Sodium in PDB 6puk: Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72

The structure of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72, PDB code: 6puk was solved by W.Awad, A.N.Keller, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.57 / 2.08
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	217.055, 69.688, 143.319, 90.00, 104.35, 90.00
R / Rfree (%)	17.6 / 20.2

The binding sites of Sodium atom in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72 (pdb code 6puk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72, PDB code: 6puk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na103 b:54.5 occ:1.00 O F:HIS84 2.5 47.2 1.0 O F:LEU87 2.5 49.5 1.0 OD1 F:ASN83 2.6 51.7 1.0 O F:HOH279 2.6 53.1 1.0 O F:HOH263 2.7 59.7 1.0 O F:HOH255 2.8 52.1 1.0 C F:HIS84 3.3 47.0 1.0 CG F:ASN83 3.5 52.6 1.0 C F:LEU87 3.7 48.8 1.0 N F:HIS84 3.9 43.7 1.0 ND2 F:ASN83 3.9 53.3 1.0 CA F:VAL85 3.9 47.4 1.0 N F:VAL85 4.0 49.0 1.0 CA F:HIS84 4.2 45.7 1.0 N F:LEU87 4.3 43.6 1.0 C F:VAL85 4.3 46.6 1.0 CA F:LEU87 4.4 45.8 1.0 O F:VAL85 4.5 47.5 1.0 CB F:LEU87 4.5 43.1 1.0 N F:SER88 4.7 47.0 1.0 C F:ASN83 4.8 43.4 1.0 CB F:ASN83 4.8 48.0 1.0 O F:HOH299 4.8 64.5 1.0 C F:SER88 4.8 54.7 1.0 CA F:SER88 4.9 54.7 1.0

Sodium binding site 2 out of 3 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na301 b:51.8 occ:1.00 O G:TYR64 2.5 47.4 1.0 O G:HOH420 2.6 50.5 1.0 O G:HOH508 2.6 55.2 1.0 O G:HOH422 2.6 51.0 1.0 OH G:TYR47 2.7 43.8 1.0 O G:PRO61 2.7 46.1 1.0 C G:PRO61 3.5 46.3 1.0 CZ G:TYR47 3.6 43.0 1.0 C G:TYR64 3.7 46.1 1.0 CE2 G:TYR47 3.8 45.0 1.0 N G:TYR64 3.9 48.8 1.0 CA G:ASN62 4.1 46.7 1.0 CB G:PRO61 4.1 45.3 1.0 N G:GLY63 4.2 46.8 1.0 N G:ASN62 4.2 42.6 1.0 CA G:PRO61 4.3 46.5 1.0 CA G:TYR64 4.4 46.2 1.0 OD1 G:ASN65 4.4 61.4 0.6 C G:ASN62 4.5 47.3 1.0 O G:HOH614 4.6 49.9 1.0 CG G:ASN65 4.7 60.1 0.6 O G:HOH602 4.7 54.9 1.0 N G:ASN65 4.8 43.4 1.0 OD1 G:ASN62 4.8 64.9 1.0 ND2 G:ASN65 4.8 62.8 0.7 C G:GLY63 4.9 49.6 1.0 CE1 G:TYR47 4.9 39.9 1.0

Sodium binding site 3 out of 3 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-JYM72 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na101 b:84.6 occ:1.00 O H:HOH240 2.3 78.0 1.0 O H:HIS84 2.5 69.5 1.0 O H:HOH242 2.6 73.1 1.0 OD1 H:ASN83 2.6 82.3 1.0 O H:LEU87 2.7 73.8 1.0 C H:HIS84 3.4 64.8 1.0 CG H:ASN83 3.5 81.1 1.0 ND2 H:ASN83 3.8 85.7 1.0 C H:LEU87 3.8 75.6 1.0 N H:HIS84 3.9 65.8 1.0 N H:VAL85 4.1 61.8 1.0 CA H:VAL85 4.1 64.9 1.0 CA H:HIS84 4.3 63.1 1.0 N H:LEU87 4.4 71.0 1.0 C H:VAL85 4.5 68.3 1.0 CA H:LEU87 4.5 73.1 1.0 CB H:LEU87 4.5 72.4 1.0 O H:VAL85 4.6 73.0 1.0 C H:ASN83 4.8 62.4 1.0 CB H:ASN83 4.8 73.3 1.0 N H:SER88 4.9 77.3 1.0 C H:SER88 5.0 83.0 1.0

W.Awad, A.N.Keller, J.Rossjohn. The Molecular Basis Underpinning the Potency and Specificity of Mait Cell Antigens To Be Published.