Sodium in PDB 5u1r: Structure of Human MR1-Diclofenac in Complex with Human Mait A-F7 Tcr

The structure of Structure of Human MR1-Diclofenac in Complex with Human Mait A-F7 Tcr, PDB code: 5u1r 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)	49.00 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	212.571, 69.650, 142.850, 90.00, 103.38, 90.00
R / Rfree (%)	18.7 / 23.8

The structure of Structure of Human MR1-Diclofenac in Complex with Human Mait A-F7 Tcr also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Structure of Human MR1-Diclofenac in Complex with Human Mait A-F7 Tcr (pdb code 5u1r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human MR1-Diclofenac in Complex with Human Mait A-F7 Tcr, PDB code: 5u1r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human MR1-Diclofenac 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-Diclofenac in Complex with Human Mait A-F7 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:63.4 occ:1.00 O C:PRO181 3.2 41.2 1.0 CD1 C:LEU183 3.6 53.8 1.0 O C:GLY204 3.8 35.1 1.0 C C:PRO181 4.3 41.0 1.0 N C:PRO181 4.5 49.0 1.0 CD C:PRO181 4.6 44.3 1.0 CB C:GLU180 4.7 43.8 1.0 C C:GLU180 4.8 41.6 1.0 C C:GLY204 4.8 36.4 1.0 OE2 C:GLU180 4.8 69.4 1.0 CA C:PRO181 4.9 41.9 1.0

Sodium binding site 2 out of 2 in the Structure of Human MR1-Diclofenac 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-Diclofenac in Complex with Human Mait A-F7 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:61.2 occ:1.00 OH E:TYR47 2.4 66.5 1.0 O E:HOH409 2.5 36.7 1.0 O E:PRO61 2.5 51.5 1.0 O E:TYR64 2.6 63.0 1.0 O E:HOH427 2.7 35.5 1.0 C E:PRO61 3.3 52.0 1.0 CZ E:TYR47 3.5 63.3 1.0 C E:TYR64 3.7 55.1 1.0 CE1 E:TYR47 3.7 61.4 1.0 N E:TYR64 3.9 55.7 1.0 CB E:PRO61 3.9 44.3 1.0 N E:ASN62 4.0 52.6 1.0 CA E:ASN62 4.0 53.9 1.0 CA E:PRO61 4.1 49.9 1.0 N E:GLY63 4.2 65.3 1.0 CA E:TYR64 4.3 53.0 1.0 OE2 E:GLU79 4.4 79.5 1.0 C E:ASN62 4.4 60.7 1.0 N E:ASN65 4.7 49.6 1.0 CE2 E:TYR47 4.7 59.8 1.0 OD1 E:ASN62 4.8 61.3 1.0 CG E:PRO61 4.8 44.6 1.0 CB E:TYR64 4.8 50.3 1.0 CA E:ASN65 4.9 51.1 1.0 C E:GLY63 5.0 59.0 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