Zinc in PDB 4bv2: Crystal Structure of SIR2 in Complex with the Inhibitor Ex-527, 2'-O-Acetyl-Adp-Ribose and Deacetylated P53-Peptide

The structure of Crystal Structure of SIR2 in Complex with the Inhibitor Ex-527, 2'-O-Acetyl-Adp-Ribose and Deacetylated P53-Peptide, PDB code: 4bv2 was solved by M.Gertz, M.Weyand, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.47 / 3.30
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	45.950, 45.950, 241.870, 90.00, 90.00, 90.00
R / Rfree (%)	24.52 / 31.781

The structure of Crystal Structure of SIR2 in Complex with the Inhibitor Ex-527, 2'-O-Acetyl-Adp-Ribose and Deacetylated P53-Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of SIR2 in Complex with the Inhibitor Ex-527, 2'-O-Acetyl-Adp-Ribose and Deacetylated P53-Peptide (pdb code 4bv2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of SIR2 in Complex with the Inhibitor Ex-527, 2'-O-Acetyl-Adp-Ribose and Deacetylated P53-Peptide, PDB code: 4bv2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of SIR2 in Complex with the Inhibitor Ex-527, 2'-O-Acetyl-Adp-Ribose and Deacetylated P53-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SIR2 in Complex with the Inhibitor Ex-527, 2'-O-Acetyl-Adp-Ribose and Deacetylated P53-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1246 b:0.8 occ:1.00 SG A:CYS124 2.3 1.0 1.0 SG A:CYS151 2.3 0.4 1.0 SG A:CYS127 2.3 0.8 1.0 SG A:CYS148 2.3 0.9 1.0 CB A:CYS124 2.9 0.1 1.0 CB A:CYS151 3.0 0.5 1.0 CB A:CYS127 3.4 0.8 1.0 CB A:CYS148 3.4 0.5 1.0 CB A:LYS129 3.5 0.3 1.0 N A:CYS151 3.6 0.7 1.0 CB A:ASP150 3.8 0.2 1.0 CA A:CYS151 3.9 0.2 1.0 N A:LYS129 3.9 0.8 1.0 CA A:CYS127 4.1 0.5 1.0 N A:CYS127 4.1 0.3 1.0 C A:ASP150 4.2 1.0 1.0 C A:CYS127 4.3 0.9 1.0 N A:GLU128 4.3 1.0 1.0 CA A:LYS129 4.3 0.9 1.0 CA A:CYS124 4.4 1.0 1.0 CA A:ASP150 4.4 0.4 1.0 N A:ASP150 4.5 1.0 1.0 CD A:LYS129 4.7 0.5 1.0 CG A:LYS129 4.7 0.0 1.0 CA A:CYS148 4.8 0.8 1.0 O A:CYS127 4.9 0.8 1.0 OH A:TYR131 5.0 0.5 1.0 C A:CYS151 5.0 0.3 1.0 N A:CYS124 5.0 0.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SIR2 in Complex with the Inhibitor Ex-527, 2'-O-Acetyl-Adp-Ribose and Deacetylated P53-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SIR2 in Complex with the Inhibitor Ex-527, 2'-O-Acetyl-Adp-Ribose and Deacetylated P53-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1249 b:0.1 occ:1.00 SG B:CYS151 2.3 0.9 1.0 SG B:CYS124 2.3 0.5 1.0 SG B:CYS127 2.3 0.5 1.0 SG B:CYS148 2.3 0.7 1.0 CB B:CYS151 3.0 1.0 1.0 CB B:CYS124 3.0 0.4 1.0 CB B:CYS127 3.4 0.1 1.0 CB B:CYS148 3.5 0.7 1.0 N B:CYS151 3.5 0.5 1.0 CB B:LYS129 3.5 0.3 1.0 CB B:ASP150 3.7 0.8 1.0 CA B:CYS151 3.9 0.8 1.0 N B:LYS129 3.9 0.8 1.0 CA B:CYS127 4.1 0.3 1.0 N B:CYS127 4.2 0.4 1.0 C B:ASP150 4.2 0.8 1.0 CA B:ASP150 4.3 0.0 1.0 C B:CYS127 4.3 0.9 1.0 CA B:LYS129 4.3 0.6 1.0 N B:GLU128 4.4 0.3 1.0 CA B:CYS124 4.4 0.9 1.0 N B:ASP150 4.5 0.5 1.0 CD B:LYS129 4.7 0.8 1.0 CG B:LYS129 4.8 0.8 1.0 CA B:CYS148 4.8 0.5 1.0 O B:CYS127 4.9 0.1 1.0 C B:CYS151 5.0 0.2 1.0

M.Gertz, F.Fischer, G.T.T.Nguyen, M.Lakshminarasimhan, M.Schutkowski, M.Weyand, C.Steegborn. Ex-527 Inhibits Sirtuins By Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism Proc.Natl.Acad.Sci.Usa V. 110 E2772 2013.
ISSN: ISSN 0027-8424
PubMed: 23840057
DOI: 10.1073/PNAS.1303628110