Sodium in PDB 6miv: Crystal Structure of the MCD1D/Xxq (JJ300)/Inktcr Ternary Complex

The structure of Crystal Structure of the MCD1D/Xxq (JJ300)/Inktcr Ternary Complex, PDB code: 6miv 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)	41.54 / 2.05
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.976, 191.441, 151.369, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.9

The binding sites of Sodium atom in the Crystal Structure of the MCD1D/Xxq (JJ300)/Inktcr Ternary Complex (pdb code 6miv). 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/Xxq (JJ300)/Inktcr Ternary Complex, PDB code: 6miv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the MCD1D/Xxq (JJ300)/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/Xxq (JJ300)/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:51.4 occ:1.00 O C:ASP120 2.8 46.8 1.0 OH C:TYR124 2.8 36.0 1.0 OD2 C:ASP141 2.8 43.6 1.0 CG2 D:THR135 3.5 44.6 1.0 CB C:ALA122 3.5 43.9 1.0 CG C:ASP141 3.6 47.1 1.0 CZ C:TYR124 3.7 39.9 1.0 CB C:ASP141 3.7 43.9 1.0 CE2 C:TYR124 3.7 41.6 1.0 C C:ASP120 4.0 46.7 1.0 CG C:ASP120 4.0 50.0 1.0 CD2 D:HIS134 4.0 51.6 1.0 CB C:ASP120 4.1 48.2 1.0 OD2 C:ASP120 4.2 49.9 1.0 OD1 C:ASP120 4.2 51.9 1.0 O C:HOH412 4.4 42.3 1.0 CG2 C:THR140 4.4 37.3 1.0 N C:ALA122 4.4 46.9 1.0 O C:THR140 4.4 42.9 1.0 CA C:ALA122 4.6 44.7 1.0 NH1 D:ARG192 4.7 36.4 1.0 CA C:ASP120 4.7 47.0 1.0 NE2 D:HIS134 4.7 51.2 1.0 OD1 C:ASP141 4.7 47.1 1.0 C C:PRO121 4.7 48.2 1.0 C C:THR140 5.0 39.0 1.0 CE1 C:TYR124 5.0 39.6 1.0 CB D:THR135 5.0 43.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the MCD1D/Xxq (JJ300)/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/Xxq (JJ300)/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:41.1 occ:1.00 O D:GLY42 2.7 28.0 1.0 O D:ARG36 2.8 22.8 1.0 NE D:ARG44 3.0 36.3 1.0 N D:ASP38 3.2 32.5 1.0 OD2 D:ASP38 3.3 40.6 1.0 NH2 D:ARG44 3.5 40.0 1.0 CA D:GLN37 3.5 28.4 1.0 CB D:HIS41 3.6 42.4 1.0 C D:ARG36 3.6 24.4 1.0 CZ D:ARG44 3.7 39.8 1.0 C D:GLY42 3.8 30.7 1.0 C D:GLN37 3.8 29.4 1.0 CG D:ARG44 3.9 31.2 1.0 N D:ARG44 3.9 26.6 1.0 N D:GLN37 3.9 26.2 1.0 CD D:ARG44 3.9 33.5 1.0 CB D:ASP38 4.1 38.8 1.0 CB D:ARG44 4.1 30.0 1.0 CG D:ASP38 4.1 40.0 1.0 CA D:LEU43 4.2 28.4 1.0 CA D:ASP38 4.2 37.1 1.0 O D:ASP38 4.2 36.0 1.0 C D:LEU43 4.3 28.0 1.0 N D:LEU43 4.4 28.6 1.0 O D:HIS41 4.4 31.4 1.0 C D:HIS41 4.4 32.8 1.0 CG D:HIS41 4.5 47.8 1.0 CG D:ARG36 4.5 26.5 1.0 CA D:HIS41 4.7 37.5 1.0 CA D:ARG44 4.7 27.8 1.0 C D:ASP38 4.7 39.4 1.0 N D:GLY42 4.8 30.4 1.0 CB D:GLN37 4.8 28.1 1.0 CA D:ARG36 4.9 25.4 1.0 CA D:GLY42 4.9 31.6 1.0 NH1 D:ARG44 5.0 40.3 1.0 O D:GLN37 5.0 27.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the MCD1D/Xxq (JJ300)/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/Xxq (JJ300)/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:70.9 occ:1.00 OD2 D:ASP218 2.3 50.5 1.0 O D:HOH522 2.8 41.0 1.0 CG D:ASP218 3.1 55.5 1.0 O D:VAL12 3.1 34.6 1.0 O D:HOH482 3.1 50.0 1.0 OD1 D:ASP218 3.1 60.7 1.0 O D:HOH419 3.2 52.7 1.0 NZ D:LYS11 3.6 43.3 1.0 CA D:ALA13 3.9 32.7 1.0 CE D:LYS11 4.0 41.9 1.0 C D:VAL12 4.1 31.4 1.0 N D:SER215 4.3 37.3 1.0 OG D:SER215 4.4 51.6 1.0 N D:ALA13 4.5 32.2 1.0 CB D:ASP218 4.5 51.6 1.0 CA D:LEU214 4.6 33.7 1.0 O D:GLY213 4.7 31.9 1.0 CB D:ALA13 4.7 32.5 1.0 CD1 D:LEU114 4.7 40.6 1.0 N D:VAL14 4.7 33.4 1.0 C D:ALA13 4.7 32.0 1.0 CB D:SER215 4.8 44.5 1.0 C D:LEU214 4.9 35.8 1.0 CD D:LYS11 5.0 39.6 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