Sodium in PDB 9eb4: Chicken YF1.7*1 Presenting N-Palmitoylated Glycine

The structure of Chicken YF1.7*1 Presenting N-Palmitoylated Glycine, PDB code: 9eb4 was solved by Y.Khandokar, C.J.Wang, J.Rossjohn, J.Le Nours, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.02 / 2.20
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.669, 55.39, 133.456, 90, 100.98, 90
R / Rfree (%)	15.7 / 22

The structure of Chicken YF1.7*1 Presenting N-Palmitoylated Glycine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Chicken YF1.7*1 Presenting N-Palmitoylated Glycine (pdb code 9eb4). 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 Chicken YF1.7*1 Presenting N-Palmitoylated Glycine, PDB code: 9eb4:

Sodium binding site 1 out of 1 in the Chicken YF1.7*1 Presenting N-Palmitoylated Glycine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Chicken YF1.7*1 Presenting N-Palmitoylated Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:39.1 occ:1.00 O A:HOH545 2.7 43.7 1.0 OG A:SER38 3.1 23.6 1.0 N A:ARG21 3.5 23.9 1.0 CG A:ARG21 3.6 35.3 1.0 CB A:SER38 3.9 27.8 1.0 CA A:PRO20 4.0 24.0 1.0 CB A:ARG21 4.1 23.9 1.0 C A:PRO20 4.3 25.3 1.0 C A:SER38 4.4 32.1 1.0 CG A:LYS39 4.4 30.8 1.0 O A:SER38 4.4 32.1 1.0 CA A:ARG21 4.4 27.5 1.0 N A:LYS39 4.6 28.3 1.0 O A:MET19 4.7 32.5 1.0 CB A:PRO20 4.7 23.0 1.0 CA A:SER38 4.7 26.3 1.0

Y.Khandokar, T.Y.Cheng, C.J.H.Wang, T.P.Cao, R.S.K.Nagampalli, K.K.Sivaraman, I.Van Rhijn, J.Rossjohn, D.B.Moody, J.L.Nours. Molecular Basis For Presentation of N-Myristoylated Peptides By the Chicken YF1∗7.1 Molecule. J.Biol.Chem. V. 301 10253 2025.
ISSN: ESSN 1083-351X
PubMed: 40412526
DOI: 10.1016/J.JBC.2025.110253