Zinc in PDB 4utx: Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- Nitro-Propionylated CPS1-Peptide

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- Nitro-Propionylated CPS1-Peptide, PDB code: 4utx 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)	48.38 / 3.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.490, 87.490, 313.790, 90.00, 90.00, 120.00
R / Rfree (%)	19.357 / 26.189

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- Nitro-Propionylated 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 3- Nitro-Propionylated CPS1-Peptide (pdb code 4utx). 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 3- Nitro-Propionylated CPS1-Peptide, PDB code: 4utx:
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 3- Nitro-Propionylated 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 3- Nitro-Propionylated CPS1-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1299 b:51.9 occ:1.00 SG A:CYS203 2.3 51.8 1.0 SG A:CYS162 2.3 52.0 1.0 SG A:CYS208 2.3 59.9 1.0 SG A:CYS165 2.3 60.4 1.0 CB A:CYS203 3.0 54.6 1.0 CB A:CYS162 3.2 50.0 1.0 CB A:CYS165 3.4 56.3 1.0 CB A:CYS208 3.4 63.0 1.0 N A:CYS165 3.6 53.7 1.0 CA A:CYS165 4.0 52.5 1.0 N A:GLY210 4.1 49.1 1.0 CB A:SER164 4.1 57.7 1.0 CA A:GLY210 4.3 48.6 1.0 NH1 A:ARG205 4.3 99.8 1.0 CA A:CYS203 4.4 55.9 1.0 CA A:CYS162 4.6 50.3 1.0 C A:SER164 4.7 52.6 1.0 CA A:CYS208 4.7 61.2 1.0 C A:CYS165 4.8 50.1 1.0 CA A:SER164 4.9 53.1 1.0 N A:GLY166 4.9 50.8 1.0 N A:ASN209 4.9 53.9 1.0 N A:SER164 4.9 55.1 1.0 C A:CYS208 5.0 56.7 1.0 CD A:ARG205 5.0 0.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- Nitro-Propionylated 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 3- Nitro-Propionylated CPS1-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1299 b:92.6 occ:1.00 SG B:CYS165 2.3 90.7 1.0 SG B:CYS208 2.3 0.2 1.0 SG B:CYS162 2.3 91.2 1.0 SG B:CYS203 2.3 0.8 1.0 CB B:CYS203 3.1 95.7 1.0 CB B:CYS162 3.2 93.3 1.0 CB B:CYS165 3.3 91.5 1.0 CB B:CYS208 3.4 0.7 1.0 N B:CYS165 3.5 87.2 1.0 CA B:CYS165 4.0 86.8 1.0 N B:GLY210 4.1 0.8 1.0 CA B:GLY210 4.4 0.7 1.0 CB B:SER164 4.4 89.2 1.0 CA B:CYS203 4.5 98.3 1.0 CA B:CYS162 4.6 85.5 1.0 C B:SER164 4.6 84.6 1.0 C B:CYS165 4.7 89.3 1.0 CA B:CYS208 4.7 0.4 1.0 N B:GLY166 4.9 94.2 1.0 CA B:SER164 4.9 84.8 1.0 N B:SER164 5.0 86.9 1.0 N B:ASN209 5.0 0.4 1.0 C B:CYS208 5.0 0.9 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