Sodium in PDB 6mji: Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex

The structure of Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex, PDB code: 6mji 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)	45.61 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.216, 191.161, 151.095, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.7

The binding sites of Sodium atom in the Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex (pdb code 6mji). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex, PDB code: 6mji:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex


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 the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:99.0 occ:1.00 O C:ASP160 2.5 55.4 1.0 OD1 D:ASP170 3.1 47.1 1.0 C C:ASP160 3.2 54.7 1.0 O C:LYS161 3.4 50.2 1.0 CG D:ASP170 3.7 44.9 1.0 CB C:CYS162 3.7 56.0 1.0 NH2 D:ARG190 3.7 52.4 1.0 N C:ASP160 3.7 50.4 1.0 CD D:PRO171 3.7 52.0 1.0 C C:LYS161 3.8 51.8 1.0 CA D:ASP170 3.8 44.6 1.0 CA C:ASP160 3.8 55.0 1.0 CB D:ASP170 3.9 44.3 1.0 O C:HOH479 4.0 51.0 1.0 CB C:ASP160 4.0 59.5 1.0 OG1 C:THR159 4.0 46.5 1.0 CB C:THR159 4.0 46.3 1.0 N C:LYS161 4.1 53.6 1.0 N C:CYS162 4.3 50.8 1.0 CA C:LYS161 4.3 53.3 1.0 C C:THR159 4.4 48.1 1.0 CA C:CYS162 4.5 51.5 1.0 CZ D:ARG190 4.5 51.5 1.0 NH1 D:ARG190 4.6 52.7 1.0 OD2 D:ASP170 4.6 46.1 1.0 N D:ASP170 4.6 42.1 1.0 SG C:CYS162 4.7 63.7 1.0 N D:PRO171 4.7 50.6 1.0 CA C:THR159 4.8 46.5 1.0 C D:ASP170 4.8 46.3 1.0 CG D:PRO171 4.9 52.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the MCD1D/Xxs (JJ304) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na605 b:64.9 occ:1.00 OE1 D:GLU131 2.3 46.6 1.0 O D:THR139 3.1 35.5 1.0 N D:SER128 3.2 47.5 1.0 CD D:GLU131 3.4 46.6 1.0 CA D:PRO127 3.7 43.5 1.0 CD1 C:LEU126 3.7 44.4 1.0 CB D:THR139 3.8 36.4 1.0 CG C:LEU126 3.8 44.7 1.0 N D:THR139 3.8 36.8 1.0 CD2 C:LEU126 3.8 45.3 1.0 CB D:GLU131 3.9 46.4 1.0 CB D:SER128 3.9 51.1 1.0 CD2 C:LEU138 4.0 43.5 1.0 C D:THR139 4.0 36.2 1.0 C D:PRO127 4.0 44.6 1.0 CA D:THR139 4.0 37.4 1.0 CG D:GLU131 4.2 46.8 1.0 CA D:SER128 4.2 49.2 1.0 CB D:PRO127 4.2 43.3 1.0 OE2 D:GLU131 4.3 45.6 1.0 OG1 D:THR139 4.5 37.3 1.0 O D:SER128 4.6 46.5 1.0 CB C:TYR124 4.6 43.9 1.0 CG2 D:THR139 4.8 37.5 1.0 N D:PRO127 4.9 42.2 1.0 CD2 C:TYR124 4.9 44.6 1.0 C D:SER128 4.9 48.3 1.0 CG C:TYR124 5.0 44.0 1.0 C D:ALA138 5.0 37.0 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