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Sodium in PDB 6fky: Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide

Protein crystallography data

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide, PDB code: 6fky 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) 48.51 / 2.98
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 87.134, 87.134, 316.677, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 27.5

Other elements in 6fky:

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-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 3- (Benzylthio)Succinyl-CPS1 Peptide (pdb code 6fky). 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- (Benzylthio)Succinyl-CPS1 Peptide, PDB code: 6fky:

Sodium binding site 1 out of 1 in 6fky

Go back to Sodium Binding Sites List in 6fky
Sodium binding site 1 out of 1 in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-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- (Benzylthio)Succinyl-CPS1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:64.1
occ:1.00
OD1 B:ASP224 3.3 72.0 1.0
OD2 B:ASP226 3.7 76.8 1.0
OD2 B:ASP224 3.8 77.0 1.0
CG B:ASP224 3.9 70.7 1.0
CG B:ASP226 4.6 76.3 1.0
CB B:ASP226 4.8 74.2 1.0

Reference:

D.Kalbas, S.Liebscher, T.Nowak, M.Meleshin, M.Pannek, C.Popp, Z.Alhalabi, F.Bordusa, W.Sippl, C.Steegborn, M.Schutkowski. Potent and Selective Inhibitors of Human Sirtuin 5. J. Med. Chem. V. 61 2460 2018.
ISSN: ISSN 1520-4804
PubMed: 29494161
DOI: 10.1021/ACS.JMEDCHEM.7B01648
Page generated: Tue Dec 15 12:15:20 2020

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