Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- Nitro-Propionylated CPS1-Peptide, PDB code: 4utx:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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 B:Na1303 b:65.6 occ:0.50 OD1 B:ASP224 2.8 83.4 1.0 OD2 B:ASP226 2.8 69.8 1.0 OD2 B:ASP224 3.3 78.7 1.0 CG B:ASP224 3.5 78.1 1.0 CG B:ASP226 4.1 73.3 1.0 CB B:ASP226 4.8 75.5 1.0 CB B:ASP224 5.0 70.7 1.0 O B:HOH2007 5.0 49.7 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