Sodium in PDB 6pum: Structure of Human Mait A-F7 Tcr in Complex with Human MR1-2'D-5-Op-Ru

The structure of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-2'D-5-Op-Ru, PDB code: 6pum 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)	48.32 / 1.96
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	218.055, 70.242, 144.022, 90.00, 104.57, 90.00
R / Rfree (%)	15.4 / 19

The binding sites of Sodium atom in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-2'D-5-Op-Ru (pdb code 6pum). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-2'D-5-Op-Ru, PDB code: 6pum:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-2'D-5-Op-Ru


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 MR1-2'D-5-Op-Ru within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:46.6 occ:1.00 OH A:TYR206 2.6 39.5 1.0 OD2 A:ASP29 2.6 48.5 1.0 O A:HOH489 3.1 46.0 1.0 O A:HOH504 3.2 54.4 1.0 O A:HOH416 3.3 42.8 1.0 CG A:ASP29 3.5 49.0 1.0 CZ A:TYR206 3.5 39.8 1.0 O A:LEU176 3.6 39.8 1.0 CB A:ASP29 3.7 37.1 1.0 CE1 A:TYR206 3.9 34.0 1.0 CE1 A:HIS3 4.1 40.6 1.0 ND1 A:HIS3 4.1 36.7 1.0 CD2 A:LEU176 4.2 33.3 1.0 CA A:LEU176 4.3 32.1 1.0 C A:LEU176 4.4 35.0 1.0 CB A:PRO207 4.4 38.5 1.0 CB A:LEU176 4.5 36.7 1.0 NE2 A:HIS31 4.5 46.7 1.0 CE2 A:TYR206 4.6 33.7 1.0 OD1 A:ASP29 4.6 45.7 1.0 CD2 A:HIS31 4.6 44.8 1.0

Sodium binding site 2 out of 4 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-2'D-5-Op-Ru


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 MR1-2'D-5-Op-Ru within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:65.7 occ:1.00 O B:HIS84 2.3 52.3 1.0 O B:HOH250 2.4 71.7 1.0 OD1 B:ASN83 2.4 76.1 1.0 O B:LEU87 2.7 74.4 1.0 O B:HOH256 2.8 74.3 1.0 O B:HOH263 2.9 68.8 1.0 CG B:ASN83 3.1 74.5 1.0 C B:HIS84 3.4 52.3 1.0 ND2 B:ASN83 3.4 78.5 1.0 N B:HIS84 3.8 54.7 1.0 C B:LEU87 3.8 70.0 1.0 CA B:VAL85 4.2 51.9 1.0 N B:VAL85 4.2 48.4 1.0 N B:LEU87 4.2 62.0 1.0 CA B:HIS84 4.3 52.3 1.0 CB B:LEU87 4.3 60.5 1.0 CA B:LEU87 4.3 62.9 1.0 CB B:ASN83 4.4 65.2 1.0 C B:VAL85 4.4 56.8 1.0 O B:VAL85 4.6 59.8 1.0 C B:ASN83 4.6 51.2 1.0 CA B:ASN83 4.8 55.8 1.0 O B:SER88 4.9 86.0 1.0 N B:SER88 5.0 73.4 1.0

Sodium binding site 3 out of 4 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-2'D-5-Op-Ru


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 MR1-2'D-5-Op-Ru within 5.0Å range: probe atom residue distance (Å) B Occ F:Na103 b:44.9 occ:1.00 O F:LEU87 2.2 41.2 1.0 O F:HOH274 2.2 54.1 1.0 OD1 F:ASN83 2.4 50.0 1.0 O F:HIS84 2.5 45.0 1.0 O F:HOH268 2.5 46.2 1.0 O F:HOH276 2.6 50.6 1.0 C F:LEU87 3.4 43.5 1.0 CG F:ASN83 3.4 50.0 1.0 C F:HIS84 3.4 45.2 1.0 ND2 F:ASN83 3.8 54.3 1.0 N F:HIS84 3.9 39.0 1.0 N F:LEU87 4.0 37.0 1.0 CA F:LEU87 4.1 39.9 1.0 CA F:VAL85 4.1 37.3 1.0 N F:VAL85 4.1 39.5 1.0 CB F:LEU87 4.2 39.6 1.0 CA F:HIS84 4.3 40.2 1.0 C F:VAL85 4.4 37.7 1.0 N F:SER88 4.4 44.4 1.0 O F:VAL85 4.4 41.3 1.0 C F:SER88 4.5 51.6 1.0 O F:SER88 4.6 53.1 1.0 CA F:SER88 4.6 48.9 1.0 O F:HOH279 4.6 53.3 1.0 CB F:ASN83 4.7 39.4 1.0 N F:GLN89 4.8 45.9 1.0 C F:ASN83 4.8 39.9 1.0 CA F:ASN83 5.0 36.8 1.0

Sodium binding site 4 out of 4 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-2'D-5-Op-Ru


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-2'D-5-Op-Ru within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:39.4 occ:1.00 O H:TYR64 2.3 37.5 1.0 O H:HOH571 2.4 44.6 1.0 OH H:TYR47 2.4 35.7 1.0 O H:HOH525 2.5 42.0 1.0 O H:HOH531 2.5 44.6 1.0 O H:PRO61 2.5 36.1 1.0 C H:PRO61 3.5 34.9 1.0 CZ H:TYR47 3.5 30.3 1.0 C H:TYR64 3.5 38.0 1.0 CE2 H:TYR47 3.7 33.4 1.0 N H:TYR64 3.8 34.2 1.0 CA H:ASN62 4.0 40.8 1.0 CB H:PRO61 4.2 35.2 1.0 N H:ASN62 4.2 38.5 1.0 N H:GLY63 4.2 36.9 1.0 O H:HOH686 4.2 52.3 1.0 CA H:TYR64 4.2 33.1 1.0 ND2 H:ASN65 4.3 41.3 0.5 CA H:PRO61 4.3 38.0 1.0 O H:HOH645 4.4 47.7 1.0 C H:ASN62 4.5 36.4 1.0 CG H:ASN65 4.5 46.4 0.5 N H:ASN65 4.6 34.5 1.0 OD1 H:ASN65 4.6 50.8 0.5 CA H:ASN65 4.8 37.9 0.5 CE1 H:TYR47 4.8 34.8 1.0 CB H:TYR64 4.8 30.8 1.0 O H:HOH674 4.8 53.2 1.0 CA H:ASN65 4.8 38.3 0.5 OD1 H:ASN62 4.8 47.0 1.0 C H:GLY63 4.8 38.7 1.0 CB H:ASN65 4.9 41.5 0.5

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