Zinc in PDB 4hda: Crystal Structure of Human SIRT5 in Complex with Fluor-De-Lys Peptide and Resveratrol

The structure of Crystal Structure of Human SIRT5 in Complex with Fluor-De-Lys Peptide and Resveratrol, PDB code: 4hda was solved by M.Gertz, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.78 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.300, 112.690, 55.890, 90.00, 90.05, 90.00
R / Rfree (%)	19.9 / 25.2

The binding sites of Zinc atom in the Crystal Structure of Human SIRT5 in Complex with Fluor-De-Lys Peptide and Resveratrol (pdb code 4hda). 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 Human SIRT5 in Complex with Fluor-De-Lys Peptide and Resveratrol, PDB code: 4hda:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human SIRT5 in Complex with Fluor-De-Lys Peptide and Resveratrol


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 Human SIRT5 in Complex with Fluor-De-Lys Peptide and Resveratrol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:34.5 occ:1.00 SG A:CYS212 2.3 38.3 1.0 SG A:CYS166 2.3 31.1 1.0 SG A:CYS169 2.3 27.2 1.0 SG A:CYS207 2.5 23.6 1.0 CB A:CYS166 3.0 29.6 1.0 CB A:CYS207 3.2 37.2 1.0 CB A:CYS212 3.4 39.7 1.0 CB A:CYS169 3.7 32.4 1.0 N A:CYS169 3.9 32.2 1.0 CB A:GLU209 3.9 35.9 1.0 CG A:GLU209 4.0 51.5 1.0 CA A:CYS169 4.2 33.1 1.0 CA A:CYS166 4.5 32.4 1.0 N A:GLY214 4.5 25.7 1.0 N A:GLY213 4.5 32.3 1.0 O A:CYS169 4.5 43.6 1.0 C A:CYS169 4.6 46.6 1.0 CA A:CYS207 4.7 25.7 1.0 CA A:CYS212 4.8 41.9 1.0 CB A:SER168 4.8 31.2 1.0 C A:CYS212 5.0 36.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human SIRT5 in Complex with Fluor-De-Lys Peptide and Resveratrol


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 Human SIRT5 in Complex with Fluor-De-Lys Peptide and Resveratrol within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:29.9 occ:1.00 SG B:CYS212 2.3 36.2 1.0 SG B:CYS169 2.3 32.0 1.0 SG B:CYS166 2.3 37.7 1.0 SG B:CYS207 2.4 21.4 1.0 CB B:CYS169 2.6 26.6 1.0 CB B:CYS166 2.9 29.8 1.0 CB B:CYS207 3.0 30.4 1.0 CB B:CYS212 3.3 31.1 1.0 N B:CYS169 3.5 35.2 1.0 CA B:CYS169 3.6 35.3 1.0 CA B:CYS166 4.4 31.5 1.0 C B:CYS169 4.5 40.3 1.0 CA B:CYS207 4.5 26.2 1.0 CG B:GLU209 4.5 35.0 1.0 N B:GLY170 4.6 38.7 1.0 C B:SER168 4.7 27.1 1.0 CA B:CYS212 4.7 33.5 1.0 CB B:SER168 4.7 36.1 1.0 N B:VAL171 4.8 34.7 1.0 CB B:GLU209 4.8 31.5 1.0 N B:GLY214 4.9 22.2 1.0 CB B:VAL171 4.9 19.4 1.0

M.Gertz, G.T.Nguyen, F.Fischer, B.Suenkel, C.Schlicker, B.Franzel, J.Tomaschewski, F.Aladini, C.Becker, D.Wolters, C.Steegborn. A Molecular Mechanism For Direct Sirtuin Activation By Resveratrol. Plos One V. 7 49761 2012.
ISSN: ESSN 1932-6203
PubMed: 23185430
DOI: 10.1371/JOURNAL.PONE.0049761