Sodium in PDB 7n5p: 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant

The structure of 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant, PDB code: 7n5p was solved by C.Szeto, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.22 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.334, 72.056, 107.671, 90, 101.28, 90
R / Rfree (%)	19 / 23.6

The binding sites of Sodium atom in the 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant (pdb code 7n5p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant, PDB code: 7n5p:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:47.3 occ:1.00 O D:ASN127 3.5 43.6 1.0 N D:LYS184 3.5 26.4 1.0 N D:GLN129 3.6 41.1 1.0 O D:LYS184 3.7 27.4 1.0 CG D:GLN129 4.0 64.1 1.0 O D:ASP182 4.0 47.8 1.0 CA D:ILE128 4.1 39.9 1.0 CD1 D:PHE183 4.2 38.5 1.0 CA D:PHE183 4.2 26.4 1.0 CG D:LYS184 4.2 38.1 1.0 CB D:GLN129 4.2 57.0 1.0 CA D:LYS184 4.4 28.7 1.0 C D:PHE183 4.4 28.5 1.0 C D:ILE128 4.4 38.7 1.0 C D:LYS184 4.4 33.4 1.0 CB D:LYS184 4.5 32.1 1.0 C D:ASN127 4.5 36.1 1.0 CE1 D:PHE183 4.5 32.6 1.0 CD1 D:ILE128 4.5 25.8 1.0 CA D:GLN129 4.6 49.4 1.0 CG D:PHE183 4.7 32.8 1.0 N D:ILE128 4.8 32.7 1.0 C D:ASP182 4.9 31.8 1.0 CB D:PHE183 5.0 28.5 1.0

Sodium binding site 2 out of 4 in the 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:41.2 occ:1.00 N D:LEU57 2.7 21.1 1.0 OE2 A:GLU154 2.8 39.3 0.9 O D:GLN59 3.0 47.9 1.0 N D:GLN58 3.2 29.3 1.0 OE1 D:GLN59 3.4 48.6 1.0 N D:GLN59 3.4 40.6 1.0 CA D:LEU57 3.5 25.1 1.0 CD A:GLU154 3.6 34.3 0.3 CA D:GLY56 3.6 20.9 1.0 C D:GLY56 3.7 22.2 1.0 CB D:LEU57 3.7 25.9 1.0 OE1 A:GLU154 3.8 40.2 0.7 C D:GLN59 3.8 50.8 1.0 C D:LEU57 3.9 27.3 1.0 CA D:GLN59 3.9 44.5 1.0 CB D:GLN59 3.9 40.9 1.0 C D:GLN58 4.0 39.0 1.0 OG1 D:THR67 4.2 46.7 1.0 CA D:GLN58 4.2 39.0 1.0 CD D:GLN59 4.3 58.5 1.0 CG D:GLN59 4.6 54.0 1.0 CG A:GLU154 4.8 37.2 1.0 O D:GLY56 4.8 20.6 1.0 O D:GLN58 4.9 39.9 1.0

Sodium binding site 3 out of 4 in the 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:41.3 occ:1.00 O E:HOH452 2.2 30.8 1.0 O E:VAL164 2.3 25.6 1.0 O E:HOH451 2.3 37.6 1.0 OH E:TYR10 2.5 30.8 1.0 O E:HOH453 2.6 35.4 1.0 O E:HOH434 2.6 34.1 1.0 C E:VAL164 3.5 26.4 1.0 CZ E:TYR10 3.6 29.0 1.0 O E:HOH430 3.9 33.1 1.0 N E:VAL164 4.2 25.4 1.0 CE2 E:TYR10 4.3 33.8 1.0 N E:GLU165 4.4 24.6 1.0 CA E:VAL164 4.4 26.8 1.0 OE2 E:GLU165 4.4 60.2 1.0 CA E:GLU165 4.4 29.7 1.0 CE1 E:TYR10 4.5 30.9 1.0 CG2 E:VAL164 4.5 26.2 1.0 CG E:GLU165 4.6 41.2 1.0

Sodium binding site 4 out of 4 in the 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 6218 Tcr in Complex with H2-Db PA224-233 with A Cysteine Mutant within 5.0Å range: probe atom residue distance (Å) B Occ E:Na302 b:41.6 occ:1.00 O E:ASP125 2.3 36.6 1.0 N E:ASN128 2.9 46.1 1.0 CB E:ASN128 3.1 45.2 1.0 C E:ASP125 3.3 43.7 1.0 CA E:ASN128 3.4 45.1 1.0 ND2 E:ASN128 3.5 60.8 1.0 C E:LEU126 3.5 39.8 1.0 CA E:LEU126 3.6 35.6 1.0 CG E:ASN128 3.7 64.0 1.0 N E:LYS127 3.7 39.9 1.0 C E:ASN128 3.7 38.6 1.0 N E:VAL129 3.9 36.6 1.0 O E:LEU126 3.9 36.6 1.0 N E:LEU126 3.9 42.0 1.0 CD1 E:LEU123 3.9 28.9 1.0 CG2 E:VAL129 4.0 26.3 1.0 C E:LYS127 4.1 49.0 1.0 CE2 E:TYR160 4.3 33.8 1.0 CA E:ASP125 4.5 47.8 1.0 O E:ASN128 4.5 39.0 1.0 CA E:LYS127 4.5 43.4 1.0 CB E:LEU123 4.5 30.3 1.0 CB E:ASP125 4.6 39.7 1.0 CG E:LEU123 4.6 30.0 1.0 CD2 E:LEU123 4.6 26.6 1.0 OD1 E:ASN128 4.7 62.8 1.0 CD2 E:TYR160 4.8 32.2 1.0 N E:ASP125 4.8 41.0 1.0 CA E:VAL129 4.9 33.2 1.0

C.Szeto, P.Zareie, R.C.Wirasinha, J.B.Zhang, A.T.Nguyen, A.Riboldi-Tunnicliffe, N.L.La Gruta, S.Gras, S.R.Daley. Covalent Tcr-Peptide-Mhc Interactions Induce T Cell Activation and Redirect T Cell Fate in the Thymus. Nat Commun V. 13 4951 2022.
ISSN: ESSN 2041-1723
PubMed: 35999236
DOI: 10.1038/S41467-022-32692-4