Sodium in PDB 4pjh: Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-G8 Tcr

The structure of Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-G8 Tcr, PDB code: 4pjh 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)	29.28 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	217.736, 71.481, 143.799, 90.00, 104.59, 90.00
R / Rfree (%)	16.9 / 19.8

The binding sites of Sodium atom in the Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-G8 Tcr (pdb code 4pjh). 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 MR1-Ac-6-Fp in Complex with Human Mait B-G8 Tcr, PDB code: 4pjh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-G8 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-G8 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:40.7 occ:1.00 O B:HOH319 2.2 45.7 1.0 O B:LEU87 2.3 37.4 1.0 O B:HOH289 2.4 50.8 1.0 O B:HIS84 2.5 29.8 1.0 OD1 B:ASN83 2.5 41.7 1.0 O B:HOH234 2.7 41.2 1.0 C B:HIS84 3.4 29.9 1.0 C B:LEU87 3.4 36.7 1.0 CG B:ASN83 3.5 55.2 1.0 ND2 B:ASN83 3.9 50.5 1.0 N B:HIS84 3.9 27.4 1.0 N B:VAL85 4.1 26.9 1.0 CA B:VAL85 4.1 27.9 1.0 CA B:LEU87 4.2 29.9 1.0 N B:LEU87 4.2 27.9 1.0 O B:HOH294 4.3 52.0 1.0 CB B:LEU87 4.3 29.8 1.0 CA B:HIS84 4.3 25.5 1.0 C B:VAL85 4.4 31.1 1.0 O B:VAL85 4.4 30.6 1.0 N B:SER88 4.5 35.6 1.0 C B:SER88 4.6 42.2 1.0 CA B:SER88 4.7 37.7 1.0 CB B:ASN83 4.7 31.4 1.0 C B:ASN83 4.8 30.1 1.0 O B:HOH300 4.8 58.9 1.0 O B:SER88 4.9 43.4 1.0 N B:GLN89 4.9 38.0 1.0

Sodium binding site 2 out of 4 in the Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-G8 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-G8 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:39.8 occ:1.00 O E:HOH493 2.3 38.8 1.0 O E:HOH442 2.3 34.9 1.0 O E:ILE4 2.3 22.2 1.0 O E:HOH440 2.4 28.5 1.0 O E:HOH517 2.4 37.0 1.0 O E:HOH540 2.6 53.9 1.0 C E:ILE4 3.6 24.6 1.0 OD1 E:ASP5 3.9 37.6 1.0 OD1 E:ASN3 4.0 38.3 1.0 N E:ILE4 4.1 21.9 1.0 O E:HOH413 4.2 29.1 1.0 O F:HOH617 4.3 48.6 1.0 O F:HOH436 4.3 34.9 1.0 CG2 E:ILE4 4.4 25.9 1.0 CA E:ILE4 4.4 20.9 1.0 N E:ASP5 4.5 21.7 1.0 CG E:ASP5 4.5 36.2 1.0 CA E:ASP5 4.6 22.7 1.0 O F:HOH574 4.8 42.8 1.0 CG E:ASN3 4.9 44.3 1.0 O E:TRP99 5.0 25.2 1.0

Sodium binding site 3 out of 4 in the Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-G8 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-Ac-6-Fp in Complex with Human Mait B-G8 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:28.0 occ:1.00 O F:TYR64 2.3 23.4 1.0 O F:HOH428 2.4 29.0 1.0 O F:PRO61 2.5 21.8 1.0 OH F:TYR47 2.5 25.0 1.0 O F:HOH437 2.5 24.7 1.0 C F:PRO61 3.3 23.8 1.0 C F:TYR64 3.4 23.9 1.0 CZ F:TYR47 3.5 25.2 1.0 CE2 F:TYR47 3.6 21.7 1.0 N F:TYR64 3.8 21.2 1.0 CB F:PRO61 4.0 21.4 1.0 N F:ASN62 4.0 23.4 1.0 CA F:ASN62 4.0 24.1 1.0 CA F:TYR64 4.1 20.1 1.0 N F:GLY63 4.2 24.5 1.0 CA F:PRO61 4.2 20.0 1.0 O F:HOH553 4.3 49.5 1.0 OE1 F:GLU79 4.4 38.4 1.0 N F:ASN65 4.5 20.5 1.0 C F:ASN62 4.5 26.9 1.0 O F:HOH592 4.6 65.7 1.0 CA F:ASN65 4.7 21.1 1.0 CB F:TYR64 4.7 19.6 1.0 CE1 F:TYR47 4.8 23.6 1.0 OD1 F:ASN62 4.8 33.7 1.0 CE F:LYS57 4.9 49.6 1.0 C F:GLY63 4.9 24.8 1.0 CG F:PRO61 5.0 26.4 1.0 CD2 F:TYR47 5.0 19.9 1.0

Sodium binding site 4 out of 4 in the Structure of Human MR1-Ac-6-Fp in Complex with Human Mait B-G8 Tcr


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 MR1-Ac-6-Fp in Complex with Human Mait B-G8 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:38.5 occ:1.00 O H:TYR64 2.3 36.1 1.0 O H:HOH486 2.4 37.0 1.0 O H:PRO61 2.5 35.6 1.0 O H:HOH473 2.5 32.6 1.0 OH H:TYR47 2.6 37.7 1.0 C H:PRO61 3.3 37.1 1.0 C H:TYR64 3.5 36.9 1.0 CZ H:TYR47 3.6 37.4 1.0 CE1 H:TYR47 3.7 31.7 1.0 N H:TYR64 3.8 33.6 1.0 CB H:PRO61 4.0 32.9 1.0 N H:ASN62 4.0 36.6 1.0 CA H:ASN62 4.0 37.8 1.0 N H:GLY63 4.2 36.9 1.0 CA H:TYR64 4.2 31.8 1.0 CA H:PRO61 4.2 31.4 1.0 C H:ASN62 4.5 39.8 1.0 N H:ASN65 4.5 35.1 1.0 O H:HOH441 4.6 38.0 1.0 OD1 H:ASN62 4.7 44.8 1.0 CB H:TYR64 4.8 29.7 1.0 CA H:ASN65 4.8 36.7 1.0 CE2 H:TYR47 4.9 34.8 1.0 C H:GLY63 4.9 38.9 1.0 CE H:LYS57 4.9 62.4 1.0 CG H:PRO61 5.0 37.3 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