Sodium in PDB 5u16: Structure of Human MR1-2-Oh-1-Na in Complex with Human Mait A-F7 Tcr

The structure of Structure of Human MR1-2-Oh-1-Na in Complex with Human Mait A-F7 Tcr, PDB code: 5u16 was solved by A.N.Keller, R.W.Birkinshaw, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.33 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	216.440, 69.850, 143.120, 90.00, 104.35, 90.00
R / Rfree (%)	17.3 / 21.9

The structure of Structure of Human MR1-2-Oh-1-Na in Complex with Human Mait A-F7 Tcr also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Structure of Human MR1-2-Oh-1-Na in Complex with Human Mait A-F7 Tcr (pdb code 5u16). 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 MR1-2-Oh-1-Na in Complex with Human Mait A-F7 Tcr, PDB code: 5u16:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Human MR1-2-Oh-1-Na 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 MR1-2-Oh-1-Na in Complex with Human Mait A-F7 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:37.9 occ:1.00 O D:HOH266 2.3 33.1 1.0 O D:LEU87 2.4 32.3 1.0 O D:HIS84 2.5 26.1 1.0 O D:HOH270 2.5 40.7 1.0 O D:HOH262 2.6 38.6 1.0 OD1 D:ASN83 2.7 34.2 1.0 C D:HIS84 3.4 31.4 1.0 CG D:ASN83 3.5 32.3 1.0 C D:LEU87 3.6 29.3 1.0 ND2 D:ASN83 3.8 36.6 1.0 N D:HIS84 3.9 23.2 1.0 CA D:VAL85 4.0 28.8 1.0 N D:VAL85 4.1 30.1 1.0 N D:LEU87 4.2 26.6 1.0 CA D:LEU87 4.3 27.8 1.0 C D:VAL85 4.3 28.7 1.0 O D:VAL85 4.3 29.5 1.0 CA D:HIS84 4.3 22.9 1.0 CB D:LEU87 4.4 27.3 1.0 N D:SER88 4.7 27.4 1.0 O D:HOH279 4.7 41.2 1.0 C D:SER88 4.8 29.8 1.0 CA D:SER88 4.8 29.4 1.0 CB D:ASN83 4.8 28.1 1.0 C D:ASN83 4.9 25.4 1.0 N D:THR86 5.0 24.4 1.0

Sodium binding site 2 out of 3 in the Structure of Human MR1-2-Oh-1-Na 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 MR1-2-Oh-1-Na in Complex with Human Mait A-F7 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:34.8 occ:1.00 O F:HOH480 2.3 33.0 1.0 O F:TYR64 2.4 30.1 1.0 OH F:TYR47 2.4 34.7 1.0 O F:HOH477 2.5 37.8 1.0 O F:PRO61 2.6 36.3 1.0 O F:HOH482 2.6 37.3 1.0 C F:PRO61 3.4 38.6 1.0 CZ F:TYR47 3.4 31.9 1.0 C F:TYR64 3.5 32.6 1.0 CE1 F:TYR47 3.6 27.1 1.0 N F:TYR64 3.8 29.7 1.0 CB F:PRO61 4.0 40.5 1.0 CA F:ASN62 4.0 42.1 1.0 N F:ASN62 4.1 41.4 1.0 N F:GLY63 4.2 38.3 1.0 CA F:PRO61 4.2 39.7 1.0 CA F:TYR64 4.2 32.7 1.0 OE2 F:GLU79 4.4 59.1 1.0 C F:ASN62 4.5 40.3 1.0 N F:ASN65 4.5 31.4 1.0 CE2 F:TYR47 4.7 33.2 1.0 CA F:ASN65 4.7 36.3 1.0 OD1 F:ASN62 4.8 50.4 1.0 CB F:TYR64 4.8 32.1 1.0 CG F:PRO61 4.9 38.5 1.0 C F:GLY63 4.9 39.2 1.0 CB F:ASN65 4.9 40.0 1.0 CD1 F:TYR47 5.0 29.4 1.0

Sodium binding site 3 out of 3 in the Structure of Human MR1-2-Oh-1-Na 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 MR1-2-Oh-1-Na in Complex with Human Mait A-F7 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:30.3 occ:1.00 O H:HOH586 2.4 33.6 1.0 O H:HOH420 2.4 27.2 1.0 O H:HOH485 2.4 26.6 1.0 O H:TYR64 2.5 29.3 1.0 O H:PRO61 2.5 20.4 1.0 OH H:TYR47 2.6 23.6 1.0 C H:PRO61 3.4 21.5 1.0 C H:TYR64 3.6 27.9 1.0 CZ H:TYR47 3.6 22.1 1.0 CE2 H:TYR47 3.8 24.8 1.0 N H:TYR64 3.8 23.3 1.0 CA H:ASN62 3.9 24.0 1.0 N H:GLY63 4.0 24.9 1.0 N H:ASN62 4.0 20.9 1.0 CB H:PRO61 4.1 18.8 1.0 CA H:PRO61 4.3 19.4 1.0 O H:HOH504 4.3 48.4 1.0 CA H:TYR64 4.3 19.7 1.0 C H:ASN62 4.3 25.9 1.0 O H:HOH610 4.5 26.9 1.0 OD1 H:ASN62 4.6 29.3 1.0 ND2 H:ASN65 4.6 58.7 1.0 N H:ASN65 4.7 25.1 1.0 O H:HOH629 4.7 33.7 1.0 C H:GLY63 4.8 25.6 1.0 CE1 H:TYR47 4.9 21.6 1.0 CA H:ASN65 4.9 28.2 1.0 CB H:TYR64 4.9 18.1 1.0 CA H:GLY63 5.0 22.8 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