Zinc in PDB 9gn1: Crystal Structure of Inactive Deacetylase (Hdah) H144A From Klebsiella Pneumoniae Subsp. Ozaenae

The structure of Crystal Structure of Inactive Deacetylase (Hdah) H144A From Klebsiella Pneumoniae Subsp. Ozaenae, PDB code: 9gn1 was solved by Q.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)	46.25 / 2.35
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	146.117, 146.117, 146.117, 90, 90, 90
R / Rfree (%)	15.3 / 20.4

The structure of Crystal Structure of Inactive Deacetylase (Hdah) H144A From Klebsiella Pneumoniae Subsp. Ozaenae also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Inactive Deacetylase (Hdah) H144A From Klebsiella Pneumoniae Subsp. Ozaenae (pdb code 9gn1). 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 Inactive Deacetylase (Hdah) H144A From Klebsiella Pneumoniae Subsp. Ozaenae, PDB code: 9gn1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Inactive Deacetylase (Hdah) H144A From Klebsiella Pneumoniae Subsp. Ozaenae


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 Inactive Deacetylase (Hdah) H144A From Klebsiella Pneumoniae Subsp. Ozaenae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:41.7 occ:1.00 OD2 A:ASP269 2.0 33.6 1.0 ND1 A:HIS183 2.1 38.4 1.0 OD1 A:ASP181 2.1 39.0 1.0 OXT A:ACT406 2.3 28.6 1.0 C A:ACT406 2.6 64.7 1.0 OD2 A:ASP181 2.7 35.2 1.0 CG A:ASP181 2.7 38.5 1.0 O A:ACT406 2.8 46.0 1.0 CE1 A:HIS183 3.0 39.5 1.0 CG A:ASP269 3.0 28.5 1.0 HE1 A:HIS183 3.1 38.3 1.0 HA3 A:GLY311 3.1 34.6 1.0 CG A:HIS183 3.2 33.6 1.0 HB2 A:HIS183 3.2 34.8 1.0 H A:HIS183 3.2 35.9 1.0 OD1 A:ASP269 3.3 29.5 1.0 HE2 A:HIS143 3.4 30.0 0.0 HE2 A:TYR313 3.5 46.8 1.0 HG12 A:VAL182 3.5 36.2 1.0 CB A:HIS183 3.7 35.4 1.0 H3 A:ACT406 3.8 34.5 0.0 CH3 A:ACT406 3.8 72.8 1.0 H A:VAL182 3.9 34.6 1.0 N A:HIS183 4.0 35.8 1.0 CA A:GLY311 4.1 34.4 1.0 NE2 A:HIS143 4.1 41.6 1.0 NE2 A:HIS183 4.2 37.2 1.0 CB A:ASP181 4.2 37.7 1.0 CD2 A:HIS183 4.2 38.6 1.0 H A:GLY311 4.2 34.8 1.0 H1 A:ACT406 4.3 34.5 0.0 CB A:ASP269 4.3 30.2 1.0 HH A:TYR313 4.3 30.0 0.0 CE2 A:TYR313 4.4 48.3 1.0 OH A:TYR313 4.4 43.2 1.0 N A:VAL182 4.4 34.8 1.0 CG1 A:VAL182 4.4 37.3 1.0 HE1 A:HIS143 4.4 44.2 1.0 HB3 A:HIS183 4.5 35.2 1.0 CA A:HIS183 4.5 34.5 1.0 H2 A:ACT406 4.5 34.5 0.0 HB2 A:ASP269 4.5 30.4 1.0 HB3 A:ASP269 4.5 30.1 1.0 H A:GLY312 4.5 37.7 1.0 HA2 A:GLY311 4.5 34.7 1.0 N A:GLY311 4.6 33.0 1.0 HB3 A:ASP181 4.6 37.7 1.0 HN3 A:IMD405 4.6 55.5 1.0 CE1 A:HIS143 4.6 47.5 1.0 O A:HOH594 4.6 57.5 1.0 HG13 A:VAL182 4.7 36.1 1.0 HB2 A:ASP181 4.7 37.3 1.0 HG11 A:VAL182 4.8 36.5 1.0 O A:HOH501 4.9 78.0 1.0 C A:GLY311 4.9 36.4 1.0 HA A:ASP181 4.9 35.4 1.0 HA3 A:GLY267 4.9 32.2 1.0 C A:ASP181 4.9 35.7 1.0 HE2 A:HIS183 5.0 30.0 0.0 CZ A:TYR313 5.0 49.2 1.0 C A:VAL182 5.0 39.3 1.0 CA A:ASP181 5.0 35.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Inactive Deacetylase (Hdah) H144A From Klebsiella Pneumoniae Subsp. Ozaenae


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 Inactive Deacetylase (Hdah) H144A From Klebsiella Pneumoniae Subsp. Ozaenae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:78.4 occ:1.00 HE2 A:HIS282 2.4 30.0 0.0 HG2 A:GLN345 2.8 37.6 1.0 HG3 A:GLN348 2.9 38.1 1.0 NE2 A:HIS282 3.3 40.8 1.0 HB3 A:ASP239 3.4 37.3 1.0 HA A:GLN345 3.4 36.9 1.0 O A:HOH630 3.5 44.7 1.0 O A:HOH629 3.5 46.8 1.0 O A:HOH528 3.7 41.4 1.0 HB2 A:ASP239 3.7 36.5 1.0 CG A:GLN345 3.8 38.6 1.0 CG A:GLN348 3.8 36.0 1.0 CB A:ASP239 3.9 36.2 1.0 OD2 A:ASP239 3.9 39.8 1.0 HB3 A:GLN345 3.9 37.2 1.0 HG2 A:GLN348 4.0 37.8 1.0 CG A:ASP239 4.0 38.5 1.0 O A:HOH632 4.0 49.8 1.0 HD2 A:HIS282 4.1 44.2 1.0 CD2 A:HIS282 4.1 46.1 1.0 CB A:GLN345 4.2 34.9 1.0 HG3 A:GLN345 4.2 37.0 1.0 CD A:GLN348 4.2 39.5 1.0 CA A:GLN345 4.2 38.5 1.0 CE1 A:HIS282 4.3 46.6 1.0 OE1 A:GLN348 4.4 40.0 1.0 HE1 A:HIS282 4.4 44.9 1.0 O A:HOH583 4.5 38.8 1.0 HE22 A:GLN345 4.6 41.2 1.0 NE2 A:GLN345 4.6 43.0 1.0 OD1 A:ASP239 4.7 38.4 1.0 CD A:GLN345 4.7 38.6 1.0 O A:GLN345 4.7 35.1 1.0 NE2 A:GLN348 4.9 39.5 1.0 CB A:GLN348 5.0 40.6 1.0 HB2 A:GLN348 5.0 40.7 1.0 HE21 A:GLN345 5.0 42.2 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.