Sodium in PDB 6cxe: Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr

The structure of Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr, PDB code: 6cxe was solved by J.Wang, D.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.05
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.437, 189.071, 150.908, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.8

The binding sites of Sodium atom in the Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr (pdb code 6cxe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr, PDB code: 6cxe:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:53.4 occ:1.00 O D:HOH430 2.6 41.5 1.0 O C:LEU99 2.8 33.6 1.0 NE C:ARG101 3.0 41.2 1.0 C C:LEU99 3.5 34.9 1.0 CD C:ARG101 3.6 37.6 1.0 O C:HOH463 3.7 37.1 1.0 CG A:GLU83 3.7 33.0 1.0 O C:GLY100 3.7 32.6 1.0 CD A:GLU83 3.7 33.2 1.0 OE2 A:GLU83 3.7 35.8 1.0 OH D:TYR50 3.7 36.2 1.0 CG C:ARG101 3.9 37.0 1.0 C C:GLY100 4.0 33.0 1.0 CZ C:ARG101 4.1 41.4 1.0 CA C:LEU99 4.1 35.4 1.0 NA A:NA307 4.2 46.5 1.0 N C:GLY100 4.3 32.6 1.0 NH2 C:ARG101 4.3 39.7 1.0 OE1 A:GLU83 4.3 35.1 1.0 NH2 A:ARG79 4.4 34.2 1.0 N C:ARG101 4.4 31.0 1.0 O C:ALA98 4.4 36.2 1.0 CA C:GLY100 4.5 32.6 1.0 CB A:GLU83 4.6 31.7 1.0 NE A:ARG79 4.6 34.5 1.0 O C:HOH432 4.6 29.7 1.0 CZ A:ARG79 4.7 35.4 1.0 OH D:TYR48 4.8 33.9 1.0 CA C:ARG101 4.9 32.4 1.0 CB C:ARG101 5.0 33.1 1.0

Sodium binding site 2 out of 4 in the Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:43.6 occ:1.00 O D:GLY42 2.7 35.7 1.0 O D:ARG36 2.8 31.4 1.0 NE D:ARG44 3.0 42.4 1.0 N D:ASP38 3.2 36.8 1.0 NH2 D:ARG44 3.4 44.4 1.0 OD2 D:ASP38 3.4 44.9 1.0 CB D:HIS41 3.6 46.7 1.0 CA D:GLN37 3.6 34.8 1.0 C D:ARG36 3.7 33.7 1.0 CZ D:ARG44 3.7 44.6 1.0 C D:GLY42 3.8 38.0 1.0 N D:ARG44 3.8 34.2 1.0 C D:GLN37 3.9 35.4 1.0 CG D:ARG44 3.9 37.4 1.0 CD D:ARG44 4.0 38.2 1.0 N D:GLN37 4.0 34.0 1.0 CA D:LEU43 4.1 36.7 1.0 CB D:ARG44 4.1 35.7 1.0 CB D:ASP38 4.2 43.0 1.0 CG D:ASP38 4.2 45.6 1.0 C D:LEU43 4.2 35.0 1.0 CA D:ASP38 4.2 40.5 1.0 O D:ASP38 4.2 43.5 1.0 N D:LEU43 4.3 36.6 1.0 O D:HIS41 4.4 37.3 1.0 C D:HIS41 4.4 38.6 1.0 CG D:HIS41 4.5 52.0 1.0 CA D:ARG44 4.6 34.8 1.0 CG D:ARG36 4.6 36.5 1.0 CA D:HIS41 4.7 42.1 1.0 C D:ASP38 4.7 43.9 1.0 N D:GLY42 4.8 35.0 1.0 CB D:GLN37 4.9 33.9 1.0 CA D:ARG36 4.9 33.5 1.0 CA D:GLY42 4.9 36.5 1.0 NH1 D:ARG44 5.0 46.2 1.0

Sodium binding site 3 out of 4 in the Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:64.1 occ:1.00 O D:HOH406 2.2 44.6 1.0 O D:GLY97 2.9 35.5 1.0 O D:HOH482 3.1 40.8 1.0 O D:THR99 3.3 34.8 1.0 O D:TYR98 3.4 35.5 1.0 OH D:TYR33 3.4 32.6 1.0 C D:TYR98 3.6 36.7 1.0 CG D:GLN100 3.7 33.8 1.0 O D:HOH410 3.8 35.1 1.0 C D:THR99 3.8 34.0 1.0 CA C:ALA98 3.9 33.7 1.0 CA D:TYR98 4.0 36.6 1.0 C D:GLY97 4.0 36.5 1.0 O D:ASP95 4.0 35.3 1.0 O D:HOH428 4.1 38.9 1.0 N D:THR99 4.1 34.8 1.0 CZ D:TYR33 4.2 32.8 1.0 CB C:ALA98 4.2 35.2 1.0 CE1 D:TYR33 4.3 33.0 1.0 CA D:GLY94 4.3 32.9 1.0 N D:GLN100 4.4 31.4 1.0 NE2 D:GLN100 4.4 32.9 1.0 N D:TYR98 4.5 35.9 1.0 N C:ALA98 4.6 33.4 1.0 CD D:GLN100 4.6 33.5 1.0 CA D:THR99 4.6 33.3 1.0 CA D:GLN100 4.6 32.7 1.0 C D:GLY94 4.8 35.6 1.0 CB D:GLN100 4.8 32.8 1.0 C C:ALA98 4.9 33.5 1.0 O C:ALA98 4.9 36.2 1.0 O C:SER97 5.0 33.8 1.0 N D:ASP95 5.0 34.8 1.0

Sodium binding site 4 out of 4 in the Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Alpha-Gsa[26,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:46.5 occ:1.00 OD1 A:ASP80 2.6 36.7 1.0 O C:LEU99 2.9 33.6 1.0 NE A:ARG79 3.0 34.5 1.0 NH2 A:ARG79 3.4 34.2 1.0 NH1 C:ARG95 3.6 32.4 1.0 CZ A:ARG79 3.6 35.4 1.0 N A:ASP80 3.6 33.3 1.0 CG A:GLU83 3.7 33.0 1.0 CB C:LEU99 3.7 35.3 1.0 CA A:ASP80 3.7 35.0 1.0 C A:ARG79 3.7 33.8 1.0 CG A:ASP80 3.8 39.8 1.0 C C:LEU99 3.8 34.9 1.0 O A:ARG79 3.8 34.0 1.0 NE C:ARG95 3.8 31.8 1.0 CZ C:ARG95 4.0 33.8 1.0 CB A:ARG79 4.0 35.5 1.0 CG A:ARG79 4.0 36.6 1.0 CD A:ARG79 4.1 36.3 1.0 CB A:GLU83 4.1 31.7 1.0 CA C:LEU99 4.2 35.4 1.0 NA C:NA301 4.2 53.4 1.0 CB A:ASP80 4.4 36.5 1.0 CA A:ARG79 4.5 34.6 1.0 CG C:ARG95 4.6 33.5 1.0 CG C:LEU99 4.7 36.1 1.0 OD2 A:ASP80 4.8 39.7 1.0 CD C:ARG95 4.8 31.9 1.0 CD1 C:LEU99 4.8 35.0 1.0 CD2 C:LEU99 4.9 36.2 1.0 O A:SER76 4.9 32.7 1.0 C A:ASP80 4.9 35.2 1.0 N C:GLY100 4.9 32.6 1.0 NH1 A:ARG79 4.9 30.7 1.0 CD A:GLU83 5.0 33.2 1.0 NH2 C:ARG95 5.0 33.4 1.0

J.Wang, J.Guillaume, J.Janssens, S.G.Remesh, G.Ying, A.Bitra, S.Van Calenbergh, D.M.Zajonc. A Molecular Switch in Mouse CD1D Modulates Natural Killer T Cell Activation By Alpha-Galactosylsphingamides. J.Biol.Chem. V. 294 14345 2019.
ISSN: ESSN 1083-351X
PubMed: 31391251
DOI: 10.1074/JBC.RA119.009963