Zinc in PDB 5g17: Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.

All present enzymatic activity of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.:
3.5.1.4;

The structure of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide., PDB code: 5g17 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)	87.68 / 1.51
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.270, 101.270, 175.220, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 15.8

The structure of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Potassium	(K)	4 atoms

The binding sites of Zinc atom in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. (pdb code 5g17). 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 (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide., PDB code: 5g17:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


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 (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn370 b:8.8 occ:0.50 OD2 A:ASP268 2.0 7.8 1.0 O1 A:6DK373 2.0 9.9 1.0 OD1 A:ASP180 2.1 7.3 1.0 O2 A:6DK373 2.1 9.2 1.0 ND1 A:HIS182 2.1 8.6 1.0 OD2 A:ASP180 2.4 7.4 1.0 CG A:ASP180 2.5 7.0 1.0 C1 A:6DK373 2.6 10.0 1.0 CG A:ASP268 3.0 7.1 1.0 CE1 A:HIS182 3.0 9.6 1.0 CG A:HIS182 3.2 8.2 1.0 OD1 A:ASP268 3.5 7.1 1.0 F1 A:6DK373 3.5 12.4 1.0 CB A:HIS182 3.6 7.3 1.0 C A:6DK373 3.7 10.9 1.0 C2 A:6DK373 3.8 12.5 1.0 C3 A:6DK373 4.0 14.7 1.0 NE2 A:HIS142 4.0 9.5 1.0 N A:HIS182 4.0 7.1 1.0 CB A:ASP180 4.1 7.6 1.0 CA A:GLY310 4.1 8.0 1.0 NE2 A:HIS182 4.2 9.5 1.0 CB A:ASP268 4.3 6.7 1.0 CE2 A:TYR312 4.3 8.5 1.0 CD2 A:HIS182 4.3 8.6 1.0 N A:VAL181 4.4 7.2 1.0 OH A:TYR312 4.4 10.5 1.0 CG1 A:VAL181 4.4 7.5 1.0 N A:GLY310 4.5 8.0 1.0 CE1 A:HIS142 4.5 8.9 1.0 F A:6DK373 4.5 13.5 1.0 CA A:HIS182 4.5 6.9 1.0 F2 A:6DK373 4.6 11.9 1.0 NE2 A:HIS143 4.6 10.2 1.0 C A:ASP180 4.8 7.5 1.0 CA A:ASP180 4.8 7.2 1.0 CZ A:TYR312 4.8 9.1 1.0 C A:GLY310 4.8 8.0 1.0 N A:GLY311 4.9 9.1 1.0 C A:VAL181 5.0 7.2 1.0

Zinc binding site 2 out of 2 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


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 (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn370 b:8.8 occ:0.50 OD2 B:ASP268 2.0 7.9 1.0 O2 B:6DK373 2.0 9.7 1.0 OD1 B:ASP180 2.1 8.0 1.0 O1 B:6DK373 2.1 9.7 1.0 ND1 B:HIS182 2.1 8.4 1.0 OD2 B:ASP180 2.4 8.6 1.0 CG B:ASP180 2.5 7.4 1.0 C1 B:6DK373 2.7 10.0 1.0 CG B:ASP268 3.0 7.0 1.0 CE1 B:HIS182 3.0 8.7 1.0 CG B:HIS182 3.2 7.6 1.0 OD1 B:ASP268 3.5 7.9 1.0 F1 B:6DK373 3.5 12.7 1.0 CB B:HIS182 3.7 7.3 1.0 C B:6DK373 3.7 11.5 1.0 C2 B:6DK373 3.8 12.1 1.0 C3 B:6DK373 4.0 14.4 1.0 NE2 B:HIS142 4.0 9.9 1.0 N B:HIS182 4.0 7.2 1.0 CB B:ASP180 4.1 7.7 1.0 CA B:GLY310 4.1 8.8 1.0 NE2 B:HIS182 4.2 8.8 1.0 CB B:ASP268 4.2 6.4 1.0 CE2 B:TYR312 4.3 8.6 1.0 CD2 B:HIS182 4.3 7.9 1.0 OH B:TYR312 4.4 11.0 1.0 N B:VAL181 4.4 7.3 1.0 CG1 B:VAL181 4.4 7.6 1.0 N B:GLY310 4.4 8.5 1.0 CE1 B:HIS142 4.5 9.6 1.0 CA B:HIS182 4.5 7.2 1.0 F2 B:6DK373 4.5 13.7 1.0 F B:6DK373 4.6 11.2 1.0 NE2 B:HIS143 4.6 9.5 1.0 C B:GLY310 4.8 8.8 1.0 CA B:ASP180 4.8 7.9 1.0 C B:ASP180 4.8 8.3 1.0 CZ B:TYR312 4.8 9.7 1.0 N B:GLY311 4.9 9.6 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