Sodium in PDB 5fa4: Structure of Hla-A2:01 with Peptide Y16R

The structure of Structure of Hla-A2:01 with Peptide Y16R, PDB code: 5fa4 was solved by S.G.Remesh, D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.86 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.525, 79.421, 58.513, 90.00, 116.42, 90.00
R / Rfree (%)	20.4 / 25.9

The binding sites of Sodium atom in the Structure of Hla-A2:01 with Peptide Y16R (pdb code 5fa4). 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 Structure of Hla-A2:01 with Peptide Y16R, PDB code: 5fa4:

Sodium binding site 1 out of 1 in the Structure of Hla-A2:01 with Peptide Y16R


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Hla-A2:01 with Peptide Y16R within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:28.0 occ:1.00 CE B:MET99 3.4 49.2 1.0 CA B:PRO14 3.8 31.7 1.0 N B:PRO14 3.9 31.3 1.0 C B:HIS13 4.2 29.6 1.0 CG B:PRO14 4.2 33.6 1.0 CD1 A:LEU206 4.2 27.9 1.0 CZ3 A:TRP204 4.2 33.3 1.0 O B:HIS13 4.2 30.6 1.0 OG B:SER11 4.3 29.7 1.0 CD B:PRO14 4.3 32.5 1.0 CB B:PRO14 4.5 32.6 1.0 O B:SER11 4.6 26.4 1.0 CD2 A:LEU206 4.6 27.1 1.0 CH2 A:TRP204 4.6 32.9 1.0 CE3 A:TRP204 4.6 32.8 1.0 O B:HOH202 4.8 25.8 1.0 OD2 B:ASP98 4.9 63.4 1.0 SD B:MET99 4.9 50.0 1.0

S.G.Remesh, M.Andreatta, G.Ying, T.Kaever, M.Nielsen, C.Mcmurtrey, W.Hildebrand, B.Peters, D.M.Zajonc. Unconventional Peptide Presentation By Major Histocompatibility Complex (Mhc) Class I Allele Hla-A*02:01: Breaking Confinement. J. Biol. Chem. V. 292 5262 2017.
ISSN: ESSN 1083-351X
PubMed: 28179428
DOI: 10.1074/JBC.M117.776542