Sodium in PDB 5u17: Structure of Human MR1-Da-6-Fp in Complex with Human Mait A-F7 Tcr

The structure of Structure of Human MR1-Da-6-Fp in Complex with Human Mait A-F7 Tcr, PDB code: 5u17 was solved by A.N.Keller, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.35 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	215.288, 69.740, 142.359, 90.00, 104.02, 90.00
R / Rfree (%)	18 / 22.4

The binding sites of Sodium atom in the Structure of Human MR1-Da-6-Fp in Complex with Human Mait A-F7 Tcr (pdb code 5u17). 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 MR1-Da-6-Fp in Complex with Human Mait A-F7 Tcr, PDB code: 5u17:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Human MR1-Da-6-Fp in Complex with Human Mait A-F7 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 Human MR1-Da-6-Fp in Complex with Human Mait A-F7 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ E:Na302 b:41.0 occ:1.00 O E:HOH466 2.3 41.1 1.0 O E:HOH491 2.4 42.8 1.0 O E:TYR64 2.4 43.5 1.0 OH E:TYR47 2.5 36.1 1.0 O E:HOH440 2.5 35.5 1.0 O E:PRO61 2.5 34.4 1.0 C E:PRO61 3.5 37.8 1.0 CZ E:TYR47 3.5 34.2 1.0 C E:TYR64 3.6 40.4 1.0 CE2 E:TYR47 3.7 35.2 1.0 OD1 E:ASN65 3.9 62.8 1.0 N E:TYR64 3.9 39.5 1.0 CB E:PRO61 4.2 36.1 1.0 CA E:ASN62 4.2 44.4 1.0 N E:GLY63 4.2 43.4 1.0 N E:ASN62 4.3 41.3 1.0 CA E:TYR64 4.3 37.8 1.0 CA E:PRO61 4.4 37.2 1.0 CG E:ASN65 4.6 62.0 1.0 C E:ASN62 4.6 41.7 1.0 N E:ASN65 4.7 38.9 1.0 CE1 E:TYR47 4.8 34.1 1.0 NZ E:LYS57 4.8 56.8 1.0 OD1 E:ASN62 4.9 49.2 1.0 CE E:LYS57 4.9 56.2 1.0 CA E:ASN65 4.9 43.6 1.0 CD E:LYS57 4.9 55.0 1.0 C E:GLY63 4.9 41.3 1.0

Sodium binding site 2 out of 3 in the Structure of Human MR1-Da-6-Fp in Complex with Human Mait A-F7 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 Human MR1-Da-6-Fp in Complex with Human Mait A-F7 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ G:Na301 b:43.7 occ:1.00 O G:HOH447 2.3 43.1 1.0 O G:TYR64 2.3 30.8 1.0 O G:HOH491 2.5 45.8 1.0 OH G:TYR47 2.5 43.0 1.0 O G:PRO61 2.6 34.3 1.0 O G:HOH451 2.6 33.6 1.0 C G:PRO61 3.4 35.2 1.0 C G:TYR64 3.5 36.2 1.0 CZ G:TYR47 3.6 37.1 1.0 CE2 G:TYR47 3.7 33.8 1.0 N G:TYR64 3.9 32.6 1.0 CA G:ASN62 4.0 37.5 1.0 NZ G:LYS57 4.1 54.7 1.0 N G:ASN62 4.1 35.7 1.0 CB G:PRO61 4.2 34.3 1.0 N G:GLY63 4.2 35.7 1.0 CA G:TYR64 4.3 34.3 1.0 CA G:PRO61 4.3 33.7 1.0 C G:ASN62 4.5 35.8 1.0 N G:ASN65 4.6 33.7 1.0 OD1 G:ASN62 4.6 40.0 1.0 CA G:ASN65 4.7 37.8 1.0 O G:HOH492 4.8 33.0 1.0 CE1 G:TYR47 4.8 36.9 1.0 CB G:TYR64 4.9 32.8 1.0 CE G:LYS57 4.9 52.8 1.0 CB G:ASN65 4.9 39.4 1.0 C G:GLY63 4.9 36.4 1.0

Sodium binding site 3 out of 3 in the Structure of Human MR1-Da-6-Fp in Complex with Human Mait A-F7 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 Human MR1-Da-6-Fp in Complex with Human Mait A-F7 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ H:Na103 b:53.3 occ:1.00 O H:LEU87 2.5 36.5 1.0 O H:HOH261 2.6 40.8 1.0 O H:HOH250 2.7 57.3 1.0 OD1 H:ASN83 2.7 36.0 1.0 O H:HIS84 2.8 28.3 1.0 O H:HOH259 2.9 46.7 1.0 CG H:ASN83 3.5 38.0 1.0 C H:LEU87 3.6 36.4 1.0 ND2 H:ASN83 3.7 41.9 1.0 C H:HIS84 3.7 28.3 1.0 N H:HIS84 4.1 30.2 1.0 CA H:VAL85 4.2 29.2 1.0 N H:LEU87 4.3 31.1 1.0 N H:VAL85 4.3 29.6 1.0 CA H:LEU87 4.4 31.4 1.0 O H:SER88 4.4 39.4 1.0 C H:VAL85 4.5 30.1 1.0 C H:SER88 4.5 41.2 1.0 CB H:LEU87 4.5 30.3 1.0 O H:VAL85 4.5 28.1 1.0 CA H:HIS84 4.6 29.5 1.0 N H:SER88 4.7 41.2 1.0 CB H:ASN83 4.8 33.3 1.0 CA H:SER88 4.8 43.3 1.0 N H:GLN89 4.9 41.0 1.0

A.N.Keller, S.B.Eckle, W.Xu, L.Liu, V.A.Hughes, J.Y.Mak, B.S.Meehan, T.Pediongco, R.W.Birkinshaw, Z.Chen, H.Wang, C.D'souza, L.Kjer-Nielsen, N.A.Gherardin, D.I.Godfrey, L.Kostenko, A.J.Corbett, A.W.Purcell, D.P.Fairlie, J.Mccluskey, J.Rossjohn. Drugs and Drug-Like Molecules Can Modulate the Function of Mucosal-Associated Invariant T Cells. Nat. Immunol. V. 18 402 2017.
ISSN: ESSN 1529-2916
PubMed: 28166217
DOI: 10.1038/NI.3679