Sodium in PDB 8dv3: Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1

The structure of Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1, PDB code: 8dv3 was solved by R.Farquhar, J.Rossjohn, A.Shahine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.58 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.816, 78.628, 92.725, 90, 90, 90
R / Rfree (%)	19.2 / 25.3

The structure of Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1 also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Iodine	(I)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1 (pdb code 8dv3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1, PDB code: 8dv3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1


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 Human CD1B Presenting Phosphatidylinositol C34:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1203 b:35.8 occ:1.00 O A:HOH1439 2.4 37.1 1.0 NE2 A:GLN82 3.4 39.8 1.0 O A:THR22 3.6 39.6 1.0 N A:ALA24 3.7 23.3 1.0 C A:THR22 3.7 37.1 1.0 N A:TRP23 3.9 32.7 1.0 CA A:TRP23 4.1 33.7 1.0 C A:TRP23 4.1 33.6 1.0 CB A:ALA24 4.2 20.9 1.0 CG A:GLN82 4.2 27.3 1.0 CD A:GLN82 4.3 31.0 1.0 CA A:THR22 4.4 29.6 1.0 CA A:ALA24 4.5 26.1 1.0 O A:HOH1403 4.8 33.1 1.0 O A:ALA24 4.8 29.2 1.0 O A:SER21 4.9 37.2 1.0 CB A:ALA78 5.0 21.3 1.0 O A:HOH1503 5.0 40.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1216 b:64.6 occ:1.00 O A:SER196 2.3 56.7 1.0 C A:SER196 3.4 57.1 1.0 O A:GLY198 3.4 59.1 1.0 CA A:PRO197 3.7 68.3 1.0 N A:GLY198 3.8 57.9 1.0 C A:PRO197 3.9 61.9 1.0 N A:PRO197 4.0 53.5 1.0 C A:GLY198 4.2 53.9 1.0 N A:SER196 4.5 54.2 1.0 O A:ARG201 4.5 39.9 1.0 CA A:SER196 4.6 51.4 1.0 O A:PRO197 4.6 58.6 1.0 CA A:GLY198 4.6 50.9 1.0

R.Farquhar, I.Van Rhijn, D.B.Moody, J.Rossjohn, A.Shahine. Alpha Beta T-Cell Receptor Recognition of Self-Phosphatidylinositol Presented By CD1B. J.Biol.Chem. V. 299 02849 2023.
ISSN: ESSN 1083-351X
PubMed: 36587766
DOI: 10.1016/J.JBC.2022.102849