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

Protein crystallography data

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

Other elements in 4utr:

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

Zinc (Zn) 2 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 1 in 4utr

Go back to Sodium Binding Sites List in 4utr
Sodium binding site 1 out of 1 in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with Glutarylated 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 Glutarylated CPS1-Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1302

b:60.7
occ:0.50
OD2 B:ASP226 2.7 68.3 1.0
OD1 B:ASP224 2.9 76.2 1.0
CG B:ASP224 3.6 70.0 1.0
OD2 B:ASP224 3.6 73.4 1.0
CG B:ASP226 4.0 67.2 1.0
CB B:ASP226 4.6 64.9 1.0
OD1 B:ASP226 4.9 65.4 1.0
CB B:ASP224 5.0 64.9 1.0

Reference:

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
Page generated: Tue Dec 15 08:41:19 2020

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