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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5ojo:

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

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Sirtuin 5 From Danio Rerio in Complex with 3-Hydroxy-3-Methylglutaryl- CPS1 Peptide, PDB code: 5ojo:

Sodium binding site 1 out of 1 in 5ojo

Go back to Sodium Binding Sites List in 5ojo
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
B:Na303

b:0.6
occ:0.50
OD2 B:ASP226 3.0 0.1 1.0
OD2 B:ASP224 3.3 77.1 1.0
OD1 B:ASP224 3.6 80.1 1.0
CG B:ASP226 3.8 99.7 1.0
CG B:ASP224 3.9 76.2 1.0
CB B:ASP226 4.0 95.6 1.0
OD1 B:ASP226 4.9 99.7 1.0

Reference:

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
Page generated: Mon Oct 7 23:12:20 2024

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