Sodium in PDB 6mj6: Crystal Structure of the MCD1D/Xxx (JJ166) /Inktcr Ternary Complex

The structure of Crystal Structure of the MCD1D/Xxx (JJ166) /Inktcr Ternary Complex, PDB code: 6mj6 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)	47.80 / 2.45
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.357, 191.020, 151.348, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.4

The structure of Crystal Structure of the MCD1D/Xxx (JJ166) /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/Xxx (JJ166) /Inktcr Ternary Complex (pdb code 6mj6). 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/Xxx (JJ166) /Inktcr Ternary Complex, PDB code: 6mj6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the MCD1D/Xxx (JJ166) /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/Xxx (JJ166) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:49.5 occ:1.00 OD1 A:ASP80 2.7 39.5 1.0 O C:LEU99 2.8 33.7 1.0 NE A:ARG79 3.0 36.2 1.0 NH2 A:ARG79 3.4 34.1 1.0 CG A:GLU83 3.6 36.8 1.0 CZ A:ARG79 3.6 36.1 1.0 O A:ARG79 3.7 34.6 1.0 C A:ARG79 3.7 33.4 1.0 N A:ASP80 3.7 32.9 1.0 CA A:ASP80 3.7 35.9 1.0 NH1 C:ARG95 3.7 34.6 1.0 CB C:LEU99 3.7 35.0 1.0 C C:LEU99 3.8 34.6 1.0 CG A:ASP80 3.8 41.5 1.0 CG A:ARG79 3.9 34.5 1.0 NE C:ARG95 3.9 33.3 1.0 CB A:ARG79 4.0 34.3 1.0 CD A:ARG79 4.0 35.6 1.0 O C:HOH418 4.0 42.9 1.0 CB A:GLU83 4.1 35.7 1.0 CZ C:ARG95 4.1 35.4 1.0 CA C:LEU99 4.2 35.0 1.0 CB A:ASP80 4.3 38.3 1.0 CA A:ARG79 4.5 34.0 1.0 CG C:ARG95 4.7 33.5 1.0 CG C:LEU99 4.7 35.6 1.0 OD2 A:ASP80 4.8 44.5 1.0 CD C:ARG95 4.9 33.5 1.0 C A:ASP80 4.9 35.3 1.0 CD1 C:LEU99 4.9 35.7 1.0 N C:GLY100 4.9 35.9 1.0 CD2 C:LEU99 4.9 35.4 1.0 O A:SER76 4.9 34.0 1.0 NH1 A:ARG79 5.0 33.6 1.0 CD A:GLU83 5.0 35.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the MCD1D/Xxx (JJ166) /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/Xxx (JJ166) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na605 b:54.7 occ:1.00 O D:HOH736 2.6 36.8 1.0 N D:ASN30 3.4 35.4 1.0 CG D:ASN30 3.4 35.2 1.0 OD1 D:ASN30 3.5 33.1 1.0 CB D:ASP95 3.6 38.5 1.0 CA D:ASP95 3.6 37.4 1.0 CB D:ASN30 3.7 35.4 1.0 ND2 D:ASN30 3.8 33.5 1.0 O D:ASN28 3.9 41.5 1.0 OE1 D:GLU96 4.1 42.0 1.0 CA D:ASN30 4.2 34.3 1.0 CA D:HIS29 4.2 39.3 1.0 C D:HIS29 4.3 38.8 1.0 O D:HOH783 4.3 29.7 1.0 C D:ASP95 4.3 37.0 1.0 N D:GLU96 4.4 38.0 1.0 O D:GLY94 4.5 36.1 1.0 N D:ASP95 4.8 36.3 1.0 C D:ASN28 4.9 43.9 1.0 N D:HIS29 5.0 40.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the MCD1D/Xxx (JJ166) /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/Xxx (JJ166) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:57.8 occ:1.00 OG A:SER28 2.7 39.4 1.0 O A:HOH416 2.8 36.0 1.0 CE3 A:TRP40 3.3 33.0 1.0 CG2 A:THR26 3.5 38.4 1.0 CB A:SER28 3.6 35.8 1.0 CZ3 A:TRP40 3.8 34.2 1.0 CD A:ARG74 3.8 32.3 1.0 CD2 A:TRP40 3.9 34.4 1.0 N A:SER28 4.1 34.5 1.0 C A:ASP27 4.3 33.6 1.0 CG A:ARG74 4.3 32.0 1.0 O A:TRP40 4.3 36.1 1.0 CG A:GLN14 4.3 32.6 1.0 O A:THR26 4.4 35.2 1.0 CG A:TRP40 4.4 35.7 1.0 CCF A:JTM309 4.5 49.2 1.0 CA A:SER28 4.5 35.7 1.0 C A:THR26 4.5 35.0 1.0 CB A:TRP40 4.5 35.6 1.0 CB A:THR26 4.5 37.9 1.0 CH2 A:TRP40 4.6 34.9 1.0 N A:ASP27 4.6 35.2 1.0 CCG A:JTM309 4.6 47.9 1.0 CA A:ASP27 4.7 35.1 1.0 O A:ASP27 4.7 31.4 1.0 CE2 A:TRP40 4.7 35.2 1.0 CD A:GLN14 4.8 33.8 1.0 NH1 A:ARG74 4.8 31.2 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