Zinc in PDB 5g10: Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide

The structure of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide, PDB code: 5g10 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)	75.94 / 1.71
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.740, 81.740, 205.210, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.4

The structure of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide (pdb code 5g10). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide, PDB code: 5g10:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1372 b:12.8 occ:0.70 OD2 A:ASP269 2.0 14.2 1.0 OD1 A:ASP181 2.0 13.2 1.0 O1 A:6DK1375 2.0 17.6 1.0 O2 A:6DK1375 2.1 17.9 1.0 ND1 A:HIS183 2.1 13.6 1.0 CG A:ASP181 2.7 12.1 1.0 OD2 A:ASP181 2.7 12.1 1.0 C1 A:6DK1375 2.7 19.5 1.0 CG A:ASP269 3.0 12.5 1.0 CE1 A:HIS183 3.0 12.8 1.0 CG A:HIS183 3.2 12.5 1.0 OD1 A:ASP269 3.3 12.3 1.0 CB A:HIS183 3.7 12.5 1.0 F1 A:6DK1375 3.7 25.4 1.0 C A:6DK1375 3.8 20.6 1.0 C2 A:6DK1375 3.8 20.7 1.0 C3 A:6DK1375 3.9 20.9 1.0 N A:HIS183 4.0 11.4 1.0 CB A:ASP181 4.1 11.4 1.0 NE2 A:HIS143 4.2 16.6 1.0 NE2 A:HIS183 4.2 12.9 1.0 CA A:GLY311 4.2 16.7 1.0 CD2 A:HIS183 4.3 13.0 1.0 N A:VAL182 4.3 10.7 1.0 CE2 A:TYR313 4.3 21.2 1.0 CB A:ASP269 4.3 12.2 1.0 CG1 A:VAL182 4.3 11.8 1.0 CA A:HIS183 4.5 11.7 1.0 OH A:TYR313 4.5 23.3 1.0 N A:GLY311 4.6 16.2 1.0 CE1 A:HIS143 4.6 16.7 1.0 F A:6DK1375 4.6 21.8 1.0 NE2 A:HIS144 4.7 16.6 1.0 F2 A:6DK1375 4.7 21.4 1.0 C A:ASP181 4.8 11.8 1.0 CA A:ASP181 4.8 11.0 1.0 CZ A:TYR313 4.9 23.4 1.0 C A:VAL182 5.0 11.4 1.0

Zinc binding site 2 out of 2 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1378 b:14.0 occ:0.70 OD2 B:ASP269 2.0 14.2 1.0 OD1 B:ASP181 2.0 13.2 1.0 O1 B:6DK1381 2.1 19.2 1.0 O2 B:6DK1381 2.1 19.8 1.0 ND1 B:HIS183 2.1 14.5 1.0 OD2 B:ASP181 2.7 13.6 1.0 CG B:ASP181 2.7 12.6 1.0 C1 B:6DK1381 2.7 20.4 1.0 CG B:ASP269 3.0 13.0 1.0 CE1 B:HIS183 3.0 14.1 1.0 CG B:HIS183 3.2 13.0 1.0 OD1 B:ASP269 3.3 12.4 1.0 CB B:HIS183 3.7 12.6 1.0 F1 B:6DK1381 3.8 23.0 1.0 C2 B:6DK1381 3.8 20.8 1.0 C B:6DK1381 3.8 21.4 1.0 C3 B:6DK1381 3.9 22.5 1.0 N B:HIS183 4.0 11.9 1.0 CB B:ASP181 4.2 12.2 1.0 NE2 B:HIS183 4.2 13.6 1.0 NE2 B:HIS143 4.2 16.4 1.0 CA B:GLY311 4.2 14.6 1.0 CE2 B:TYR313 4.3 17.2 1.0 CD2 B:HIS183 4.3 12.5 1.0 CB B:ASP269 4.3 12.9 1.0 N B:VAL182 4.3 11.6 1.0 CG1 B:VAL182 4.4 12.6 1.0 OH B:TYR313 4.5 22.3 1.0 CA B:HIS183 4.5 12.2 1.0 N B:GLY311 4.6 15.1 1.0 F B:6DK1381 4.6 23.6 1.0 CE1 B:HIS143 4.7 17.0 1.0 NE2 B:HIS144 4.8 18.6 1.0 F2 B:6DK1381 4.8 22.9 1.0 C B:ASP181 4.8 11.6 1.0 CA B:ASP181 4.8 11.9 1.0 CZ B:TYR313 4.9 18.3 1.0 C B:VAL182 5.0 12.3 1.0

A.Kramer, T.Wagner, O.Yildiz, F.J.Meyer-Almes. Crystal Structure of A Histone Deacetylase Homologue From Pseudomonas Aeruginosa. Biochemistry V. 55 6858 2016.
ISSN: ISSN 1520-4995
PubMed: 27951649
DOI: 10.1021/ACS.BIOCHEM.6B00613