Sodium in PDB 7wj2: Crystal Structure of Hla-C*1402 Complexed with 8-Mer Hiv Gag Peptide

The structure of Crystal Structure of Hla-C*1402 Complexed with 8-Mer Hiv Gag Peptide, PDB code: 7wj2 was solved by J.Kuroha, D.Morita, M.Asa, M.Sugita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.44 / 1.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.655, 76.885, 62.053, 90, 119.54, 90
R / Rfree (%)	15.6 / 17.8

The binding sites of Sodium atom in the Crystal Structure of Hla-C*1402 Complexed with 8-Mer Hiv Gag Peptide (pdb code 7wj2). 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 Hla-C*1402 Complexed with 8-Mer Hiv Gag Peptide, PDB code: 7wj2:

Sodium binding site 1 out of 1 in the Crystal Structure of Hla-C*1402 Complexed with 8-Mer Hiv Gag 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 Hla-C*1402 Complexed with 8-Mer Hiv Gag Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:27.0 occ:1.00 O B:HOH314 2.7 31.1 1.0 O B:HOH202 2.8 36.1 1.0 O A:HOH486 2.8 17.1 1.0 N A:GLU232 3.0 13.5 0.5 N A:GLU232 3.0 13.4 0.5 CD B:LYS6 3.0 23.6 0.5 CB A:GLU232 3.4 15.7 0.5 NE2 B:GLN8 3.4 13.5 1.0 CB A:GLU232 3.5 16.4 0.5 CG A:GLU232 3.5 19.3 0.5 CA A:GLU232 3.8 13.4 0.5 CA A:VAL231 3.8 16.0 1.0 CA A:GLU232 3.8 13.5 0.5 CD B:GLN8 3.9 11.5 1.0 CG B:LYS6 3.9 20.1 0.5 C A:VAL231 3.9 13.5 1.0 CB A:VAL231 3.9 16.8 1.0 CG B:GLN8 4.3 11.7 1.0 CE B:LYS6 4.3 25.8 0.5 CD A:GLU232 4.3 21.4 0.5 CG1 A:VAL231 4.3 19.3 1.0 OE1 A:GLU232 4.5 21.7 0.5 NZ B:LYS6 4.5 27.9 0.5 OE1 B:GLN8 4.5 12.3 1.0 OE1 A:GLU232 4.6 22.3 0.5 O A:GLU232 4.7 11.5 0.5 O A:GLU232 4.7 11.4 0.5 CD B:LYS6 4.7 19.6 0.5 C A:GLU232 4.8 11.2 0.5 O A:HOH404 4.8 36.2 1.0 CG A:GLU232 4.8 18.2 0.5 C A:GLU232 4.8 11.1 0.5 OE2 A:GLU232 5.0 23.5 0.5

M.Asa, D.Morita, J.Kuroha, T.Mizutani, N.Mori, B.Mikami, M.Sugita. Crystal Structures of N-Myristoylated Lipopeptide-Bound Hla Class I Complexes Indicate Reorganization of B-Pocket Architecture Upon Ligand Binding. J.Biol.Chem. V. 298 02100 2022.
ISSN: ESSN 1083-351X
PubMed: 35667438
DOI: 10.1016/J.JBC.2022.102100