Sodium in PDB 5efi: Crystal Structure of Mouse CD1D in Complex with the P99P Lipopeptide

The structure of Crystal Structure of Mouse CD1D in Complex with the P99P Lipopeptide, PDB code: 5efi was solved by E.Girardi, J.Wang, D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.12 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.190, 107.850, 110.340, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24.4

The binding sites of Sodium atom in the Crystal Structure of Mouse CD1D in Complex with the P99P Lipopeptide (pdb code 5efi). 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 Mouse CD1D in Complex with the P99P Lipopeptide, PDB code: 5efi:

Sodium binding site 1 out of 1 in the Crystal Structure of Mouse CD1D in Complex with the P99P Lipopeptide


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 Mouse CD1D in Complex with the P99P Lipopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:45.7 occ:1.00 O A:TRP40 2.6 37.5 1.0 O A:THR26 2.9 37.1 1.0 C A:THR26 3.6 35.9 1.0 O3 A:CIT310 3.6 58.5 1.0 C A:TRP40 3.6 38.3 1.0 NH1 A:ARG74 3.6 47.2 1.0 CD A:ARG74 3.6 45.0 1.0 CD2 A:TRP40 3.7 40.0 1.0 N A:SER28 3.7 30.8 1.0 CA A:ASP27 3.7 33.2 1.0 CG A:TRP40 3.8 39.7 1.0 CE3 A:TRP40 3.8 38.8 1.0 C A:ASP27 3.9 31.2 1.0 OG A:SER28 4.0 30.3 1.0 N A:ASP27 4.0 33.9 1.0 O A:SER41 4.0 44.1 1.0 CB A:TRP40 4.0 37.6 1.0 C A:SER41 4.1 43.1 1.0 CG2 A:THR26 4.1 34.6 1.0 CB A:SER28 4.2 30.0 1.0 CE2 A:TRP40 4.2 42.4 1.0 N A:ASN42 4.3 43.7 1.0 CD1 A:TRP40 4.4 41.8 1.0 NE A:ARG74 4.4 47.5 1.0 CZ A:ARG74 4.4 48.5 1.0 CA A:TRP40 4.5 37.5 1.0 CZ3 A:TRP40 4.5 39.8 1.0 CB A:THR26 4.5 36.4 1.0 N A:SER41 4.5 40.0 1.0 CA A:ASN42 4.5 45.7 1.0 C5 A:CIT310 4.6 59.8 1.0 CA A:SER28 4.6 29.4 1.0 NE1 A:TRP40 4.6 43.5 1.0 O4 A:CIT310 4.6 60.8 1.0 CA A:SER41 4.7 41.4 1.0 CA A:THR26 4.7 36.4 1.0 CG A:ARG74 4.8 44.7 1.0 O A:ASP27 4.8 30.0 1.0 CZ2 A:TRP40 4.8 43.4 1.0 CH2 A:TRP40 4.9 42.0 1.0

E.Girardi, J.Wang, D.M.Zajonc. Structure of An Alpha-Helical Peptide and Lipopeptide Bound to the Nonclassical Major Histocompatibility Complex (Mhc) Class I Molecule CD1D. J.Biol.Chem. V. 291 10677 2016.
ISSN: ESSN 1083-351X
PubMed: 27006394
DOI: 10.1074/JBC.M115.702118