Sodium in PDB 6mja: Crystal Structure of the MCD1D/Xxo (JJ294) /Inktcr Ternary Complex

The structure of Crystal Structure of the MCD1D/Xxo (JJ294) /Inktcr Ternary Complex, PDB code: 6mja 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)	45.68 / 2.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.037, 191.486, 151.131, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.7

The binding sites of Sodium atom in the Crystal Structure of the MCD1D/Xxo (JJ294) /Inktcr Ternary Complex (pdb code 6mja). 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/Xxo (JJ294) /Inktcr Ternary Complex, PDB code: 6mja:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the MCD1D/Xxo (JJ294) /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/Xxo (JJ294) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:55.5 occ:1.00 O D:HOH785 2.5 41.7 1.0 O C:ARG95 2.9 31.3 1.0 CA C:GLY100 3.6 35.8 1.0 N C:ARG95 3.6 32.4 1.0 CE1 C:HIS32 3.6 29.7 1.0 CA C:GLY93 3.7 30.6 1.0 O C:SER97 3.8 31.6 1.0 N C:ASP94 3.8 31.4 1.0 C C:GLY100 3.9 36.7 1.0 C C:ARG95 3.9 31.6 1.0 C C:GLY93 3.9 31.1 1.0 CB D:TYR98 4.0 37.1 1.0 O C:ARG101 4.1 32.6 1.0 CD2 C:LEU102 4.1 31.9 1.0 CA C:ARG95 4.2 32.2 1.0 N C:ARG101 4.3 36.1 1.0 O C:GLY100 4.3 37.5 1.0 CB C:ARG95 4.3 33.6 1.0 N C:GLY100 4.4 35.2 1.0 O D:TYR98 4.4 36.7 1.0 NE2 C:HIS32 4.5 30.5 1.0 C C:ARG101 4.5 34.5 1.0 ND1 C:HIS32 4.6 29.3 1.0 OD1 C:ASP94 4.6 34.2 1.0 C C:ASP94 4.7 32.6 1.0 CA D:TYR98 4.7 36.8 1.0 O C:GLY93 4.8 30.8 1.0 CA C:ASP94 4.9 32.2 1.0 C C:SER97 4.9 31.4 1.0 CG C:LEU102 5.0 32.6 1.0 CA C:ARG101 5.0 35.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the MCD1D/Xxo (JJ294) /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/Xxo (JJ294) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:90.7 occ:1.00 O A:GLU92 2.2 61.0 1.0 O A:VAL85 2.6 36.6 1.0 C A:GLU92 3.2 61.4 1.0 N A:SER89 3.2 53.7 1.0 CA A:SER89 3.4 56.0 1.0 N A:GLU92 3.5 62.3 1.0 C A:MET88 3.5 49.9 1.0 C A:VAL85 3.6 35.3 1.0 CA A:GLU92 3.7 63.4 1.0 CG1 A:VAL85 3.8 34.7 1.0 O A:MET88 3.9 51.3 1.0 CA A:VAL85 3.9 34.2 1.0 CB A:MET88 3.9 46.8 1.0 CB A:SER89 4.0 56.2 1.0 CB A:GLU92 4.0 65.9 1.0 CA A:MET88 4.2 47.2 1.0 OG A:SER89 4.2 58.8 1.0 N A:LYS91 4.3 63.9 1.0 N A:ASP93 4.3 60.7 1.0 N A:MET88 4.4 43.8 1.0 CB A:VAL85 4.4 34.5 1.0 CA A:PRO90 4.4 61.2 1.0 C A:PRO90 4.5 62.0 1.0 C A:LYS91 4.6 63.8 1.0 C A:SER89 4.6 58.2 1.0 CA A:ASP93 4.7 59.6 1.0 N A:LYS86 4.8 35.2 1.0 CA A:LYS91 5.0 64.5 1.0 N A:PRO90 5.0 61.0 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