Zinc in PDB 5g12: Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.

The structure of Pseudomonas Aeruginosa Hdah (Y313F) Unliganded., PDB code: 5g12 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)	75.79 / 2.02
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.560, 81.560, 205.150, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.4

The structure of Pseudomonas Aeruginosa Hdah (Y313F) Unliganded. also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded. (pdb code 5g12). 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 (Y313F) Unliganded., PDB code: 5g12:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.


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 (Y313F) Unliganded. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1372 b:16.7 occ:0.70 OD2 A:ASP269 2.0 16.5 1.0 OD1 A:ASP181 2.0 14.0 1.0 ND1 A:HIS183 2.1 14.9 1.0 O A:HOH2077 2.3 24.8 1.0 O A:HOH2094 2.4 37.7 1.0 OD2 A:ASP181 2.7 14.2 1.0 CG A:ASP181 2.7 14.0 1.0 CE1 A:HIS183 2.9 15.2 1.0 CG A:ASP269 3.0 15.9 1.0 CG A:HIS183 3.2 14.2 1.0 OD1 A:ASP269 3.3 17.1 1.0 CB A:HIS183 3.7 14.1 1.0 N A:HIS183 4.1 13.6 1.0 NE2 A:HIS183 4.1 14.7 1.0 CA A:GLY311 4.2 20.5 1.0 CB A:ASP181 4.2 13.8 1.0 NE2 A:HIS143 4.2 21.8 1.0 O A:HOH2076 4.2 43.3 1.0 CE2 A:PHE313 4.3 22.4 0.5 CD2 A:HIS183 4.3 14.6 1.0 CB A:ASP269 4.3 14.8 1.0 N A:VAL182 4.3 12.8 1.0 CG1 A:VAL182 4.3 13.4 1.0 CA A:HIS183 4.5 13.5 1.0 N A:GLY311 4.6 19.6 1.0 NE2 A:HIS144 4.6 18.3 1.0 CE1 A:HIS143 4.6 21.5 1.0 CZ A:PHE313 4.7 22.5 0.5 C A:ASP181 4.8 12.9 1.0 CA A:ASP181 4.8 13.1 1.0 C A:GLY311 4.9 20.2 1.0 C A:VAL182 5.0 13.0 1.0

Zinc binding site 2 out of 2 in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.


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 (Y313F) Unliganded. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1377 b:18.6 occ:0.70 OD2 B:ASP269 2.0 17.5 1.0 OD1 B:ASP181 2.0 15.8 1.0 ND1 B:HIS183 2.1 16.1 1.0 O B:HOH2063 2.2 28.0 1.0 O B:HOH2081 2.5 42.5 1.0 OD2 B:ASP181 2.7 16.1 1.0 CG B:ASP181 2.7 15.1 1.0 CE1 B:HIS183 2.9 16.4 1.0 CG B:ASP269 3.0 15.7 1.0 CG B:HIS183 3.2 15.2 1.0 OD1 B:ASP269 3.4 16.1 1.0 CB B:HIS183 3.7 14.3 1.0 O B:HOH2064 3.8 56.2 1.0 N B:HIS183 4.0 14.2 1.0 NE2 B:HIS183 4.1 16.1 1.0 CA B:GLY311 4.1 21.8 1.0 NE2 B:HIS143 4.2 21.4 1.0 CB B:ASP181 4.2 14.6 1.0 CD2 B:HIS183 4.3 15.7 1.0 CE2 B:PHE313 4.3 25.5 0.5 CG1 B:VAL182 4.3 13.6 1.0 CB B:ASP269 4.3 14.3 1.0 N B:VAL182 4.3 14.2 1.0 CA B:HIS183 4.5 14.1 1.0 N B:GLY311 4.6 22.2 1.0 NE2 B:HIS144 4.6 21.1 1.0 CE1 B:HIS143 4.6 20.7 1.0 CZ B:PHE313 4.7 26.4 0.5 C B:ASP181 4.8 14.2 1.0 CA B:ASP181 4.9 14.2 1.0 C B:VAL182 5.0 13.7 1.0 C B:GLY311 5.0 22.4 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