Sodium in PDB 6cxf: Structure of Alpha-Gsa[26,P5P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr

The structure of Structure of Alpha-Gsa[26,P5P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr, PDB code: 6cxf 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)	41.50 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.933, 191.781, 151.378, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.9

The binding sites of Sodium atom in the Structure of Alpha-Gsa[26,P5P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr (pdb code 6cxf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Alpha-Gsa[26,P5P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr, PDB code: 6cxf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of Alpha-Gsa[26,P5P] 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,P5P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:43.9 occ:1.00 OD1 A:ASP80 2.6 43.6 1.0 O C:LEU99 2.8 26.8 1.0 NE A:ARG79 3.1 34.4 1.0 NH2 A:ARG79 3.5 36.8 1.0 O A:ARG79 3.6 28.4 1.0 CG A:ASP80 3.7 43.8 1.0 CZ A:ARG79 3.7 34.0 1.0 CB C:LEU99 3.7 32.5 1.0 CA A:ASP80 3.7 33.7 1.0 C A:ARG79 3.7 29.7 1.0 NH1 C:ARG95 3.7 28.1 1.0 C C:LEU99 3.7 29.5 1.0 N A:ASP80 3.8 30.9 1.0 CB A:GLU83 3.9 34.9 1.0 CG A:ARG79 3.9 31.4 1.0 NE C:ARG95 4.0 27.4 1.0 CD A:ARG79 4.1 32.8 1.0 CZ C:ARG95 4.1 28.0 1.0 CG A:GLU83 4.1 36.4 1.0 CB A:ARG79 4.1 30.8 1.0 CA C:LEU99 4.2 31.3 1.0 CB A:ASP80 4.3 37.2 1.0 CA A:ARG79 4.6 29.8 1.0 CG C:LEU99 4.6 34.9 1.0 OD2 A:ASP80 4.6 48.5 1.0 CD1 C:LEU99 4.7 35.3 1.0 CG C:ARG95 4.7 26.2 1.0 CD2 C:LEU99 4.8 35.5 1.0 N C:GLY100 4.8 29.7 1.0 OE1 A:GLU83 4.8 33.0 1.0 C A:ASP80 4.9 33.0 1.0 CD A:GLU83 4.9 34.8 1.0 NH1 A:ARG79 4.9 32.7 1.0 CD C:ARG95 4.9 26.2 1.0

Sodium binding site 2 out of 6 in the Structure of Alpha-Gsa[26,P5P] 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,P5P] 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:39.8 occ:1.00 OG1 C:THR108 2.6 28.1 1.0 O C:GLN22 2.9 28.7 1.0 NE2 C:GLN6 3.1 25.4 1.0 O C:SER7 3.3 28.5 1.0 CB C:THR108 3.5 28.6 1.0 N C:GLN22 3.5 32.9 1.0 CB C:LEU21 3.6 33.5 1.0 CB C:GLN6 3.7 28.8 1.0 CH2 C:TRP35 3.8 23.9 1.0 C C:GLN22 3.8 32.0 1.0 CG C:GLN6 3.8 28.3 1.0 C C:LEU21 3.9 31.3 1.0 CZ3 C:TRP35 3.9 23.0 1.0 CG C:LEU21 3.9 34.4 1.0 CD C:GLN6 3.9 27.6 1.0 CA C:LEU21 4.0 31.9 1.0 N C:SER7 4.1 29.8 1.0 C C:SER7 4.2 29.9 1.0 CA C:GLN22 4.3 34.2 1.0 CG2 C:THR108 4.3 28.5 1.0 CA C:GLN6 4.3 29.4 1.0 CD2 C:LEU21 4.3 34.4 1.0 C C:GLN6 4.5 29.0 1.0 O C:PRO8 4.6 32.4 1.0 CA C:THR108 4.7 29.1 1.0 O C:LEU21 4.7 27.8 1.0 N C:THR108 4.7 28.1 1.0 O C:TYR88 4.8 25.6 1.0 N C:CYS23 4.8 32.9 1.0 CA C:SER7 4.8 29.8 1.0 N C:PRO8 4.9 30.8 1.0

Sodium binding site 3 out of 6 in the Structure of Alpha-Gsa[26,P5P] 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,P5P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:58.0 occ:1.00 OH C:TYR124 2.8 32.4 1.0 OD2 C:ASP141 2.9 51.0 1.0 O C:ASP120 2.9 54.0 1.0 CG2 D:THR135 3.5 53.3 1.0 CG C:ASP141 3.6 50.1 1.0 CB C:ALA122 3.7 42.6 1.0 CZ C:TYR124 3.7 35.4 1.0 CE2 C:TYR124 3.7 37.3 1.0 CB C:ASP141 3.8 46.6 1.0 CG C:ASP120 4.0 56.7 1.0 C C:ASP120 4.0 51.8 1.0 CD2 D:HIS134 4.1 56.7 1.0 CB C:ASP120 4.1 56.1 1.0 OD1 C:ASP120 4.2 60.1 1.0 OD2 C:ASP120 4.3 53.1 1.0 CG2 C:THR140 4.3 39.0 1.0 O C:HOH406 4.3 34.9 1.0 N C:ALA122 4.5 44.4 1.0 OD1 C:ASP141 4.6 54.7 1.0 NH1 D:ARG192 4.6 43.6 1.0 CA C:ALA122 4.7 42.1 1.0 CA C:ASP120 4.7 54.0 1.0 O C:THR140 4.8 39.2 1.0 C C:PRO121 4.9 46.5 1.0 CB D:THR135 5.0 52.0 1.0 NE2 D:HIS134 5.0 56.5 1.0

Sodium binding site 4 out of 6 in the Structure of Alpha-Gsa[26,P5P] 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,P5P] 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:35.3 occ:1.00 O D:ARG36 2.7 27.7 1.0 O D:GLY42 2.9 31.0 1.0 NE D:ARG44 3.0 37.7 1.0 OD2 D:ASP38 3.4 45.1 1.0 N D:ASP38 3.4 38.1 1.0 C D:ARG36 3.6 28.8 1.0 NH2 D:ARG44 3.7 41.2 1.0 CZ D:ARG44 3.7 40.4 1.0 CA D:GLN37 3.7 31.9 1.0 CB D:HIS41 3.7 43.7 1.0 N D:ARG44 3.8 28.4 1.0 CG D:ARG44 3.8 33.9 1.0 CD D:ARG44 3.9 35.7 1.0 C D:GLY42 3.9 31.1 1.0 C D:GLN37 4.0 33.4 1.0 CB D:ARG44 4.0 31.2 1.0 N D:GLN37 4.1 30.9 1.0 CG D:ASP38 4.1 45.1 1.0 CB D:ASP38 4.1 42.8 1.0 CA D:LEU43 4.1 30.2 1.0 C D:LEU43 4.2 28.9 1.0 CA D:ASP38 4.3 41.3 1.0 O D:ASP38 4.4 40.4 1.0 N D:LEU43 4.4 28.8 1.0 CA D:ARG44 4.5 29.8 1.0 CG D:ARG36 4.5 30.8 1.0 C D:HIS41 4.6 34.3 1.0 O D:HIS41 4.6 30.6 1.0 CG D:HIS41 4.6 48.5 1.0 CA D:HIS41 4.8 39.8 1.0 N D:GLY42 4.8 31.3 1.0 CA D:ARG36 4.9 28.5 1.0 C D:ASP38 4.9 41.7 1.0 NH1 D:ARG44 4.9 41.6 1.0

Sodium binding site 5 out of 6 in the Structure of Alpha-Gsa[26,P5P] 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 5 of Structure of Alpha-Gsa[26,P5P] 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:56.8 occ:1.00 O D:TYR212 2.5 32.5 1.0 O D:HIS151 3.1 40.7 1.0 O D:PRO149 3.3 39.2 1.0 CE1 D:PHE211 3.4 25.3 1.0 N D:HIS151 3.6 42.1 1.0 CG D:PRO149 3.6 36.0 1.0 CB D:HIS151 3.6 41.0 1.0 C D:TYR212 3.6 31.9 1.0 CD D:PRO149 3.7 35.0 1.0 N D:PRO149 3.7 34.5 1.0 C D:PRO149 3.7 38.4 1.0 C D:HIS151 3.8 41.1 1.0 CD1 D:PHE211 3.8 25.8 1.0 CA D:HIS151 3.8 41.2 1.0 N D:TYR212 3.9 30.6 1.0 CZ D:PHE211 4.0 25.2 1.0 CA D:PRO149 4.1 36.1 1.0 CG2 D:VAL12 4.1 39.7 1.0 CA D:TYR212 4.2 31.9 1.0 CB D:PRO149 4.3 36.4 1.0 C D:TYR148 4.3 32.4 1.0 O D:TYR148 4.4 32.0 1.0 CB D:TYR212 4.5 32.7 1.0 N D:ASP150 4.5 39.5 1.0 CG D:PHE211 4.6 25.6 1.0 C D:ASP150 4.6 43.3 1.0 CG D:HIS151 4.7 42.2 1.0 N D:GLY213 4.7 32.3 1.0 CE2 D:PHE211 4.7 25.1 1.0 N D:VAL152 5.0 40.7 1.0 CG1 D:VAL152 5.0 39.8 1.0 C D:PHE211 5.0 29.1 1.0 CD2 D:PHE211 5.0 25.3 1.0

Sodium binding site 6 out of 6 in the Structure of Alpha-Gsa[26,P5P] 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 6 of Structure of Alpha-Gsa[26,P5P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:52.2 occ:1.00 O D:TRP157 3.2 27.8 1.0 O D:HIS204 3.3 32.6 1.0 N D:GLY160 3.3 28.8 1.0 N D:ASN159 3.5 27.7 1.0 C D:TRP157 3.5 26.9 1.0 CB D:ARG206 3.8 30.6 1.0 CB D:TRP157 3.8 26.4 1.0 C D:VAL158 3.9 27.6 1.0 N D:VAL158 4.0 26.8 1.0 CA D:VAL158 4.0 27.8 1.0 CA D:ASN159 4.1 28.2 1.0 N D:ARG206 4.1 29.6 1.0 ND1 D:HIS204 4.1 42.4 1.0 CA D:GLY160 4.1 30.2 1.0 C D:HIS204 4.1 33.1 1.0 C D:ASN159 4.2 28.7 1.0 CA D:TRP157 4.3 26.4 1.0 C D:PHE205 4.5 28.4 1.0 CB D:HIS204 4.6 36.8 1.0 CA D:ARG206 4.6 30.6 1.0 CG D:HIS204 4.6 39.8 1.0 CA D:PHE205 4.7 29.4 1.0 O D:VAL158 4.7 28.3 1.0 N D:PHE205 4.8 30.4 1.0 NE D:ARG206 4.8 32.8 1.0 CE1 D:HIS204 4.9 41.2 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