Sodium in PDB 6miy: Crystal Structure of the MCD1D/Xxa (JJ239)/Inktcr Ternary Complex

The structure of Crystal Structure of the MCD1D/Xxa (JJ239)/Inktcr Ternary Complex, PDB code: 6miy 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)	47.42 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.865, 192.477, 150.418, 90.00, 90.79, 90.00
R / Rfree (%)	19.2 / 24.7

The structure of Crystal Structure of the MCD1D/Xxa (JJ239)/Inktcr Ternary Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the MCD1D/Xxa (JJ239)/Inktcr Ternary Complex (pdb code 6miy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the MCD1D/Xxa (JJ239)/Inktcr Ternary Complex, PDB code: 6miy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the MCD1D/Xxa (JJ239)/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/Xxa (JJ239)/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:75.5 occ:1.00 OH C:TYR124 2.8 55.3 1.0 O C:ASP120 2.8 72.2 1.0 CG2 D:THR135 3.5 68.5 1.0 OD2 C:ASP141 3.6 72.4 1.0 CG C:ASP141 3.7 71.6 1.0 CB C:ALA122 3.8 62.4 1.0 OD2 C:ASP120 3.8 79.4 1.0 CZ C:TYR124 3.8 56.5 1.0 CB C:ASP141 3.8 69.0 1.0 CG C:ASP120 3.9 80.2 1.0 CE2 C:TYR124 3.9 57.8 1.0 C C:ASP120 4.0 73.3 1.0 CD2 D:HIS134 4.0 74.4 1.0 CB C:ASP120 4.1 78.3 1.0 OD1 C:ASP120 4.4 81.3 1.0 OD1 C:ASP141 4.4 73.4 1.0 N C:ALA122 4.6 66.0 1.0 CG2 C:THR140 4.6 63.4 1.0 NH1 D:ARG192 4.7 59.4 1.0 CA C:ASP120 4.7 77.4 1.0 O C:THR140 4.7 63.3 1.0 NE2 D:HIS134 4.7 75.4 1.0 C C:PRO121 4.8 68.1 1.0 CA C:ALA122 4.8 63.5 1.0 CB D:THR135 5.0 68.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the MCD1D/Xxa (JJ239)/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/Xxa (JJ239)/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:71.6 occ:1.00 O D:VAL163 2.9 52.7 1.0 N D:TRP156 3.5 43.4 1.0 OE2 D:GLU162 3.6 60.1 1.0 ND1 D:HIS164 3.7 56.0 1.0 CG D:GLU162 3.9 56.4 1.0 CE1 D:HIS164 3.9 57.3 1.0 CA D:SER155 3.9 45.3 1.0 C D:VAL163 4.0 53.3 1.0 CB D:SER155 4.1 45.4 1.0 O D:TRP156 4.1 45.8 1.0 CD D:GLU162 4.2 57.5 1.0 C D:SER155 4.3 44.2 1.0 CA D:TRP156 4.4 44.3 1.0 CG D:HIS164 4.5 55.9 1.0 CB D:TRP156 4.5 44.2 1.0 CA D:HIS164 4.5 52.7 1.0 N D:HIS164 4.6 53.9 1.0 NE2 D:HIS164 4.7 57.9 1.0 N D:VAL163 4.7 53.0 1.0 CG1 D:VAL167 4.8 51.1 1.0 C D:TRP156 4.8 46.0 1.0 O D:LEU154 4.9 48.4 1.0 CD2 D:HIS164 5.0 57.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the MCD1D/Xxa (JJ239)/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/Xxa (JJ239)/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Na302 b:63.7 occ:1.00 OG1 G:THR108 2.6 46.0 1.0 O G:GLN22 2.7 50.2 1.0 NE2 G:GLN6 3.1 47.6 1.0 O G:SER7 3.3 46.7 1.0 CB G:THR108 3.4 46.0 1.0 N G:GLN22 3.6 53.7 1.0 CB G:LEU21 3.7 51.1 1.0 C G:GLN22 3.7 53.3 1.0 CB G:GLN6 3.8 49.3 1.0 CH2 G:TRP35 3.8 41.1 1.0 N G:SER7 3.8 48.1 1.0 CG G:GLN6 3.9 49.8 1.0 CG G:LEU21 3.9 52.0 1.0 CZ3 G:TRP35 4.0 41.1 1.0 CD G:GLN6 4.0 49.7 1.0 C G:LEU21 4.0 51.2 1.0 C G:SER7 4.0 47.4 1.0 CA G:LEU21 4.1 50.6 1.0 CG2 G:THR108 4.1 46.3 1.0 CA G:GLN22 4.3 55.4 1.0 CD2 G:LEU21 4.3 52.1 1.0 CA G:GLN6 4.3 48.1 1.0 C G:GLN6 4.4 47.4 1.0 O G:PRO8 4.5 51.3 1.0 CA G:SER7 4.6 47.7 1.0 CA G:THR108 4.7 45.8 1.0 O G:TYR88 4.7 41.7 1.0 O G:LEU21 4.7 52.7 1.0 N G:PRO8 4.8 48.0 1.0 N G:THR108 4.8 45.4 1.0 N G:CYS23 4.8 53.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the MCD1D/Xxa (JJ239)/Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the MCD1D/Xxa (JJ239)/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:54.7 occ:1.00 O H:GLY42 2.6 54.6 1.0 O H:ARG36 2.8 42.6 1.0 NE H:ARG44 3.2 52.8 1.0 N H:ASP38 3.4 50.7 1.0 OD2 H:ASP38 3.4 61.4 1.0 NH2 H:ARG44 3.7 53.5 1.0 C H:ARG36 3.7 44.0 1.0 CB H:HIS41 3.7 61.0 1.0 CA H:GLN37 3.8 45.4 1.0 C H:GLY42 3.8 52.9 1.0 CZ H:ARG44 3.8 53.5 1.0 CG H:ARG44 3.8 49.0 1.0 N H:ARG44 3.8 46.7 1.0 C H:GLN37 3.9 47.2 1.0 CB H:ASP38 4.0 56.7 1.0 CB H:ARG44 4.0 47.1 1.0 CD H:ARG44 4.0 50.8 1.0 CG H:ASP38 4.0 59.0 1.0 N H:GLN37 4.1 45.2 1.0 CA H:ASP38 4.2 54.1 1.0 CA H:LEU43 4.3 49.6 1.0 O H:ASP38 4.3 55.9 1.0 C H:LEU43 4.3 47.6 1.0 CG H:ARG36 4.5 44.0 1.0 N H:LEU43 4.5 50.5 1.0 C H:HIS41 4.5 55.7 1.0 CA H:ARG44 4.6 46.0 1.0 O H:HIS41 4.7 54.2 1.0 CG H:HIS41 4.7 64.3 1.0 N H:GLY42 4.7 53.6 1.0 CA H:HIS41 4.8 59.1 1.0 C H:ASP38 4.8 55.6 1.0 CA H:GLY42 4.9 53.6 1.0 CA H:ARG36 4.9 44.0 1.0 O H:GLN37 4.9 46.6 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