Sodium in PDB 4pje: Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-B10 Tcr

The structure of Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-B10 Tcr, PDB code: 4pje was solved by R.W.Birkinshaw, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.55 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	219.040, 72.460, 143.360, 90.00, 104.50, 90.00
R / Rfree (%)	17.1 / 19.7

The structure of Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-B10 Tcr also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-B10 Tcr (pdb code 4pje). 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-Ac-6-Fp in Complex with Human Mait B-B10 Tcr, PDB code: 4pje:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-B10 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-Ac-6-Fp in Complex with Human Mait B-B10 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ F:Na302 b:27.4 occ:1.00 O F:TYR64 2.2 23.4 1.0 O F:HOH446 2.4 33.9 1.0 OH F:TYR47 2.4 23.6 1.0 O F:PRO61 2.5 23.2 1.0 O F:HOH424 2.6 27.6 1.0 O F:HOH437 2.6 26.6 1.0 C F:TYR64 3.4 24.4 1.0 C F:PRO61 3.4 25.1 1.0 CZ F:TYR47 3.4 23.2 1.0 CE1 F:TYR47 3.6 22.1 1.0 N F:TYR64 3.8 24.1 1.0 CB F:PRO61 4.1 21.7 1.0 CA F:TYR64 4.2 21.9 1.0 CA F:ASN62 4.2 26.2 1.0 N F:ASN62 4.2 24.4 1.0 N F:GLY63 4.2 27.2 1.0 CA F:PRO61 4.3 21.1 1.0 O F:HOH568 4.4 52.5 1.0 N F:ASN65 4.4 21.8 1.0 C F:ASN62 4.6 29.7 1.0 CA F:ASN65 4.7 22.1 1.0 CE2 F:TYR47 4.7 22.5 1.0 CB F:TYR64 4.7 21.1 1.0 CE F:LYS57 4.8 56.3 1.0 C F:GLY63 4.9 27.7 1.0 OD1 F:ASN62 4.9 34.2 1.0 CD1 F:TYR47 5.0 21.8 1.0

Sodium binding site 2 out of 2 in the Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-B10 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-Ac-6-Fp in Complex with Human Mait B-B10 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:32.4 occ:1.00 O H:HOH592 2.3 34.9 1.0 O H:TYR64 2.3 31.9 1.0 O H:HOH460 2.4 32.4 1.0 OH H:TYR47 2.5 32.0 1.0 O H:PRO61 2.5 28.8 1.0 O H:HOH468 2.6 33.5 1.0 C H:PRO61 3.4 30.0 1.0 C H:TYR64 3.5 33.2 1.0 CZ H:TYR47 3.5 35.4 1.0 CE2 H:TYR47 3.7 27.6 1.0 N H:TYR64 3.9 31.7 1.0 CB H:PRO61 4.1 28.1 1.0 CA H:ASN62 4.1 30.3 1.0 N H:ASN62 4.1 28.9 1.0 N H:GLY63 4.2 31.9 1.0 CA H:TYR64 4.2 29.6 1.0 CA H:PRO61 4.3 25.7 1.0 C H:ASN62 4.5 33.4 1.0 O H:HOH432 4.5 37.0 1.0 N H:ASN65 4.5 30.2 1.0 OD1 H:ASN62 4.8 40.7 1.0 CA H:ASN65 4.8 31.3 1.0 CE1 H:TYR47 4.8 30.4 1.0 CB H:TYR64 4.8 27.4 1.0 C H:GLY63 4.9 33.3 1.0

S.B.Eckle, R.W.Birkinshaw, L.Kostenko, A.J.Corbett, H.E.Mcwilliam, R.Reantragoon, Z.Chen, N.A.Gherardin, T.Beddoe, L.Liu, O.Patel, B.Meehan, D.P.Fairlie, J.A.Villadangos, D.I.Godfrey, L.Kjer-Nielsen, J.Mccluskey, J.Rossjohn. A Molecular Basis Underpinning the T Cell Receptor Heterogeneity of Mucosal-Associated Invariant T Cells. J.Exp.Med. V. 211 1585 2014.
ISSN: ESSN 1540-9538
PubMed: 25049336
DOI: 10.1084/JEM.20140484