Sodium in PDB 6mjq: Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex

The structure of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex, PDB code: 6mjq 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)	49.75 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.967, 191.858, 150.957, 90.00, 90.02, 90.00
R / Rfree (%)	21.5 / 25.8

The structure of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex (pdb code 6mjq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex, PDB code: 6mjq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the MCD1D/Xxp (JJ295) /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/Xxp (JJ295) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:45.0 occ:1.00 O D:GLY42 2.8 53.5 1.0 O D:ARG36 2.9 39.6 1.0 NE D:ARG44 3.4 48.2 1.0 OD2 D:ASP38 3.4 52.7 1.0 N D:ASP38 3.6 48.0 1.0 NH2 D:ARG44 3.7 48.3 1.0 C D:ARG36 3.8 39.8 1.0 CB D:HIS41 3.9 57.0 1.0 CG D:ASP38 3.9 52.0 1.0 CA D:GLN37 3.9 42.9 1.0 CB D:ASP38 4.0 51.2 1.0 CZ D:ARG44 4.0 48.5 1.0 C D:GLY42 4.0 52.5 1.0 C D:GLN37 4.0 44.9 1.0 N D:ARG44 4.1 47.0 1.0 CB D:ARG44 4.2 46.7 1.0 N D:GLN37 4.2 41.6 1.0 CG D:ARG44 4.2 47.4 1.0 CG D:ARG36 4.2 38.1 1.0 CA D:ASP38 4.3 50.3 1.0 CD D:ARG44 4.4 47.9 1.0 CA D:LEU43 4.6 49.7 1.0 C D:LEU43 4.7 48.3 1.0 CG D:HIS41 4.7 57.8 1.0 O D:ASP38 4.7 51.3 1.0 N D:LEU43 4.8 51.0 1.0 C D:HIS41 4.8 54.9 1.0 CA D:ARG44 4.8 46.4 1.0 N D:GLY42 4.8 53.7 1.0 OD1 D:ASP38 4.9 52.6 1.0 CA D:ARG36 4.9 38.5 1.0 CA D:HIS41 5.0 56.0 1.0 O D:GLN37 5.0 44.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the MCD1D/Xxp (JJ295) /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/Xxp (JJ295) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:57.2 occ:1.00 O H:THR20 3.6 51.9 1.0 CE H:LYS11 3.9 49.7 1.0 NZ H:LYS11 3.9 50.2 1.0 CD H:PRO8 4.1 53.5 1.0 CD H:LYS11 4.2 49.2 1.0 CG H:PRO8 4.2 53.3 1.0 N H:THR20 4.2 52.5 1.0 C H:THR20 4.5 52.2 1.0 CA H:THR20 4.8 52.6 1.0 CG H:LYS11 4.8 48.9 1.0 CG1 H:VAL19 4.9 52.9 1.0 CB H:THR20 5.0 53.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:44.4 occ:1.00 O H:GLY42 2.8 52.2 1.0 O H:ARG36 2.9 39.1 1.0 NE H:ARG44 3.4 46.7 1.0 OD2 H:ASP38 3.4 51.4 1.0 N H:ASP38 3.6 46.9 1.0 NH2 H:ARG44 3.7 46.7 1.0 C H:ARG36 3.8 39.4 1.0 CB H:HIS41 3.9 55.6 1.0 CG H:ASP38 3.9 50.8 1.0 CB H:ASP38 4.0 50.1 1.0 CA H:GLN37 4.0 41.7 1.0 CZ H:ARG44 4.0 46.9 1.0 C H:GLN37 4.0 43.6 1.0 C H:GLY42 4.0 51.0 1.0 N H:ARG44 4.1 45.7 1.0 CB H:ARG44 4.2 45.2 1.0 N H:GLN37 4.2 40.8 1.0 CG H:ARG36 4.2 38.2 1.0 CG H:ARG44 4.2 45.9 1.0 CA H:ASP38 4.3 49.2 1.0 CD H:ARG44 4.4 46.5 1.0 CA H:LEU43 4.6 48.1 1.0 C H:LEU43 4.7 46.8 1.0 O H:ASP38 4.7 50.6 1.0 CG H:HIS41 4.7 56.4 1.0 N H:LEU43 4.8 49.3 1.0 C H:HIS41 4.8 53.3 1.0 CA H:ARG44 4.8 44.9 1.0 OD1 H:ASP38 4.9 51.5 1.0 N H:GLY42 4.9 52.0 1.0 CA H:ARG36 4.9 38.4 1.0 CA H:HIS41 5.0 54.6 1.0 CD H:ARG36 5.0 38.2 1.0 O H:GLN37 5.0 43.2 1.0 NE H:ARG36 5.0 38.1 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