Sodium in PDB 6cx5: Structure of Alpha-Gsa[8,8P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr

The structure of Structure of Alpha-Gsa[8,8P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr, PDB code: 6cx5 was solved by J.Wang, D.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.769, 190.790, 150.879, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.8

The binding sites of Sodium atom in the Structure of Alpha-Gsa[8,8P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr (pdb code 6cx5). 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 Alpha-Gsa[8,8P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr, PDB code: 6cx5:

Sodium binding site 1 out of 1 in the Structure of Alpha-Gsa[8,8P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Alpha-Gsa[8,8P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:34.5 occ:1.00 OD1 A:ASP80 2.6 26.5 1.0 O C:LEU99 2.8 22.2 1.0 CD A:ARG79 3.2 31.3 1.0 NH1 A:ARG79 3.3 32.2 1.0 CB C:LEU99 3.6 24.3 1.0 N A:ASP80 3.7 28.2 1.0 CA A:ASP80 3.7 27.9 1.0 NH1 C:ARG95 3.7 27.6 1.0 C C:LEU99 3.7 24.0 1.0 O A:ARG79 3.7 26.0 1.0 C A:ARG79 3.7 27.4 1.0 CG A:ASP80 3.7 29.2 1.0 NE C:ARG95 3.9 26.3 1.0 CB A:GLU83 3.9 31.1 1.0 CZ C:ARG95 4.0 27.3 1.0 NE A:ARG79 4.1 32.8 1.0 CA C:LEU99 4.1 24.1 1.0 CZ A:ARG79 4.1 33.0 1.0 CG A:GLU83 4.1 32.0 1.0 CB A:ARG79 4.2 27.9 1.0 CG A:ARG79 4.2 29.1 1.0 CB A:ASP80 4.3 28.1 1.0 CA A:ARG79 4.6 27.4 1.0 CG C:ARG95 4.6 27.0 1.0 CG C:LEU99 4.7 25.7 1.0 OD2 A:ASP80 4.8 28.0 1.0 CD1 C:LEU99 4.8 26.5 1.0 C A:ASP80 4.8 27.5 1.0 CD C:ARG95 4.9 26.5 1.0 N C:GLY100 4.9 24.2 1.0 CD2 C:LEU99 4.9 26.3 1.0 O A:SER76 5.0 31.2 1.0

J.Wang, J.Guillaume, J.Janssens, S.G.Remesh, G.Ying, A.Bitra, S.Van Calenbergh, D.M.Zajonc. A Molecular Switch in Mouse CD1D Modulates Natural Killer T Cell Activation By Alpha-Galactosylsphingamides. J.Biol.Chem. V. 294 14345 2019.
ISSN: ESSN 1083-351X
PubMed: 31391251
DOI: 10.1074/JBC.RA119.009963