Sodium in PDB 9eb6: Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein Circ

The structure of Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein Circ, PDB code: 9eb6 was solved by Y.Khandokar, C.J.H.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)	38.95 / 1.90
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	55.289, 55.41, 137.904, 90, 97.92, 90
R / Rfree (%)	17.1 / 22.1

The structure of Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein Circ also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein Circ (pdb code 9eb6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein Circ, PDB code: 9eb6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein Circ


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 Myristoylated Peptide Derived From Tegument Protein Circ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:63.2 occ:1.00 O A:HOH421 2.2 63.9 1.0 CD1 A:LEU79 2.4 47.2 0.3 O A:PRO80 2.8 59.2 1.0 CG A:LEU79 3.7 42.7 0.3 C A:GLU81 3.9 57.7 1.0 C A:PRO80 3.9 56.1 1.0 CA A:GLU81 4.0 54.5 1.0 O A:GLU81 4.0 60.7 1.0 N A:ARG82 4.2 77.0 1.0 CG A:ARG82 4.4 76.2 1.0 N A:GLU81 4.4 50.6 1.0 O A:LEU79 4.4 49.6 1.0 CB A:LEU79 4.5 44.6 0.7 CE1 A:HIS90 4.6 42.0 1.0 CB A:LEU79 4.6 44.9 0.3 CD2 A:LEU79 4.7 41.9 0.3 NE2 A:HIS90 4.7 36.6 1.0 C A:LEU79 4.8 50.9 1.0 C A:ARG82 4.8 75.2 1.0 CA A:ARG82 5.0 71.4 1.0

Sodium binding site 2 out of 2 in the Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein Circ


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein Circ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:53.4 occ:1.00 O1 A:PGE301 2.2 39.9 1.0 O A:HOH578 2.8 40.6 1.0 H1 A:PGE301 2.8 53.0 1.0 HO1 A:PGE301 2.8 47.9 1.0 CL A:CL305 3.0 68.5 1.0 O A:HOH458 3.0 37.8 1.0 C1 A:PGE301 3.0 44.1 1.0 H2 A:PGE301 3.5 44.1 1.0 H12 A:PGE301 3.8 53.0 1.0 C2 A:PGE301 3.8 36.7 1.0 CZ A:PHE268 3.9 27.2 1.0 CA A:GLY266 3.9 36.6 1.0 O A:HOH447 4.2 36.7 1.0 H32 A:PGE301 4.3 59.4 1.0 H22 A:PGE301 4.4 44.1 1.0 CD2 A:LEU262 4.4 36.8 1.0 CE2 A:PHE268 4.4 27.6 1.0 CE1 A:PHE268 4.7 32.0 1.0 N A:GLY266 4.7 31.7 1.0 O A:HOH423 4.8 41.7 1.0 CD1 A:LEU262 4.8 27.2 1.0 H6 A:PGE301 4.8 65.8 1.0 O2 A:PGE301 4.9 58.2 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