Sodium in PDB 7z50: Structure of the Highly Diabetogenic 4.1-T Cell Receptor Targeting A Hybrid Insulin Peptide Bound to I-AG7.

The structure of Structure of the Highly Diabetogenic 4.1-T Cell Receptor Targeting A Hybrid Insulin Peptide Bound to I-AG7., PDB code: 7z50 was solved by J.Lopez-Sagaseta, E.Erausquin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.82 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	213.615, 133.457, 102.56, 90, 103.69, 90
R / Rfree (%)	22.1 / 26.1

The structure of Structure of the Highly Diabetogenic 4.1-T Cell Receptor Targeting A Hybrid Insulin Peptide Bound to I-AG7. also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of the Highly Diabetogenic 4.1-T Cell Receptor Targeting A Hybrid Insulin Peptide Bound to I-AG7. (pdb code 7z50). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Highly Diabetogenic 4.1-T Cell Receptor Targeting A Hybrid Insulin Peptide Bound to I-AG7., PDB code: 7z50:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Highly Diabetogenic 4.1-T Cell Receptor Targeting A Hybrid Insulin Peptide Bound to I-AG7.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Highly Diabetogenic 4.1-T Cell Receptor Targeting A Hybrid Insulin Peptide Bound to I-AG7. within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:47.4 occ:0.50 O F:GLN223 2.9 85.6 1.0 O F:ARG225 3.0 68.1 1.0 O F:ASP224 3.1 69.4 1.0 C F:ASP224 3.6 72.4 1.0 C F:ARG225 3.8 65.1 1.0 CD1 F:TRP221 3.9 63.5 1.0 C F:GLN223 4.0 78.7 1.0 CA F:ASP224 4.1 78.2 1.0 NE1 F:TRP221 4.2 61.9 1.0 N F:ARG225 4.3 69.7 1.0 N F:ALA226 4.5 61.9 1.0 CA F:ALA226 4.5 59.5 1.0 N F:ASP224 4.5 80.7 1.0 CA F:ARG225 4.6 60.8 1.0 N F:LYS227 4.7 60.0 1.0 C F:ALA226 4.9 62.9 1.0

Sodium binding site 2 out of 2 in the Structure of the Highly Diabetogenic 4.1-T Cell Receptor Targeting A Hybrid Insulin Peptide Bound to I-AG7.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Highly Diabetogenic 4.1-T Cell Receptor Targeting A Hybrid Insulin Peptide Bound to I-AG7. within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:47.6 occ:1.00 O E:GLN40 2.7 58.8 1.0 O H:PHE102 2.9 50.0 1.0 O E:LEU42 2.9 59.4 1.0 O H:GLY103 3.0 56.0 1.0 C H:GLY103 3.3 58.1 1.0 C H:PHE102 3.7 48.3 1.0 N H:ALA104 3.8 55.4 1.0 C E:GLN40 3.9 52.6 1.0 CA H:GLY103 4.0 46.7 1.0 C E:LEU42 4.0 53.2 1.0 CA H:ALA104 4.1 53.3 1.0 N H:GLY103 4.2 40.8 1.0 CG E:GLU43 4.2 56.0 1.0 N E:LEU42 4.3 63.6 1.0 NE2 E:GLN40 4.5 88.2 1.0 O H:HOH410 4.6 47.9 1.0 C E:GLY41 4.6 62.1 1.0 CA H:PHE102 4.7 46.4 1.0 CB H:PHE102 4.7 39.8 1.0 CA E:GLY41 4.8 48.8 1.0 CA E:LEU42 4.8 54.6 1.0 CA E:GLN40 4.8 57.5 1.0 N E:GLU43 4.8 51.0 1.0 N E:GLY41 4.8 50.8 1.0 CA E:GLU43 4.9 52.2 1.0 CB E:GLN40 4.9 55.5 1.0 CB H:ALA104 5.0 48.8 1.0

E.Erausquin, P.Serra, D.Parras, P.Santamaria, J.Lopez-Sagaseta. Structural Plasticity in I-A G7 Links Autoreactivity to Hybrid Insulin Peptides in Type I Diabetes. Front Immunol V. 13 24311 2022.
ISSN: ESSN 1664-3224
PubMed: 35967292
DOI: 10.3389/FIMMU.2022.924311