Sodium in PDB 7byd: Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104

The structure of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104, PDB code: 7byd was solved by D.Morita, M.Sugita, C.Iwashita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.96 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.937, 95.071, 123.352, 90, 90.89, 90
R / Rfree (%)	18.5 / 25

The structure of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Iodine	(I)	19 atoms

The binding sites of Sodium atom in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 (pdb code 7byd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104, PDB code: 7byd:

Sodium binding site 1 out of 1 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range: probe atom residue distance (Å) B Occ I:Na206 b:22.6 occ:1.00 OD1 I:ASP137 2.3 57.7 1.0 N I:ASP137 3.4 25.6 1.0 CG I:ASP137 3.5 47.3 1.0 CG I:PRO191 3.6 33.9 1.0 CA I:PHE136 3.8 22.6 1.0 CB I:PHE136 3.9 23.9 1.0 CB I:PRO113 4.0 38.3 1.0 C I:PHE136 4.1 25.6 1.0 CG I:PRO115 4.1 34.0 1.0 CB I:ASP137 4.1 30.9 1.0 CB I:PRO191 4.2 32.7 1.0 CD I:PRO115 4.3 30.8 1.0 CB I:PRO115 4.4 27.6 1.0 CA I:ASP137 4.4 27.2 1.0 OD2 I:ASP137 4.5 52.7 1.0 CG I:PRO113 4.6 46.5 1.0 CD I:PRO191 4.9 33.9 1.0

D.Morita, C.Iwashita, T.Mizutani, N.Mori, B.Mikami, M.Sugita. Crystal Structure of the Ternary Complex of Tcr, Mhc Class I and Lipopeptides. Int.Immunol. V. 32 805 2020.
ISSN: ESSN 1460-2377
PubMed: 32720986
DOI: 10.1093/INTIMM/DXAA050