Magnesium in PDB 9eb5: Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein MDV023

The structure of Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein MDV023, PDB code: 9eb5 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)	48.13 / 2.08
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.116, 55.429, 133.412, 90, 101.43, 90
R / Rfree (%)	18.6 / 24.3

The structure of Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein MDV023 also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein MDV023 (pdb code 9eb5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein MDV023, PDB code: 9eb5:

Magnesium binding site 1 out of 1 in the Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein MDV023


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Chicken YF1.7*1 Presenting Myristoylated Peptide Derived From Tegument Protein MDV023 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:36.9 occ:1.00 O B:HOH246 2.9 29.8 1.0 N B:THR71 3.2 21.7 1.0 CA B:PHE70 3.7 20.2 1.0 C B:PHE70 4.0 21.4 1.0 CB B:PHE70 4.1 19.7 1.0 CB B:THR71 4.2 23.8 1.0 CA B:THR71 4.2 22.5 1.0 O B:THR71 4.3 24.4 1.0 OG1 B:THR71 4.4 23.7 1.0 C B:THR71 4.6 22.9 1.0 NZ B:LYS41 4.7 33.3 1.0 O B:HOH277 4.8 29.7 1.0 O B:HOH201 4.9 30.1 1.0 N B:PHE70 5.0 19.4 1.0 O B:ASP69 5.0 24.2 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