Zinc in PDB 5g1b: Bordetella Alcaligenes Hdah Native

All present enzymatic activity of Bordetella Alcaligenes Hdah Native:
3.5.1.4;

The structure of Bordetella Alcaligenes Hdah Native, PDB code: 5g1b was solved by A.Kraemer, F.J.Meyer-Almes, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.56 / 1.70
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.660, 100.660, 175.110, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 19.1

The structure of Bordetella Alcaligenes Hdah Native also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Bordetella Alcaligenes Hdah Native (pdb code 5g1b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bordetella Alcaligenes Hdah Native, PDB code: 5g1b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bordetella Alcaligenes Hdah Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bordetella Alcaligenes Hdah Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn370 b:18.0 occ:0.60 OD2 A:ASP268 1.9 13.0 1.0 O A:HOH2309 2.0 25.1 1.0 OD1 A:ASP180 2.1 11.6 1.0 O A:HOH2277 2.1 20.3 1.0 ND1 A:HIS182 2.2 15.4 1.0 OD2 A:ASP180 2.5 14.0 1.0 CG A:ASP180 2.6 10.9 1.0 CG A:ASP268 3.0 11.4 1.0 CE1 A:HIS182 3.1 13.6 1.0 CG A:HIS182 3.2 13.0 1.0 OD1 A:ASP268 3.4 10.2 1.0 CB A:HIS182 3.6 10.5 1.0 NE2 A:HIS142 4.0 15.7 1.0 N A:HIS182 4.0 10.1 1.0 CB A:ASP180 4.1 9.1 1.0 CA A:GLY310 4.1 11.5 1.0 NE2 A:HIS182 4.2 14.1 1.0 CB A:ASP268 4.2 11.3 1.0 CE2 A:TYR312 4.3 15.1 1.0 CD2 A:HIS182 4.3 13.2 1.0 OH A:TYR312 4.3 19.0 1.0 CE1 A:HIS142 4.4 15.1 1.0 CG1 A:VAL181 4.4 10.4 1.0 O A:HOH2285 4.4 41.6 1.0 CA A:HIS182 4.4 11.2 1.0 N A:VAL181 4.4 11.7 1.0 N A:GLY310 4.5 11.3 1.0 NE2 A:HIS143 4.6 17.9 1.0 CZ A:TYR312 4.8 15.5 1.0 C A:GLY310 4.8 13.3 1.0 CA A:ASP180 4.8 12.5 1.0 C A:ASP180 4.9 12.6 1.0 N A:GLY311 4.9 13.7 1.0 C A:VAL181 5.0 10.6 1.0

Zinc binding site 2 out of 2 in the Bordetella Alcaligenes Hdah Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bordetella Alcaligenes Hdah Native within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn370 b:13.7 occ:0.60 OD2 B:ASP268 1.9 11.8 1.0 OD1 B:ASP180 2.1 9.8 1.0 O B:HOH2253 2.1 25.2 1.0 ND1 B:HIS182 2.1 12.9 1.0 O B:HOH2228 2.2 19.6 1.0 OD2 B:ASP180 2.5 14.2 1.0 CG B:ASP180 2.6 10.4 1.0 CG B:ASP268 3.0 11.1 1.0 CE1 B:HIS182 3.0 13.7 1.0 CG B:HIS182 3.2 12.1 1.0 OD1 B:ASP268 3.4 9.1 1.0 CB B:HIS182 3.6 9.0 1.0 N B:HIS182 4.0 9.3 1.0 NE2 B:HIS142 4.0 14.0 1.0 CB B:ASP180 4.1 8.5 1.0 CA B:GLY310 4.2 11.5 1.0 NE2 B:HIS182 4.2 12.8 1.0 CB B:ASP268 4.2 8.9 1.0 CE2 B:TYR312 4.3 14.5 1.0 CD2 B:HIS182 4.3 12.6 1.0 CG1 B:VAL181 4.3 9.4 1.0 O B:HOH2232 4.3 47.1 1.0 OH B:TYR312 4.4 17.2 1.0 N B:VAL181 4.4 10.0 1.0 CE1 B:HIS142 4.4 13.1 1.0 CA B:HIS182 4.4 9.0 1.0 N B:GLY310 4.5 10.9 1.0 NE2 B:HIS143 4.7 18.8 1.0 CZ B:TYR312 4.8 14.5 1.0 C B:ASP180 4.8 10.4 1.0 CA B:ASP180 4.8 10.3 1.0 C B:GLY310 4.8 12.0 1.0 N B:GLY311 4.9 12.0 1.0 C B:VAL181 4.9 9.4 1.0

C.Meyners, A.Kramer, O.Yildiz, F.J.Meyer-Almes. The Thermodynamic Signature of Ligand Binding to Histone Deacetylase-Like Amidohydrolases Is Most Sensitive to the Flexibility in the L2-Loop Lining the Active Site Pocket. Biochim. Biophys. Acta V.1861 1855 2017.
ISSN: ISSN 0006-3002
PubMed: 28389333
DOI: 10.1016/J.BBAGEN.2017.04.001