Zinc in PDB 4utr: Crystal Structure of Zebrafish Sirtuin 5 in Complex with Glutarylated CPS1-Peptide

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with Glutarylated CPS1-Peptide, PDB code: 4utr was solved by M.Pannek, M.Gertz, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.53 / 2.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.220, 87.220, 314.040, 90.00, 90.00, 120.00
R / Rfree (%)	21.332 / 26.17

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with Glutarylated CPS1-Peptide also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with Glutarylated CPS1-Peptide (pdb code 4utr). 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 Zebrafish Sirtuin 5 in Complex with Glutarylated CPS1-Peptide, PDB code: 4utr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with Glutarylated CPS1-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 Zebrafish Sirtuin 5 in Complex with Glutarylated CPS1-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1300 b:44.0 occ:1.00 SG A:CYS203 2.3 56.9 1.0 SG A:CYS165 2.3 50.5 1.0 SG A:CYS162 2.3 52.4 1.0 SG A:CYS208 2.3 55.5 1.0 CB A:CYS203 3.1 56.8 1.0 CB A:CYS162 3.2 50.2 1.0 CB A:CYS165 3.2 53.3 1.0 CB A:CYS208 3.3 59.8 1.0 N A:CYS165 3.8 48.2 1.0 NH1 A:ARG205 3.9 86.5 1.0 CA A:CYS165 4.0 50.4 1.0 N A:GLY210 4.4 50.5 1.0 CA A:CYS203 4.5 55.7 1.0 CA A:CYS162 4.6 49.0 1.0 CB A:SER164 4.7 49.5 1.0 C A:CYS165 4.7 48.7 1.0 CA A:CYS208 4.7 61.8 1.0 CG A:ARG205 4.7 73.4 1.0 CA A:GLY210 4.8 50.1 1.0 N A:GLY166 4.9 46.4 1.0 C A:SER164 4.9 48.1 1.0 N A:ASN209 4.9 54.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with Glutarylated CPS1-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 Zebrafish Sirtuin 5 in Complex with Glutarylated CPS1-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1299 b:86.6 occ:1.00 SG B:CYS208 2.3 0.8 1.0 SG B:CYS165 2.3 94.0 1.0 SG B:CYS162 2.3 0.3 1.0 SG B:CYS203 2.3 0.8 1.0 CB B:CYS165 3.1 97.5 1.0 CB B:CYS203 3.1 0.1 1.0 CB B:CYS162 3.2 94.9 1.0 CB B:CYS208 3.3 0.5 1.0 N B:CYS165 3.7 93.6 1.0 CA B:CYS165 3.9 93.0 1.0 N B:GLY210 4.4 0.4 1.0 CA B:CYS203 4.6 0.9 1.0 C B:CYS165 4.6 87.9 1.0 CB B:ARG205 4.6 0.5 1.0 CA B:CYS208 4.7 0.7 1.0 CA B:CYS162 4.7 86.3 1.0 CA B:GLY210 4.8 0.2 1.0 C B:SER164 4.8 93.8 1.0 N B:GLY166 4.8 82.8 1.0 CB B:SER164 4.8 92.9 1.0 CD B:ARG205 4.9 0.4 1.0 N B:ASN209 4.9 0.1 1.0

C.Roessler, T.Nowak, M.Pannek, M.Gertz, G.T.Nguyen, M.Scharfe, I.Born, W.Sippl, C.Steegborn, M.Schutkowski. Chemical Probing of the Human Sirtuin 5 Active Site Reveals Its Substrate Acyl Specificity and Peptide-Based Inhibitors. Angew.Chem.Int.Ed.Engl. V. 53 10728 2014.
ISSN: ISSN 1433-7851
PubMed: 25111069
DOI: 10.1002/ANIE.201402679