Zinc in PDB 9gky: Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid

The structure of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid, PDB code: 9gky was solved by L.G.Graf, S.Schulze, G.J.Palm, M.Lammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.14 / 1.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.11, 51.15, 108.82, 90, 102.22, 90
R / Rfree (%)	15.8 / 17.9

The structure of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Potassium	(K)	9 atoms

The binding sites of Zinc atom in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid (pdb code 9gky). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid, PDB code: 9gky:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:9.7 occ:0.80 HD1 A:HIS176 1.2 8.6 0.0 OD1 A:ASP174 1.9 10.5 1.0 OD2 A:ASP251 2.0 11.6 1.0 ND1 A:HIS176 2.1 10.5 1.0 O2 A:DKA401 2.1 12.7 0.8 O1 A:DKA401 2.5 13.8 0.8 CG A:ASP174 2.6 11.2 1.0 C1 A:DKA401 2.6 12.2 0.8 OD2 A:ASP174 2.6 12.6 1.0 CG A:ASP251 2.9 10.6 1.0 CE1 A:HIS176 3.0 10.8 1.0 HE1 A:HIS176 3.1 10.8 1.0 HB2 A:HIS176 3.2 10.6 1.0 H A:HIS176 3.2 10.1 1.0 CG A:HIS176 3.2 10.6 1.0 HG12 A:VAL175 3.2 10.0 1.0 OD1 A:ASP251 3.3 10.8 1.0 HE2 A:TYR294 3.4 12.3 1.0 HA3 A:GLY292 3.4 10.5 1.0 HE2 A:HIS136 3.5 9.5 0.0 H4 A:IMD402 3.5 14.7 1.0 CB A:HIS176 3.6 10.9 1.0 H A:VAL175 3.8 9.8 1.0 N A:HIS176 3.9 10.1 1.0 HE1 A:HIS136 4.1 11.4 1.0 CB A:ASP174 4.1 10.0 1.0 C2 A:DKA401 4.1 13.5 0.8 NE2 A:HIS136 4.2 11.2 1.0 HE2 A:HIS137 4.2 8.5 0.0 NE2 A:HIS176 4.2 11.0 1.0 CG1 A:VAL175 4.2 10.3 1.0 CB A:ASP251 4.2 9.9 1.0 N A:VAL175 4.3 9.6 1.0 CD2 A:HIS176 4.3 11.2 1.0 C4 A:IMD402 4.3 14.5 1.0 CE2 A:TYR294 4.3 12.1 1.0 H A:GLY292 4.3 10.4 1.0 CA A:GLY292 4.4 10.5 1.0 HB2 A:ASP251 4.4 10.1 1.0 CA A:HIS176 4.4 10.4 1.0 HN3 A:IMD402 4.4 15.3 1.0 H22 A:DKA401 4.4 13.5 0.8 HB3 A:ASP174 4.4 10.2 1.0 CE1 A:HIS136 4.4 11.4 1.0 HB3 A:ASP251 4.5 10.0 1.0 HB3 A:HIS176 4.5 10.8 1.0 H21 A:DKA401 4.5 13.7 0.8 H A:GLY293 4.5 10.5 1.0 HG11 A:VAL175 4.5 10.2 1.0 HG13 A:VAL175 4.5 10.2 1.0 HB2 A:ASP174 4.6 10.2 1.0 N3 A:IMD402 4.7 16.1 1.0 C A:ASP174 4.8 10.2 1.0 N A:GLY292 4.8 10.4 1.0 CA A:ASP174 4.8 9.7 1.0 O A:HOH520 4.8 15.0 1.0 C A:VAL175 4.8 10.2 1.0 OH A:TYR294 4.9 15.8 1.0 HA A:ASP174 4.9 9.8 1.0 NE2 A:HIS137 4.9 10.5 1.0 HE2 A:HIS176 4.9 8.8 0.0 CA A:VAL175 5.0 10.2 1.0 HA2 A:GLY292 5.0 10.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:9.9 occ:0.70 HD1 B:HIS176 1.2 8.5 0.0 OD2 B:ASP251 2.0 12.3 1.0 OD1 B:ASP174 2.0 11.9 1.0 ND1 B:HIS176 2.1 11.6 1.0 O1 B:DKA401 2.1 13.4 0.7 O2 B:DKA401 2.4 14.7 0.7 C1 B:DKA401 2.6 13.2 0.7 CG B:ASP174 2.6 11.9 1.0 OD2 B:ASP174 2.7 14.5 1.0 CG B:ASP251 2.9 11.1 1.0 CE1 B:HIS176 3.0 12.7 1.0 H B:HIS176 3.1 10.4 1.0 HE1 B:HIS176 3.1 12.5 1.0 HB2 B:HIS176 3.1 11.6 1.0 HG12 B:VAL175 3.2 10.7 1.0 CG B:HIS176 3.2 11.3 1.0 OD1 B:ASP251 3.3 10.9 1.0 HE2 B:TYR294 3.4 13.8 1.0 HE2 B:HIS136 3.4 9.9 0.0 HA3 B:GLY292 3.5 10.1 1.0 H5 B:IMD402 3.5 16.1 0.7 CB B:HIS176 3.7 12.1 1.0 H B:VAL175 3.8 10.8 1.0 N B:HIS176 3.9 10.2 1.0 HE1 B:HIS136 4.1 12.6 1.0 HE2 B:HIS137 4.1 9.4 0.0 CB B:ASP174 4.1 11.4 1.0 NE2 B:HIS136 4.1 13.1 1.0 CG1 B:VAL175 4.1 10.9 1.0 C2 B:DKA401 4.1 14.0 0.7 NE2 B:HIS176 4.2 13.4 1.0 N B:VAL175 4.2 10.8 1.0 CB B:ASP251 4.2 10.3 1.0 CD2 B:HIS176 4.3 12.5 1.0 C5 B:IMD402 4.3 16.8 0.7 CE2 B:TYR294 4.3 13.9 1.0 HB2 B:ASP251 4.4 10.6 1.0 HN1 B:IMD402 4.4 15.6 0.7 CA B:HIS176 4.4 11.3 1.0 CA B:GLY292 4.4 9.8 1.0 H B:GLY292 4.4 9.9 1.0 HG11 B:VAL175 4.4 11.0 1.0 HB3 B:ASP174 4.4 11.4 1.0 H22 B:DKA401 4.4 14.4 0.7 CE1 B:HIS136 4.5 12.6 1.0 HB3 B:ASP251 4.5 10.4 1.0 HB3 B:HIS176 4.5 12.0 1.0 H21 B:DKA401 4.5 14.6 0.7 HG13 B:VAL175 4.5 10.8 1.0 H B:GLY293 4.6 10.9 1.0 HB2 B:ASP174 4.6 11.2 1.0 N1 B:IMD402 4.7 14.8 0.7 C B:ASP174 4.7 11.2 1.0 CA B:ASP174 4.8 10.7 1.0 C B:VAL175 4.8 10.9 1.0 N B:GLY292 4.8 9.9 1.0 OH B:TYR294 4.9 16.8 1.0 O B:HOH529 4.9 17.3 1.0 NE2 B:HIS137 4.9 13.2 1.0 HA B:ASP174 4.9 10.8 1.0 CA B:VAL175 4.9 11.0 1.0 HE2 B:HIS176 4.9 9.7 0.0 H31 B:DKA401 5.0 15.6 0.7 HA2 B:GLY292 5.0 10.1 1.0

L.G.Graf, C.Moreno-Yruela, C.Qin, S.Schulze, G.J.Palm, O.Schmoeker, N.Wang, D.Hocking, L.Jebeli, B.Girbardt, L.Berndt, D.M.Weis, M.Janetzky, D.Zuehlke, S.Sievers, R.A.Strugnell, C.A.Olsen, K.Hofmann, M.Lammers. Distribution and Diversity of Classical Deacylases in Bacteria Nature Communications 2024.