Sodium in PDB 6mj4: Crystal Structure of MCD1D/Inktcr Ternary Complex Bound to Glycolipid (Xxw)

The structure of Crystal Structure of MCD1D/Inktcr Ternary Complex Bound to Glycolipid (Xxw), PDB code: 6mj4 was solved by D.M.Zajonc, A.Bitra, J.Janssens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.10 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.948, 190.723, 151.145, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.4

The binding sites of Sodium atom in the Crystal Structure of MCD1D/Inktcr Ternary Complex Bound to Glycolipid (Xxw) (pdb code 6mj4). 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 MCD1D/Inktcr Ternary Complex Bound to Glycolipid (Xxw), PDB code: 6mj4:

Sodium binding site 1 out of 1 in the Crystal Structure of MCD1D/Inktcr Ternary Complex Bound to Glycolipid (Xxw)


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 MCD1D/Inktcr Ternary Complex Bound to Glycolipid (Xxw) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:43.3 occ:1.00 OE1 D:GLU131 2.3 32.4 1.0 O D:THR139 3.1 25.3 1.0 N D:SER128 3.2 33.8 1.0 CD D:GLU131 3.4 33.5 1.0 CA D:PRO127 3.6 31.4 1.0 N D:THR139 3.7 25.9 1.0 CG C:LEU126 3.8 32.9 1.0 CD2 C:LEU126 3.8 32.5 1.0 CB D:THR139 3.8 26.2 1.0 CD1 C:LEU126 3.8 32.6 1.0 CB D:GLU131 3.9 32.9 1.0 CB D:SER128 3.9 36.4 1.0 C D:PRO127 3.9 32.5 1.0 C D:THR139 3.9 25.5 1.0 CA D:THR139 4.0 26.3 1.0 CD2 C:LEU138 4.0 29.2 1.0 CB D:PRO127 4.1 31.6 1.0 CA D:SER128 4.1 35.1 1.0 CG D:GLU131 4.2 32.9 1.0 OE2 D:GLU131 4.3 34.5 1.0 OG1 D:THR139 4.4 26.7 1.0 O D:SER128 4.5 33.2 1.0 CB C:TYR124 4.8 32.9 1.0 N D:PRO127 4.8 30.8 1.0 C D:SER128 4.9 34.2 1.0 C D:ALA138 4.9 25.9 1.0 CD2 C:TYR124 4.9 33.4 1.0 CG2 D:THR139 5.0 26.3 1.0

J.Janssens, A.Bitra, J.Wang, T.Decruy, K.Venken, J.Van Der Eycken, D.Elewaut, D.M.Zajonc, S.Van Calenbergh. 4"-O-Alkylated Alpha-Galactosylceramide Analogues As Inkt-Cell Antigens: Synthetic, Biological, and Structural Studies. Chemmedchem V. 14 147 2019.
ISSN: ESSN 1860-7187
PubMed: 30556652
DOI: 10.1002/CMDC.201800649