Zinc in PDB 1q17: Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide

The structure of Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide, PDB code: 1q17 was solved by K.Zhao, X.Chai, R.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.88 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.159, 109.682, 85.825, 90.00, 104.90, 90.00
R / Rfree (%)	18.6 / 24.7

The structure of Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide (pdb code 1q17). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide, PDB code: 1q17:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:53.2 occ:1.00 SG A:CYS170 2.3 52.6 1.0 SG A:CYS173 2.4 53.1 1.0 SG A:CYS146 2.4 51.1 1.0 SG A:CYS143 2.5 53.2 1.0 CB A:CYS170 3.1 45.9 1.0 CB A:CYS173 3.2 53.8 1.0 CB A:CYS146 3.3 48.8 1.0 CB A:CYS143 3.3 35.1 1.0 N A:CYS146 3.4 51.3 1.0 N A:CYS173 3.8 55.8 1.0 CA A:CYS146 3.9 53.7 1.0 CG2 A:VAL172 4.0 49.4 1.0 CA A:CYS173 4.0 52.1 1.0 C A:GLY145 4.5 52.0 1.0 CA A:CYS170 4.6 50.5 1.0 CA A:GLY145 4.6 47.1 1.0 C A:CYS173 4.6 47.6 1.0 CB A:GLU175 4.7 64.4 1.0 N A:GLY174 4.7 45.8 1.0 C A:CYS146 4.7 50.0 1.0 N A:GLU175 4.7 58.9 1.0 CA A:CYS143 4.8 43.9 1.0 CB A:LYS148 4.8 52.8 1.0 N A:GLY147 4.8 46.2 1.0 N A:GLY145 4.8 48.7 1.0 OH A:TYR150 4.9 65.7 1.0 C A:VAL172 4.9 60.5 1.0 CG A:GLU175 5.0 74.6 1.0 N A:LYS148 5.0 43.3 1.0

Zinc binding site 2 out of 3 in the Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:61.9 occ:1.00 SG B:CYS170 2.4 55.8 1.0 SG B:CYS146 2.5 66.6 1.0 SG B:CYS173 2.5 75.7 1.0 SG B:CYS143 2.5 56.2 1.0 CB B:CYS143 3.3 55.0 1.0 CB B:CYS173 3.3 72.6 1.0 N B:CYS146 3.5 63.4 1.0 CB B:CYS170 3.5 62.1 1.0 CB B:CYS146 3.5 68.0 1.0 CG1 B:VAL172 3.7 76.9 1.0 CA B:CYS146 4.1 67.6 1.0 N B:CYS173 4.3 78.1 1.0 CA B:CYS173 4.4 74.9 1.0 C B:GLY145 4.5 60.3 1.0 CB B:LYS148 4.5 69.8 1.0 N B:GLY147 4.5 68.0 1.0 CA B:GLY145 4.6 59.0 1.0 N B:LYS148 4.7 64.4 1.0 C B:CYS146 4.7 70.2 1.0 CA B:CYS143 4.7 55.8 1.0 N B:GLY145 4.8 62.0 1.0 CB B:GLU175 4.9 79.5 1.0 CA B:CYS170 4.9 62.1 1.0 C B:VAL172 5.0 76.0 1.0

Zinc binding site 3 out of 3 in the Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:63.3 occ:1.00 SG C:CYS170 2.3 48.2 1.0 SG C:CYS146 2.3 68.9 1.0 SG C:CYS173 2.4 62.7 1.0 SG C:CYS143 2.5 57.3 1.0 CB C:CYS146 2.9 51.7 1.0 CB C:CYS173 3.1 63.5 1.0 CB C:CYS170 3.1 55.3 1.0 CB C:CYS143 3.2 50.8 1.0 N C:CYS146 3.3 51.1 1.0 CA C:CYS146 3.6 55.1 1.0 CG1 C:VAL172 3.9 79.0 1.0 N C:CYS173 4.1 66.9 1.0 CA C:CYS173 4.1 63.9 1.0 N C:GLY147 4.3 51.1 1.0 C C:CYS146 4.3 53.4 1.0 C C:GLY145 4.4 50.4 1.0 N C:LYS148 4.6 55.0 1.0 CA C:CYS170 4.6 52.4 1.0 CB C:LYS148 4.7 60.2 1.0 C C:VAL172 4.7 68.5 1.0 CA C:CYS143 4.7 52.1 1.0 C C:CYS173 4.7 60.7 1.0 CA C:GLY145 4.7 49.9 1.0 N C:GLY145 4.8 55.4 1.0 CB C:GLU175 4.9 48.3 1.0 N C:GLY174 4.9 56.4 1.0 N C:GLU175 5.0 57.0 1.0

K.Zhao, X.Chai, R.Marmorstein. Structure of the Yeast HST2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl Adp Ribose and Histone Peptide. Structure V. 11 1403 2003.
ISSN: ISSN 0969-2126
PubMed: 14604530
DOI: 10.1016/J.STR.2003.09.016