Bromine in PDB 2vcg: Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17

The structure of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17, PDB code: 2vcg was solved by A.Dickmanns, A.Strasser, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	117.85 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.664, 93.633, 121.664, 90.00, 103.99, 90.00
R / Rfree (%)	15.6 / 20.6

The structure of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 also contains other interesting chemical elements:

Potassium	(K)	8 atoms
Chlorine	(Cl)	1 atom
Zinc	(Zn)	5 atoms

The binding sites of Bromine atom in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 (pdb code 2vcg). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17, PDB code: 2vcg:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1378 b:44.0 occ:0.50 BR1 A:S171378 0.0 44.0 0.5 CZ A:S171378 1.9 40.4 0.5 CE1 A:S171378 2.8 39.1 0.5 CE2 A:S171378 2.9 39.5 0.5 O D:HOH2399 3.0 41.8 1.0 O D:HOH2401 3.4 39.5 1.0 O D:GLU346 3.5 23.3 1.0 O D:HOH2097 3.5 66.8 1.0 CG A:PRO216 3.8 18.4 1.0 C D:GLU346 3.9 22.5 1.0 CA D:PHE347 3.9 21.8 1.0 N D:PHE347 4.1 22.1 1.0 CD1 A:S171378 4.1 38.1 0.5 CD2 A:S171378 4.2 38.5 0.5 CB A:PRO216 4.3 18.5 1.0 O D:HOH2400 4.3 17.4 1.0 CD A:PRO216 4.5 16.8 1.0 O D:PHE347 4.7 21.0 1.0 CG A:S171378 4.7 37.5 0.5 O A:HOH2251 4.7 29.7 1.0 C D:PHE347 4.7 20.8 1.0 CB D:GLU346 4.7 23.5 1.0 O D:HOH2212 4.8 41.6 1.0 CA D:GLU346 4.9 23.1 1.0 CB D:PHE347 5.0 22.4 1.0 O D:HOH2398 5.0 41.7 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br1379 b:53.0 occ:0.50 BR1 B:S171379 0.0 53.0 0.5 CZ B:S171379 1.9 49.1 0.5 CE1 B:S171379 2.8 48.6 0.5 CE2 B:S171379 2.8 48.4 0.5 CA B:GLY105 3.8 30.2 1.0 O B:ASP104 3.8 29.4 1.0 O B:GLY105 3.9 30.4 1.0 C B:GLY105 4.1 30.4 1.0 O B:HOH2172 4.1 44.1 1.0 CD1 B:S171379 4.1 47.1 0.5 CD2 B:S171379 4.1 47.2 0.5 C B:ASP104 4.6 29.5 1.0 N B:GLY105 4.6 29.9 1.0 CG B:S171379 4.6 45.4 0.5 O B:HOH2173 4.8 40.2 1.0 O B:HOH2174 4.9 46.0 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br1380 b:41.5 occ:0.50 BR1 C:S171380 0.0 41.5 0.5 CZ C:S171380 1.9 38.6 0.5 O B:HOH2401 2.8 55.4 1.0 CE1 C:S171380 2.9 37.9 0.5 CE2 C:S171380 2.9 37.8 0.5 O B:HOH2402 3.6 25.3 1.0 O B:GLU346 3.7 16.2 1.0 CD B:GLU346 3.9 28.6 1.0 OE1 B:GLU346 3.9 32.8 1.0 C B:GLU346 4.0 16.1 1.0 CG C:PRO216 4.1 13.0 1.0 CA B:PHE347 4.1 15.5 1.0 CG B:GLU346 4.1 23.1 1.0 O C:HOH2024 4.2 40.5 1.0 CD1 C:S171380 4.2 36.6 0.5 CD2 C:S171380 4.2 36.8 0.5 N B:PHE347 4.2 15.6 1.0 OE2 B:GLU346 4.3 31.3 1.0 CG C:S171380 4.7 35.6 0.5 CB B:GLU346 4.7 17.3 1.0 CB C:PRO216 4.7 12.6 1.0 O B:HOH2210 4.8 32.5 1.0 CD C:PRO216 4.9 11.2 1.0 C B:PHE347 5.0 14.4 1.0 O B:PHE347 5.0 14.1 1.0 CA B:GLU346 5.0 16.5 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range: probe atom residue distance (Å) B Occ D:Br1381 b:39.9 occ:0.50 BR1 D:S171381 0.0 39.9 0.5 CZ D:S171381 1.9 36.0 0.5 CE1 D:S171381 2.8 35.2 0.5 CE2 D:S171381 2.9 35.5 0.5 O A:HOH2356 3.3 48.5 1.0 O A:GLU346 3.6 21.1 1.0 CG A:GLU346 3.7 25.6 1.0 OE1 A:GLU346 3.7 32.4 1.0 O A:HOH2355 3.8 43.1 1.0 C A:GLU346 3.9 21.0 1.0 CG D:PRO216 4.0 15.1 1.0 CA A:PHE347 4.0 20.3 1.0 CD1 D:S171381 4.1 33.7 0.5 CD A:GLU346 4.2 30.2 1.0 N A:PHE347 4.2 20.7 1.0 CD2 D:S171381 4.2 33.9 0.5 O A:HOH2353 4.4 65.6 1.0 O A:HOH2359 4.6 19.7 1.0 CB D:PRO216 4.6 14.5 1.0 CB A:GLU346 4.6 22.0 1.0 CG D:S171381 4.7 32.6 0.5 O D:HOH2039 4.7 37.7 1.0 CD D:PRO216 4.7 13.9 1.0 O A:PHE347 4.9 19.2 1.0 CA A:GLU346 4.9 21.5 1.0 C A:PHE347 4.9 19.5 1.0 CB A:PHE347 5.0 20.4 1.0

S.Schaefer, L.Saunders, E.Eliseeva, A.Velena, M.Jung, A.Schwienhorst, A.Strasser, A.Dickmanns, R.Ficner, S.Schlimme, W.Sippl, E.Verdin, M.Jung. Phenylalanine-Containing Hydroxamic Acids As Selective Inhibitors of Class Iib Histone Deacetylases (Hdacs). Bioorg.Med.Chem. V. 16 2011 2008.
ISSN: ISSN 0968-0896
PubMed: 18054239
DOI: 10.1016/J.BMC.2007.10.092