Sodium in PDB 6tdp: Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule in Complex with One Gl Dipeptide in the A Pocket.

The structure of Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule in Complex with One Gl Dipeptide in the A Pocket., PDB code: 6tdp was solved by R.Anjanappa, M.Garcia Alai, S.Springer, R.Meijers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.23 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.340, 81.134, 56.450, 90.00, 112.29, 90.00
R / Rfree (%)	19 / 22.7

The binding sites of Sodium atom in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule in Complex with One Gl Dipeptide in the A Pocket. (pdb code 6tdp). 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 the Disulfide Engineered Hla-A0201 Molecule in Complex with One Gl Dipeptide in the A Pocket., PDB code: 6tdp:

Sodium binding site 1 out of 1 in the Crystal Structure of the Disulfide Engineered Hla-A0201 Molecule in Complex with One Gl Dipeptide in the A Pocket.


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 the Disulfide Engineered Hla-A0201 Molecule in Complex with One Gl Dipeptide in the A Pocket. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:25.2 occ:1.00 OE1 A:GLU63 2.7 18.0 1.0 OH A:TYR7 2.7 16.7 1.0 OH A:TYR59 3.0 14.9 1.0 CD A:GLU63 3.5 20.0 1.0 CZ A:TYR7 3.6 14.1 1.0 CG A:GLU63 3.7 18.0 1.0 CG2 A:VAL34 3.7 13.6 1.0 CE1 A:TYR7 3.7 12.8 1.0 CZ A:TYR59 3.9 17.1 1.0 CG1 A:VAL34 4.0 15.2 1.0 CE1 A:PHE33 4.0 13.5 1.0 CE A:MET45 4.0 17.9 1.0 CA A:GLY302 4.1 18.2 1.0 CB A:GLU63 4.2 15.8 1.0 N A:GLY302 4.3 15.8 1.0 N A:LEU303 4.3 20.9 1.0 CB A:VAL34 4.3 12.9 1.0 CZ A:PHE33 4.4 13.8 1.0 OH A:TYR171 4.4 16.5 1.0 CE2 A:TYR59 4.5 15.2 1.0 OE2 A:GLU63 4.6 23.7 1.0 C A:GLY302 4.6 19.4 1.0 CG A:LEU303 4.6 21.2 1.0 CE1 A:TYR59 4.7 17.4 1.0 CG A:MET45 4.8 13.7 1.0 CE2 A:TYR7 4.9 13.6 1.0 SD A:MET45 4.9 16.7 1.0

R.Anjanappa, M.Garcia-Alai, J.D.Kopicki, J.Lockhauserbaumer, M.Aboelmagd, J.Hinrichs, I.M.Nemtanu, C.Uetrecht, M.Zacharias, S.Springer, R.Meijers. Structures of Peptide-Free and Partially Loaded Mhc Class I Molecules Reveal Mechanisms of Peptide Selection. Nat Commun V. 11 1314 2020.
ISSN: ESSN 2041-1723
PubMed: 32161266
DOI: 10.1038/S41467-020-14862-4