Zinc in PDB 9gn6: Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha

The structure of Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha, PDB code: 9gn6 was solved by C.Qin, 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)	46.28 / 1.95
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	146.206, 146.206, 146.206, 90, 90, 90
R / Rfree (%)	13.7 / 17.6

The structure of Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha (pdb code 9gn6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha, PDB code: 9gn6:

Zinc binding site 1 out of 1 in the Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha


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 Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:37.8 occ:1.00 HO1 A:SHH404 1.8 34.4 0.0 O1 A:SHH404 1.9 37.8 1.0 OD2 A:ASP269 1.9 32.5 0.7 ND1 A:HIS183 2.1 32.5 1.0 OD1 A:ASP181 2.2 36.9 1.0 OD2 A:ASP269 2.2 25.2 0.3 OD2 A:ASP181 2.5 34.3 1.0 CG A:ASP181 2.6 40.4 1.0 O2 A:SHH404 2.8 47.3 1.0 N1 A:SHH404 2.8 52.5 1.0 CG A:ASP269 2.9 36.8 0.7 CG A:ASP269 3.0 30.2 0.3 CE1 A:HIS183 3.0 37.7 1.0 HB2 A:HIS183 3.1 34.1 1.0 C1 A:SHH404 3.1 49.8 1.0 CG A:HIS183 3.1 37.9 1.0 HE1 A:HIS183 3.1 35.7 1.0 HA3 A:GLY311 3.2 38.5 1.0 OD1 A:ASP269 3.2 37.2 0.7 OD1 A:ASP269 3.2 30.5 0.3 H A:HIS183 3.3 36.4 1.0 HE2 A:HIS143 3.3 30.0 0.0 HG12 A:VAL182 3.4 35.7 1.0 HN1 A:SHH404 3.5 47.7 1.0 CB A:HIS183 3.6 33.0 1.0 HE2 A:TYR313 3.6 39.3 1.0 H A:VAL182 3.9 37.6 1.0 N A:HIS183 4.0 38.5 1.0 HE2 A:HIS144 4.0 30.0 0.0 NE2 A:HIS143 4.0 44.9 1.0 HE1 A:HIS143 4.1 43.7 1.0 CB A:ASP181 4.1 39.9 1.0 NE2 A:HIS183 4.2 36.6 1.0 CA A:GLY311 4.2 39.5 1.0 CB A:ASP269 4.2 33.5 0.7 CD2 A:HIS183 4.2 36.7 1.0 CB A:ASP269 4.3 30.2 0.3 H A:GLY311 4.3 38.6 1.0 CG1 A:VAL182 4.3 35.2 1.0 HB2 A:ASP269 4.3 30.7 0.3 N A:VAL182 4.4 39.2 1.0 HB3 A:HIS183 4.4 34.6 1.0 HH A:TYR313 4.4 30.0 0.0 HB3 A:ASP269 4.4 34.0 0.7 HB2 A:ASP269 4.4 34.3 0.7 CE1 A:HIS143 4.4 44.5 1.0 CA A:HIS183 4.5 33.7 1.0 OH A:TYR313 4.5 43.9 1.0 CE2 A:TYR313 4.5 36.1 1.0 C2 A:SHH404 4.5 43.0 1.0 HB3 A:ASP181 4.5 40.8 1.0 HG13 A:VAL182 4.6 35.4 1.0 HB3 A:ASP269 4.6 30.3 0.3 HB2 A:ASP181 4.6 40.2 1.0 N A:GLY311 4.6 37.8 1.0 H31 A:SHH404 4.6 46.3 1.0 HA2 A:GLY311 4.6 38.5 1.0 HG11 A:VAL182 4.7 35.9 1.0 H A:GLY312 4.8 38.2 1.0 NE2 A:HIS144 4.8 39.1 1.0 H32 A:SHH404 4.8 46.2 1.0 C A:ASP181 4.8 36.9 1.0 CA A:ASP181 4.9 41.1 1.0 HA A:ASP181 4.9 39.5 1.0 C A:VAL182 4.9 36.2 1.0 HA3 A:GLY267 4.9 39.2 1.0 HE2 A:HIS183 4.9 30.0 0.0 C3 A:SHH404 4.9 45.7 1.0 H21 A:SHH404 5.0 45.2 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.