBV805 3.5 24.6 1.0
CE1 A:PHE643 3.6 11.8 1.0
CE1 A:PHE583 3.6 11.4 1.0
C A:GLY582 3.6 12.5 1.0
C06 A:HBV805 3.7 25.3 1.0
OG A:SER531 3.7 11.2 1.0
CD2 A:PHE643 3.8 11.2 1.0
CZ A:PHE583 3.8 11.5 1.0
CD1 A:PHE583 3.9 11.7 1.0
O A:GLY582 4.0 13.1 1.0
C08 A:HBV805 4.1 24.8 1.0
CD1 A:PHE643 4.1 10.8 1.0
N01 A:HBV805 4.1 23.9 1.0
CG A:PHE643 4.2 11.7 1.0
N A:GLY582 4.3 12.1 1.0
CE2 A:PHE583 4.3 11.8 1.0
CG A:PHE583 4.4 12.1 1.0
N A:PHE583 4.4 11.3 1.0
O A:SER531 4.5 13.9 1.0
C01 A:HBV805 4.5 24.5 1.0
CD2 A:PHE583 4.5 11.8 1.0
CA A:SER531 4.8 12.9 1.0
CD2 A:HIS574 5.0 9.7 1.0
C07 A:HBV805 5.0 26.5 1.0

Reference:

N.J.Porter, J.D.Osko, D.Diedrich, T.Kurz, J.M.Hooker, F.K.Hansen, D.W.Christianson. Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. J. Med. Chem. V. 61 8054 2018.
ISSN: ISSN 1520-4804
PubMed: 30118224
DOI: 10.1021/ACS.JMEDCHEM.8B01013
Page generated: Sun Dec 13 12:48:24 2020

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