Chlorine in PDB 5wgi: Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa

The structure of Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa, PDB code: 5wgi 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)	47.04 / 1.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.439, 69.639, 50.193, 90.00, 110.42, 90.00
R / Rfree (%)	10.6 / 12.6

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

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

The binding sites of Chlorine atom in the Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa (pdb code 5wgi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa, PDB code: 5wgi:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl805 b:10.3 occ:0.84 HH11 A:ARG451 2.5 14.4 1.0 HD2 A:ARG451 3.1 11.6 1.0 HD21 A:LEU493 3.1 10.2 1.0 NH1 A:ARG451 3.2 12.0 1.0 O A:HOH1316 3.2 16.3 1.0 HG21 A:THR540 3.2 11.9 1.0 HG23 A:THR540 3.4 11.9 1.0 HD11 A:LEU544 3.4 11.0 1.0 HH12 A:ARG451 3.5 14.4 1.0 HD11 A:LEU493 3.5 13.7 1.0 HD21 A:LEU544 3.6 9.7 1.0 CG2 A:THR540 3.6 9.9 1.0 HG22 A:THR540 3.7 11.9 1.0 CD A:ARG451 3.9 9.7 1.0 HD3 A:ARG451 3.9 11.6 1.0 CD2 A:LEU493 4.1 8.5 1.0 HG A:LEU493 4.2 9.9 1.0 CZ A:ARG451 4.3 10.5 1.0 CD1 A:LEU544 4.4 9.2 1.0 CD1 A:LEU493 4.4 11.4 1.0 HG A:LEU544 4.4 9.3 1.0 CD2 A:LEU544 4.5 8.0 1.0 CG A:LEU493 4.5 8.3 1.0 HD23 A:LEU493 4.5 10.2 1.0 NE A:ARG451 4.5 10.8 1.0 HD22 A:LEU493 4.7 10.2 1.0 CG A:LEU544 4.7 7.7 1.0 HD12 A:LEU544 4.8 11.0 1.0 O A:HOH1190 4.8 26.6 0.4 HB3 A:ARG451 4.9 10.4 1.0 HD13 A:LEU544 4.9 11.0 1.0 HD12 A:LEU493 4.9 13.7 1.0 HD13 A:LEU493 4.9 13.7 1.0 HD22 A:LEU544 5.0 9.7 1.0 HD23 A:LEU544 5.0 9.7 1.0

Chlorine binding site 2 out of 3 in the Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl806 b:13.3 occ:1.00 H A:SER484 2.4 10.2 1.0 HA A:ARG481 2.6 10.1 1.0 HG A:SER484 2.6 17.7 1.0 HB3 A:LEU483 3.0 11.2 1.0 O A:HOH1279 3.1 30.8 1.0 HB3 A:SER484 3.1 16.0 1.0 N A:SER484 3.2 8.5 1.0 H A:LEU483 3.2 9.3 1.0 OG A:SER484 3.3 14.8 1.0 HA A:GLU478 3.3 10.1 1.0 O A:HOH1225 3.4 34.8 1.0 CA A:ARG481 3.5 8.4 1.0 CB A:SER484 3.6 13.3 1.0 O A:HOH1070 3.6 30.4 1.0 N A:LEU483 3.7 7.8 1.0 HD2 A:ARG481 3.7 14.5 1.0 C A:ARG481 3.7 7.9 1.0 O A:GLU478 3.8 9.1 1.0 CB A:LEU483 3.8 9.3 1.0 CA A:SER484 4.0 9.8 1.0 N A:LEU482 4.1 7.3 1.0 CA A:LEU483 4.1 8.2 1.0 H A:ARG481 4.1 9.3 1.0 C A:LEU483 4.1 8.5 1.0 HB3 A:ARG481 4.1 11.3 1.0 H A:LEU482 4.2 8.7 1.0 CA A:GLU478 4.2 8.4 1.0 O A:ARG481 4.2 10.6 1.0 HD3 A:ARG481 4.2 14.5 1.0 O A:HIS477 4.3 8.9 1.0 HB2 A:LEU483 4.3 11.2 1.0 N A:ARG481 4.3 7.8 1.0 CB A:ARG481 4.4 9.4 1.0 CD A:ARG481 4.4 12.1 1.0 C A:GLU478 4.5 8.2 1.0 C A:LEU482 4.5 7.6 1.0 HB2 A:SER484 4.5 16.0 1.0 HD23 A:LEU483 4.5 13.1 1.0 HA A:SER484 4.6 11.7 1.0 HG2 A:GLU478 4.6 14.3 1.0 O A:HOH1226 4.7 27.4 1.0 HG A:LEU483 4.8 12.0 1.0 HB3 A:GLU478 4.8 11.4 1.0 CG A:LEU483 4.8 10.0 1.0 H A:ARG485 4.9 9.7 1.0 CA A:LEU482 4.9 7.7 1.0 CB A:GLU478 5.0 9.5 1.0 O A:HOH1255 5.0 35.1 1.0

Chlorine binding site 3 out of 3 in the Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl807 b:21.8 occ:1.00 H A:ARG520 2.3 12.2 1.0 HD2 A:PRO519 2.8 14.7 1.0 HB2 A:ARG520 3.0 13.8 1.0 HB3 A:LYS518 3.0 15.4 1.0 N A:ARG520 3.1 10.2 1.0 HB2 A:PRO519 3.2 14.6 1.0 HB3 A:ARG520 3.4 13.8 1.0 CD A:PRO519 3.5 12.3 1.0 CB A:ARG520 3.6 11.6 1.0 N A:PRO519 3.7 10.8 1.0 CB A:PRO519 3.9 12.2 1.0 CB A:LYS518 3.9 12.8 1.0 CA A:ARG520 4.0 10.6 1.0 HB2 A:LYS518 4.0 15.4 1.0 C A:PRO519 4.0 10.6 1.0 CA A:PRO519 4.1 10.7 1.0 HG2 A:PRO519 4.1 15.4 1.0 CG A:PRO519 4.1 12.8 1.0 C A:LYS518 4.3 10.9 1.0 HD3 A:PRO519 4.3 14.7 1.0 HA A:ARG520 4.4 12.7 1.0 HD2 A:LYS518 4.6 26.1 1.0 CA A:LYS518 4.7 11.0 1.0 HB3 A:PRO519 4.7 14.6 1.0 H A:ASP521 4.8 11.7 1.0 HG3 A:LYS518 4.8 19.5 1.0 CG A:LYS518 4.9 16.3 1.0 CG A:ARG520 4.9 13.1 1.0 O A:LYS518 4.9 10.0 1.0 HG3 A:ARG520 5.0 15.7 1.0 HA A:LYS518 5.0 13.2 1.0

N.J.Porter, A.Mahendran, R.Breslow, D.W.Christianson. Unusual Zinc-Binding Mode of HDAC6-Selective Hydroxamate Inhibitors. Proc. Natl. Acad. Sci. V. 114 13459 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29203661
DOI: 10.1073/PNAS.1718823114