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Sodium in PDB 6omg: Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex

Protein crystallography data

The structure of Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex, PDB code: 6omg was solved by M.Z.Dirk, A.Bitra, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.11 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 78.692, 191.250, 151.290, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex (pdb code 6omg). 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 Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex, PDB code: 6omg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6omg

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Sodium binding site 1 out of 5 in the Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na603

b:32.6
occ:1.00
 OG1 C:THR108 2.8 22.6 1.0
O C:GLN22 2.8 21.5 1.0
NE2 C:GLN6 2.9 24.6 1.0
N C:GLN22 3.5 26.3 1.0
CH2 C:TRP35 3.5 22.6 1.0
CB C:LEU21 3.5 29.6 1.0
O C:SER7 3.5 26.7 1.0
CB C:GLN6 3.5 26.5 1.0
CZ3 C:TRP35 3.6 23.6 1.0
C C:GLN22 3.7 25.4 1.0
CB C:THR108 3.7 24.7 1.0
CG C:GLN6 3.7 26.1 1.0
CD C:GLN6 3.8 26.7 1.0
C C:LEU21 3.9 27.4 1.0
CG C:LEU21 4.0 32.2 1.0
CA C:LEU21 4.0 27.8 1.0
N C:SER7 4.1 26.2 1.0
CA C:GLN6 4.1 25.8 1.0
CA C:GLN22 4.2 27.4 1.0
C C:SER7 4.3 25.2 1.0
CD2 C:LEU21 4.4 31.5 1.0
C C:GLN6 4.5 26.0 1.0
CG2 C:THR108 4.6 24.9 1.0
N C:CYS23 4.7 25.1 1.0
N C:THR108 4.7 24.9 1.0
O C:LEU21 4.8 27.7 1.0
O C:TYR88 4.8 25.1 1.0
CZ2 C:TRP35 4.8 23.0 1.0
CA C:THR108 4.8 25.4 1.0
O C:PRO8 4.8 27.8 1.0
CA C:SER7 4.9 26.9 1.0
CE3 C:TRP35 4.9 23.0 1.0
OE1 C:GLN6 5.0 26.7 1.0

Sodium binding site 2 out of 5 in 6omg

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Sodium binding site 2 out of 5 in the Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:38.1
occ:1.00
 O D:GLY42 2.8 27.9 1.0
O D:ARG36 2.8 19.4 1.0
NE D:ARG44 3.0 33.3 1.0
N D:ASP38 3.2 30.1 1.0
OD2 D:ASP38 3.4 38.4 1.0
CB D:HIS41 3.6 40.7 1.0
CA D:GLN37 3.6 26.7 1.0
C D:ARG36 3.6 22.3 1.0
NH2 D:ARG44 3.6 38.8 1.0
CZ D:ARG44 3.7 38.0 1.0
CG D:ARG44 3.8 29.7 1.0
N D:ARG44 3.8 25.8 1.0
C D:GLN37 3.8 27.3 1.0
C D:GLY42 3.8 28.3 1.0
CD D:ARG44 3.9 30.7 1.0
N D:GLN37 3.9 24.8 1.0
CB D:ARG44 4.0 27.8 1.0
CB D:ASP38 4.1 34.0 1.0
CG D:ASP38 4.1 35.9 1.0
CA D:LEU43 4.1 26.0 1.0
C D:LEU43 4.2 25.8 1.0
CA D:ASP38 4.2 33.4 1.0
O D:ASP38 4.2 32.0 1.0
N D:LEU43 4.4 27.3 1.0
CG D:HIS41 4.4 44.5 1.0
C D:HIS41 4.5 30.4 1.0
CG D:ARG36 4.5 24.1 1.0
O D:HIS41 4.5 30.3 1.0
CA D:ARG44 4.6 26.2 1.0
CA D:HIS41 4.6 36.0 1.0
C D:ASP38 4.7 35.6 1.0
N D:GLY42 4.8 26.7 1.0
CB D:GLN37 4.9 26.9 1.0
CA D:ARG36 4.9 23.3 1.0
CA D:GLY42 5.0 28.3 1.0
O D:GLN37 5.0 25.7 1.0
NH1 D:ARG44 5.0 37.9 1.0

Sodium binding site 3 out of 5 in 6omg

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Sodium binding site 3 out of 5 in the Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na311

b:36.4
occ:1.00
 OD1 A:ASP80 2.6 30.3 1.0
O C:LEU99 2.8 23.4 1.0
NE A:ARG79 3.0 26.6 1.0
NH2 A:ARG79 3.3 25.1 1.0
N A:ASP80 3.5 26.2 1.0
CA A:ASP80 3.5 27.4 1.0
CG A:GLU83 3.6 26.3 1.0
CZ A:ARG79 3.6 26.3 1.0
C A:ARG79 3.6 25.6 1.0
CB C:LEU99 3.7 26.5 1.0
O A:ARG79 3.7 25.8 1.0
CG A:ASP80 3.7 32.9 1.0
NH1 C:ARG95 3.8 25.3 1.0
C C:LEU99 3.8 24.8 1.0
CB A:ARG79 3.9 25.2 1.0
CG A:ARG79 4.0 26.8 1.0
NE C:ARG95 4.0 24.2 1.0
CB A:GLU83 4.0 25.1 1.0
CD A:ARG79 4.1 26.0 1.0
CA C:LEU99 4.1 25.4 1.0
O C:HOH742 4.1 31.1 1.0
CZ C:ARG95 4.2 24.8 1.0
CB A:ASP80 4.2 29.1 1.0
CA A:ARG79 4.4 25.9 1.0
CG C:ARG95 4.7 25.0 1.0
CG C:LEU99 4.7 28.6 1.0
C A:ASP80 4.7 26.9 1.0
OD2 A:ASP80 4.8 37.4 1.0
O A:SER76 4.8 22.2 1.0
CD2 C:LEU99 4.8 29.9 1.0
O A:ASP80 4.9 24.8 1.0
NH1 A:ARG79 4.9 24.3 1.0
N C:GLY100 4.9 26.6 1.0
CD A:GLU83 4.9 26.4 1.0

Sodium binding site 4 out of 5 in 6omg

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Sodium binding site 4 out of 5 in the Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:39.2
occ:1.00
 O A:PRO52 2.6 29.8 1.0
NA A:NA313 2.6 44.0 1.0
O A:HOH450 2.9 33.2 1.0
N A:GLN55 3.1 25.7 1.0
CB A:GLN55 3.2 27.6 1.0
C A:TRP53 3.5 26.0 1.0
N A:SER54 3.5 25.2 1.0
CA A:TRP53 3.6 26.2 1.0
C A:PRO52 3.6 29.1 1.0
CA A:GLN55 3.7 26.9 1.0
N A:TRP53 3.9 27.2 1.0
O A:TRP53 4.0 27.2 1.0
C A:SER54 4.2 25.6 1.0
O A:HOH505 4.3 48.2 0.5
N A:GLY56 4.3 27.6 1.0
C A:GLN55 4.3 26.9 1.0
CA A:SER54 4.4 25.9 1.0
CG A:GLN55 4.6 28.5 1.0
CE2 A:PHE49 4.6 31.6 1.0
OE1 A:GLN55 4.7 29.5 1.0
CD2 A:PHE49 4.8 33.9 1.0
O A:GLY56 4.8 31.9 1.0
O A:HOH448 4.8 45.1 1.0
CD A:GLN55 4.9 28.3 1.0
CA A:PRO52 4.9 29.9 1.0
CB A:TRP53 4.9 26.6 1.0
O A:LYS51 5.0 28.6 1.0

Sodium binding site 5 out of 5 in 6omg

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Sodium binding site 5 out of 5 in the Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na313

b:44.0
occ:1.00
 NA A:NA312 2.6 39.2 1.0
O A:GLY56 2.8 31.9 1.0
O A:HOH448 3.5 45.1 1.0
N A:GLY56 3.7 27.6 1.0
CA A:TRP53 3.8 26.2 1.0
C A:GLY56 3.8 31.7 1.0
O A:TRP53 3.8 27.2 1.0
C A:TRP53 4.0 26.0 1.0
CA A:GLY56 4.1 29.7 1.0
O A:PRO52 4.2 29.8 1.0
C A:GLN55 4.2 26.9 1.0
CB A:GLN55 4.2 27.6 1.0
N A:GLN55 4.3 25.7 1.0
O A:HOH517 4.3 45.4 1.0
CB A:ALA178 4.4 35.5 1.0
CA A:GLN55 4.5 26.9 1.0
CB A:TRP53 4.5 26.6 1.0
O A:HOH450 4.6 33.2 1.0
N A:SER54 4.8 25.2 1.0
N A:TRP53 4.8 27.2 1.0
O A:GLN55 4.9 26.7 1.0
C A:PRO52 4.9 29.1 1.0

Reference:

M.Z.Dirk, A.Bitra, J.Wang. Structure of Mouse CD1D- Glc-Dag (Sn-1 C18:0, Sn-2 C18:1C9)-Inkt Tcr Ternary Complex To Be Published.
Page generated: Tue Dec 15 12:43:28 2020

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