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Sodium in PDB 6cx7: Structure of Alpha-Gsa[12,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr

Protein crystallography data

The structure of Structure of Alpha-Gsa[12,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr, PDB code: 6cx7 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 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.809, 191.115, 152.378, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Alpha-Gsa[12,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr (pdb code 6cx7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Alpha-Gsa[12,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr, PDB code: 6cx7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6cx7

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Sodium binding site 1 out of 5 in the Structure of Alpha-Gsa[12,6P] 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[12,6P] 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:57.5
occ:1.00
 OG1 C:THR108 2.7 37.7 1.0
NE2 C:GLN6 2.9 40.4 1.0
O C:GLN22 2.9 40.4 1.0
CB C:THR108 3.5 41.2 1.0
O C:SER7 3.6 46.3 1.0
N C:GLN22 3.6 47.3 1.0
CB C:GLN6 3.7 44.2 1.0
CH2 C:TRP35 3.7 35.4 1.0
CB C:LEU21 3.8 47.6 1.0
CZ3 C:TRP35 3.8 34.6 1.0
CG C:GLN6 3.8 44.9 1.0
C C:GLN22 3.8 46.4 1.0
CD C:GLN6 3.8 43.6 1.0
CG C:LEU21 4.0 49.3 1.0
N C:SER7 4.0 44.2 1.0
C C:LEU21 4.0 46.7 1.0
CA C:LEU21 4.1 46.9 1.0
CD2 C:LEU21 4.2 52.4 1.0
CA C:GLN6 4.3 42.5 1.0
C C:SER7 4.3 45.4 1.0
CA C:GLN22 4.3 50.5 1.0
CG2 C:THR108 4.4 42.2 1.0
C C:GLN6 4.5 42.9 1.0
N C:THR108 4.6 42.0 1.0
CA C:THR108 4.6 42.9 1.0
O C:TYR88 4.7 39.1 1.0
N C:CYS23 4.8 46.3 1.0
O C:LEU21 4.8 45.6 1.0
CA C:SER7 4.8 45.2 1.0
O C:PRO8 4.8 52.7 1.0

Sodium binding site 2 out of 5 in 6cx7

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Sodium binding site 2 out of 5 in the Structure of Alpha-Gsa[12,6P] 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[12,6P] 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:70.0
occ:1.00
 OH C:TYR124 2.8 61.7 1.0
O C:ASP120 2.9 65.2 1.0
OD2 C:ASP141 3.3 81.1 1.0
CG2 D:THR135 3.6 67.9 1.0
CG C:ASP141 3.7 77.3 1.0
CB C:ALA122 3.7 64.0 1.0
CZ C:TYR124 3.8 64.8 1.0
CB C:ASP141 3.8 70.8 1.0
CE2 C:TYR124 3.9 67.3 1.0
CG C:ASP120 3.9 69.8 1.0
CD2 D:HIS134 3.9 77.0 1.0
OD2 C:ASP120 4.1 68.5 1.0
C C:ASP120 4.1 65.7 1.0
CB C:ASP120 4.1 68.8 1.0
OD1 C:ASP120 4.2 72.2 1.0
CG2 C:THR140 4.4 60.2 1.0
N C:ALA122 4.5 63.6 1.0
OD1 C:ASP141 4.5 80.9 1.0
O C:THR140 4.7 57.2 1.0
CA C:ALA122 4.7 63.1 1.0
NE2 D:HIS134 4.7 77.8 1.0
CA C:ASP120 4.7 69.2 1.0
NH1 D:ARG192 4.8 71.3 1.0
C C:PRO121 4.8 60.8 1.0
CG D:HIS134 5.0 73.9 1.0

Sodium binding site 3 out of 5 in 6cx7

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Sodium binding site 3 out of 5 in the Structure of Alpha-Gsa[12,6P] 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[12,6P] 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:58.7
occ:1.00
 O D:GLY42 2.8 55.4 1.0
O D:ARG36 2.9 42.2 1.0
NE D:ARG44 3.1 58.7 1.0
N D:ASP38 3.4 53.9 1.0
NH2 D:ARG44 3.7 56.0 1.0
OD2 D:ASP38 3.7 67.6 1.0
C D:ARG36 3.7 43.0 1.0
CB D:HIS41 3.7 63.6 1.0
CA D:GLN37 3.7 45.2 1.0
CZ D:ARG44 3.8 57.8 1.0
N D:ARG44 3.8 46.3 1.0
CG D:ARG44 3.8 54.9 1.0
C D:GLY42 3.9 54.6 1.0
CD D:ARG44 3.9 56.3 1.0
C D:GLN37 4.0 46.0 1.0
CB D:ARG44 4.0 50.1 1.0
N D:GLN37 4.1 45.6 1.0
CB D:ASP38 4.1 59.4 1.0
CA D:LEU43 4.1 48.9 1.0
C D:LEU43 4.2 47.5 1.0
CG D:ASP38 4.3 63.4 1.0
CA D:ASP38 4.3 58.0 1.0
N D:LEU43 4.4 50.3 1.0
O D:ASP38 4.4 59.2 1.0
CA D:ARG44 4.5 47.0 1.0
C D:HIS41 4.5 58.2 1.0
CG D:ARG36 4.6 43.2 1.0
CG D:HIS41 4.6 71.3 1.0
O D:HIS41 4.6 55.7 1.0
CA D:HIS41 4.8 61.1 1.0
N D:GLY42 4.8 55.0 1.0
C D:ASP38 4.9 60.2 1.0
CA D:ARG36 5.0 42.8 1.0
NH1 D:ARG44 5.0 56.0 1.0
O D:LEU43 5.0 47.9 1.0
CA D:GLY42 5.0 54.5 1.0

Sodium binding site 4 out of 5 in 6cx7

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Sodium binding site 4 out of 5 in the Structure of Alpha-Gsa[12,6P] 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[12,6P] 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:58.5
occ:1.00
 O D:TRP157 3.1 47.4 1.0
O D:HIS204 3.2 48.2 1.0
N D:GLY160 3.4 47.2 1.0
N D:ASN159 3.5 48.9 1.0
C D:TRP157 3.5 46.6 1.0
CB D:ARG206 3.8 46.1 1.0
CB D:TRP157 3.8 43.0 1.0
C D:VAL158 3.9 52.4 1.0
N D:VAL158 4.0 46.8 1.0
CA D:VAL158 4.0 49.4 1.0
C D:HIS204 4.1 48.9 1.0
CA D:ASN159 4.1 48.5 1.0
N D:ARG206 4.2 45.1 1.0
CA D:GLY160 4.2 47.1 1.0
CA D:TRP157 4.3 44.5 1.0
ND1 D:HIS204 4.3 56.6 1.0
C D:ASN159 4.3 50.0 1.0
C D:PHE205 4.5 46.6 1.0
CG D:HIS204 4.6 53.6 1.0
CB D:HIS204 4.6 49.5 1.0
CA D:ARG206 4.6 47.1 1.0
N D:PHE205 4.7 47.3 1.0
CA D:PHE205 4.7 47.5 1.0
NE D:ARG206 4.7 47.4 1.0
CD D:ARG206 4.8 48.0 1.0
O D:VAL158 4.8 51.6 1.0
CG D:ARG206 4.9 47.4 1.0
CE1 D:HIS204 5.0 58.9 1.0
CA D:HIS204 5.0 48.6 1.0

Sodium binding site 5 out of 5 in 6cx7

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Sodium binding site 5 out of 5 in the Structure of Alpha-Gsa[12,6P] 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 5 of Structure of Alpha-Gsa[12,6P] Bound By CD1D and in Complex with the VA14VB8.2 Tcr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:64.2
occ:1.00
 OE1 A:GLN99 2.6 48.0 1.0
O A:GLU97 3.0 46.0 1.0
N A:GLY122 3.2 51.6 1.0
O A:ALA119 3.2 46.7 1.0
N A:GLN121 3.4 47.7 1.0
CD A:GLN99 3.5 45.2 1.0
C A:ALA119 3.5 45.0 1.0
C A:GLU97 3.5 44.5 1.0
N A:GLN99 3.6 42.1 1.0
N A:PHE120 3.7 46.5 1.0
CG A:GLN99 3.8 44.6 1.0
CG A:GLU97 3.8 54.9 1.0
C A:PHE120 3.8 47.9 1.0
CA A:PHE120 3.8 47.3 1.0
CA A:ILE98 3.9 42.2 1.0
CB A:GLN99 3.9 43.5 1.0
CA A:GLY122 3.9 51.5 1.0
C A:ILE98 4.0 42.3 1.0
N A:ILE98 4.0 42.0 1.0
CB A:ALA119 4.0 45.1 1.0
CA A:GLN121 4.0 46.8 1.0
CB A:GLU97 4.1 49.7 1.0
C A:GLN121 4.1 51.0 1.0
CA A:ALA119 4.4 44.6 1.0
CA A:GLU97 4.4 47.9 1.0
CA A:GLN99 4.4 42.2 1.0
CE1 B:HIS31 4.5 0.5 1.0
O A:PHE120 4.7 53.0 1.0
NE2 A:GLN99 4.7 44.7 1.0
O A:ILE98 4.8 43.9 1.0
C A:GLY122 4.9 53.8 1.0
NE2 B:HIS31 4.9 0.9 1.0
N A:LYS123 5.0 56.0 1.0

Reference:

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
Page generated: Tue Oct 8 06:49:02 2024

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