Zinc in PDB 5ojo: Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide

All present enzymatic activity of Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide:
6.3.4.16;

The structure of Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide, PDB code: 5ojo was solved by M.Pannek, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.67 / 3.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.540, 87.540, 316.920, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 26.6

The structure of Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide (pdb code 5ojo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide, PDB code: 5ojo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:59.2 occ:1.00 SG A:CYS203 2.3 67.2 1.0 SG A:CYS162 2.3 62.3 1.0 SG A:CYS208 2.3 75.3 1.0 SG A:CYS165 2.3 75.1 1.0 CB A:CYS203 3.1 66.5 1.0 CB A:CYS162 3.3 60.7 1.0 CB A:CYS165 3.3 73.8 1.0 CB A:CYS208 3.4 74.7 1.0 N A:CYS165 3.7 67.7 1.0 NH2 A:ARG205 3.9 91.6 1.0 CA A:CYS165 4.1 69.6 1.0 N A:GLY210 4.4 58.9 1.0 CA A:CYS203 4.6 64.3 1.0 CB A:SER164 4.7 68.2 1.0 CA A:CYS162 4.7 58.6 1.0 CA A:GLY210 4.7 57.3 1.0 CA A:CYS208 4.8 75.2 1.0 C A:CYS165 4.8 66.7 1.0 C A:SER164 4.9 67.1 1.0 N A:GLY166 5.0 62.6 1.0

Zinc binding site 2 out of 2 in the Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.3 occ:1.00 SG B:CYS208 2.3 1.0 1.0 SG B:CYS165 2.3 0.7 1.0 SG B:CYS203 2.4 0.1 1.0 SG B:CYS162 2.4 0.8 1.0 CB B:CYS162 3.3 0.0 1.0 CB B:CYS203 3.3 0.6 1.0 CB B:CYS165 3.3 0.1 1.0 CB B:CYS208 3.4 0.6 1.0 N B:CYS165 3.7 0.7 1.0 CA B:CYS165 4.0 0.2 1.0 CG B:ARG205 4.4 0.6 1.0 N B:GLY210 4.6 0.5 1.0 CD B:ARG205 4.6 0.3 1.0 CB B:SER164 4.7 0.4 1.0 CA B:CYS162 4.7 0.9 1.0 C B:CYS165 4.7 0.2 1.0 CA B:CYS208 4.8 0.6 1.0 CA B:CYS203 4.8 0.1 1.0 C B:SER164 4.8 0.1 1.0 OE1 B:GLU167 4.8 0.9 1.0 CA B:GLY210 4.9 0.3 1.0 N B:GLY166 4.9 0.1 1.0 CB B:GLU167 5.0 0.8 1.0

M.Pannek, Z.Simic, M.Fuszard, M.Meleshin, D.Rotili, A.Mai, M.Schutkowski, C.Steegborn. Crystal Structures of the Mitochondrial Deacylase Sirtuin 4 Reveal Isoform-Specific Acyl Recognition and Regulation Features. Nat Commun V. 8 1513 2017.
ISSN: ESSN 2041-1723
PubMed: 29138502
DOI: 10.1038/S41467-017-01701-2