Sodium in PDB 6v7z: Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D22

The structure of Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D22, PDB code: 6v7z was solved by A.Shahine, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.31 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.717, 121.933, 172.136, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 25.2

The structure of Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D22 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D22 (pdb code 6v7z). 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 Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D22, PDB code: 6v7z:

Sodium binding site 1 out of 1 in the Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D22


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D22 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:68.4 occ:1.00 NH2 D:ARG45 3.5 0.5 1.0 N D:LYS48 3.8 0.5 1.0 NH1 D:ARG45 3.9 0.1 1.0 CZ D:ARG45 4.2 0.1 1.0 CA D:GLU47 4.2 0.3 1.0 CB D:GLU47 4.3 1.0 1.0 C D:GLU47 4.5 0.1 1.0 CA D:LYS48 4.7 0.4 1.0 CG D:GLU47 4.9 0.9 1.0

A.Shahine, J.Rossjohn. A Single-Domain Bispecific Antibody Targeting CD1D and the Nkt T-Cell Receptor Induces A Potent Antitumor Response. Nat Cancer 2020.
ISSN: ESSN 2662-1347
DOI: 10.1038/S43018-020-00111-6