Sodium in PDB 6lt6: Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with Lysophosphatidylcholine

The structure of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with Lysophosphatidylcholine, PDB code: 6lt6 was solved by Y.Shima, D.Morita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.19 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.451, 81.028, 106.108, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.2

The binding sites of Sodium atom in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with Lysophosphatidylcholine (pdb code 6lt6). 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 Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with Lysophosphatidylcholine, PDB code: 6lt6:

Sodium binding site 1 out of 1 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with Lysophosphatidylcholine


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 Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with Lysophosphatidylcholine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:38.7 occ:1.00 O B:HOH222 2.2 42.6 1.0 O B:HIS84 2.4 27.3 1.0 O B:HOH270 2.5 38.4 1.0 O B:LEU87 2.5 26.9 1.0 O B:HOH201 2.5 33.4 1.0 O B:HOH254 2.6 37.6 1.0 C B:HIS84 3.3 34.1 1.0 C B:LEU87 3.7 31.1 1.0 N B:HIS84 3.9 31.2 1.0 CA B:VAL85 4.1 23.1 1.0 N B:VAL85 4.1 27.0 1.0 CA B:HIS84 4.2 38.5 1.0 N B:LEU87 4.2 24.6 1.0 ND2 B:ASN83 4.3 50.4 1.0 CA B:LEU87 4.3 31.9 1.0 C B:VAL85 4.4 28.1 1.0 N B:GLY89 4.4 45.4 1.0 O B:VAL85 4.4 31.6 1.0 CB B:LEU87 4.4 24.2 1.0 O1 B:EDO104 4.5 51.3 1.0 N B:SER88 4.7 32.6 1.0 C B:ASN83 4.8 39.1 1.0 O B:GLY89 4.9 41.0 1.0 CA B:SER88 4.9 41.2 1.0 CB B:ASN83 5.0 30.4 1.0

Y.Shima, D.Morita, T.Mizutani, N.Mori, B.Mikami, M.Sugita. Crystal Structures of Lysophospholipid-Bound Mhc Class I Molecules. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32269076
DOI: 10.1074/JBC.RA119.011932