Sodium in PDB 8sgb: Crystal Structure of CD1D-Lipid Complexed with Beta-2-Microglobulin, Tcr Alpha-Chain and Tcr Beta-Chain

The structure of Crystal Structure of CD1D-Lipid Complexed with Beta-2-Microglobulin, Tcr Alpha-Chain and Tcr Beta-Chain, PDB code: 8sgb was solved by K.T.O.Chan Yew Poa, J.Le Nours, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.36 / 2.80
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	136.785, 136.785, 69.797, 90, 90, 90
R / Rfree (%)	20.8 / 24.9

The binding sites of Sodium atom in the Crystal Structure of CD1D-Lipid Complexed with Beta-2-Microglobulin, Tcr Alpha-Chain and Tcr Beta-Chain (pdb code 8sgb). 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 CD1D-Lipid Complexed with Beta-2-Microglobulin, Tcr Alpha-Chain and Tcr Beta-Chain, PDB code: 8sgb:

Sodium binding site 1 out of 1 in the Crystal Structure of CD1D-Lipid Complexed with Beta-2-Microglobulin, Tcr Alpha-Chain and Tcr Beta-Chain


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 CD1D-Lipid Complexed with Beta-2-Microglobulin, Tcr Alpha-Chain and Tcr Beta-Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:67.2 occ:1.00 O A:VAL158 2.2 53.3 1.0 N A:LEU162 2.4 48.2 1.0 O A:GLN159 2.5 51.6 1.0 CB A:LEU162 2.7 63.7 1.0 C A:GLN159 2.7 56.5 1.0 CA A:LEU162 2.9 47.9 1.0 CA A:GLN159 2.9 55.1 1.0 CD1 A:LEU162 2.9 64.2 1.0 N A:ASN163 3.0 54.9 1.0 C A:VAL158 3.2 54.6 1.0 CG A:LEU162 3.3 60.5 1.0 C A:LEU162 3.4 55.1 1.0 N A:GLN159 3.5 63.8 1.0 N A:LEU161 3.5 55.3 1.0 C A:LEU161 3.5 52.9 1.0 N A:TRP160 3.5 52.9 1.0 C A:TRP160 3.9 55.1 1.0 CA A:LEU161 4.0 52.8 1.0 CD2 A:LEU162 4.1 64.1 1.0 CA A:TRP160 4.3 59.9 1.0 CB A:GLN159 4.3 53.2 1.0 CA A:ASN163 4.3 58.5 1.0 CB A:ASN163 4.5 62.5 1.0 CA A:VAL158 4.6 50.5 1.0 O A:LEU161 4.6 51.8 1.0 CB A:LEU161 4.6 53.5 1.0 O A:TRP160 4.6 51.8 1.0 CG1 A:VAL158 4.7 50.0 1.0 O A:LEU162 4.7 55.5 1.0 CG A:ASN163 4.7 76.7 1.0 O A:THR157 4.9 56.3 1.0 OD1 A:ASN163 5.0 66.4 1.0

K.T.O.Chan Yew Poa, J.Le Nours, J.Rossjohn, D.G.Godfrey, C.D.S.Almeida, D.G.Pellicci, B.Moody. Semi-Invariant Human Type II Natural Killer T Cells Recognise CD1D Independently of Bound Lipids. To Be Published.