Sodium in PDB 5j6h: Recognition of the Mhc Class Ib Molecule H2-Q10 By the Natural Killer Cell Receptor LY49C

The structure of Recognition of the Mhc Class Ib Molecule H2-Q10 By the Natural Killer Cell Receptor LY49C, PDB code: 5j6h was solved by R.Berry, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.47 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.420, 81.660, 97.920, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 24.3

The binding sites of Sodium atom in the Recognition of the Mhc Class Ib Molecule H2-Q10 By the Natural Killer Cell Receptor LY49C (pdb code 5j6h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Recognition of the Mhc Class Ib Molecule H2-Q10 By the Natural Killer Cell Receptor LY49C, PDB code: 5j6h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Recognition of the Mhc Class Ib Molecule H2-Q10 By the Natural Killer Cell Receptor LY49C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Recognition of the Mhc Class Ib Molecule H2-Q10 By the Natural Killer Cell Receptor LY49C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:35.5 occ:1.00 OE1 A:GLN96 2.7 29.8 1.0 OG1 A:THR94 2.9 33.3 1.0 N A:GLY120 3.0 21.8 1.0 N A:ASP119 3.1 18.4 1.0 O A:THR94 3.2 19.4 1.0 O A:ALA117 3.3 18.3 1.0 C A:ALA117 3.4 18.8 1.0 C A:TYR118 3.5 21.1 1.0 CD A:GLN96 3.5 29.6 1.0 CG A:GLN96 3.5 17.5 1.0 N A:TYR118 3.6 15.5 1.0 CA A:TYR118 3.6 15.9 1.0 C A:THR94 3.6 21.0 1.0 N A:GLN96 3.7 17.5 1.0 CB A:ALA117 3.7 16.7 1.0 CA A:ASP119 3.8 17.7 1.0 CB A:THR94 3.8 28.1 1.0 CA A:GLY120 3.8 22.4 1.0 C A:ASP119 3.9 22.8 1.0 CB A:GLN96 3.9 17.8 1.0 C A:ILE95 4.0 19.0 1.0 CA A:ILE95 4.0 17.3 1.0 N A:ILE95 4.0 17.4 1.0 O A:TYR118 4.2 21.9 1.0 CA A:ALA117 4.2 16.6 1.0 NE2 B:HIS31 4.3 29.0 1.0 CA A:THR94 4.4 18.2 1.0 CA A:GLN96 4.4 17.1 1.0 N A:ARG121 4.7 24.4 1.0 C A:GLY120 4.7 27.7 1.0 O A:ILE95 4.7 16.4 1.0 NE2 A:GLN96 4.8 16.2 1.0

Sodium binding site 2 out of 2 in the Recognition of the Mhc Class Ib Molecule H2-Q10 By the Natural Killer Cell Receptor LY49C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Recognition of the Mhc Class Ib Molecule H2-Q10 By the Natural Killer Cell Receptor LY49C within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:45.6 occ:1.00 OD1 B:ASN24 2.5 36.1 1.0 NH2 B:ARG12 3.0 34.7 1.0 CB B:HIS67 3.2 24.6 1.0 CG B:HIS67 3.2 29.2 1.0 ND1 B:HIS67 3.5 33.1 1.0 CA A:GLY237 3.5 22.4 1.0 O A:ALA236 3.6 23.2 1.0 CG2 B:ILE22 3.6 24.6 1.0 CG B:ASN24 3.7 36.2 1.0 CD2 B:HIS67 3.8 31.0 1.0 CZ B:ARG12 3.9 48.1 1.0 CD2 B:LEU65 3.9 16.8 1.0 NE B:ARG12 3.9 34.7 1.0 CE1 B:HIS67 4.1 33.0 1.0 ND2 B:ASN24 4.2 26.7 1.0 C A:GLY237 4.3 30.5 1.0 C A:ALA236 4.3 24.6 1.0 N A:GLY237 4.3 21.9 1.0 NE2 B:HIS67 4.3 32.2 1.0 O A:GLY237 4.3 31.0 1.0 CA B:HIS67 4.7 23.3 1.0 CG B:LEU65 4.8 17.1 1.0 CB B:ASN24 4.9 22.2 1.0 CB B:ILE22 4.9 27.3 1.0

L.C.Sullivan, R.Berry, N.Sosnin, J.M.Widjaja, F.A.Deuss, G.R.Balaji, N.L.Lagruta, M.Mirams, J.A.Trapani, J.Rossjohn, A.G.Brooks, D.M.Andrews. Recognition of the Major Histocompatibility Complex (Mhc) Class Ib Molecule H2-Q10 By the Natural Killer Cell Receptor LY49C. J.Biol.Chem. V. 291 18740 2016.
ISSN: ESSN 1083-351X
PubMed: 27385590
DOI: 10.1074/JBC.M116.737130