Sodium in PDB 7qhp: Structure of I-AG7 with A Bound Hybrid Insulin Peptide

The structure of Structure of I-AG7 with A Bound Hybrid Insulin Peptide, PDB code: 7qhp 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)	54.41 / 1.82
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.996, 108.819, 98.055, 90, 90, 90
R / Rfree (%)	18.3 / 21.9

The binding sites of Sodium atom in the Structure of I-AG7 with A Bound Hybrid Insulin Peptide (pdb code 7qhp). 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 I-AG7 with A Bound Hybrid Insulin Peptide, PDB code: 7qhp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of I-AG7 with A Bound Hybrid Insulin Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of I-AG7 with A Bound Hybrid Insulin Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:47.2 occ:1.00 N B:ARG68 3.2 26.7 1.0 O B:GLN64 3.4 29.0 1.0 C B:TYR65 3.5 30.0 1.0 N B:GLU67 3.6 26.5 1.0 O B:TYR65 3.6 28.8 1.0 CA B:TYR65 3.7 28.3 1.0 CB B:GLU67 3.8 30.8 1.0 CB B:ARG68 3.8 30.4 1.0 CA B:GLU67 4.0 25.7 1.0 C B:GLU67 4.0 24.9 1.0 N B:LEU66 4.0 25.8 1.0 CA B:ARG68 4.1 30.8 1.0 C B:GLN64 4.2 36.7 1.0 N B:TYR65 4.2 33.1 1.0 NH1 B:ARG68 4.4 33.6 1.0 C B:LEU66 4.5 27.9 1.0 CZ B:ARG68 4.9 30.6 1.0 CA B:LEU66 4.9 30.5 1.0 CB B:TYR65 5.0 23.9 1.0

Sodium binding site 2 out of 2 in the Structure of I-AG7 with A Bound Hybrid Insulin Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of I-AG7 with A Bound Hybrid Insulin Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:48.0 occ:1.00 CD2 B:HIS173 2.5 48.1 1.0 O B:LYS127 3.1 31.9 1.0 O B:HIS173 3.1 30.6 1.0 NE2 B:HIS173 3.4 45.5 1.0 CG B:HIS173 3.6 45.2 1.0 CG B:GLU175 3.6 47.8 1.0 C B:HIS173 3.7 34.2 1.0 C B:LYS127 3.7 27.9 1.0 CB B:ARG129 3.8 41.6 1.0 N B:ARG129 3.8 33.8 1.0 CD B:GLU175 3.9 58.9 1.0 N B:GLU175 4.0 32.3 1.0 CG B:LYS127 4.0 35.4 1.0 OE1 B:GLU175 4.1 58.0 1.0 CB B:LYS127 4.1 32.7 1.0 N B:VAL174 4.1 32.8 1.0 CB B:HIS173 4.1 36.6 1.0 N B:VAL128 4.2 30.3 1.0 CA B:VAL128 4.2 33.2 1.0 C B:VAL128 4.2 38.0 1.0 CA B:VAL174 4.2 34.5 1.0 CB B:GLU175 4.3 37.5 1.0 C B:VAL174 4.4 31.0 1.0 CA B:ARG129 4.5 37.8 1.0 CA B:HIS173 4.5 34.6 1.0 CA B:LYS127 4.6 27.9 1.0 OE2 B:GLU175 4.6 68.1 1.0 CE1 B:HIS173 4.6 41.6 1.0 ND1 B:HIS173 4.7 50.4 1.0 CA B:GLU175 4.8 39.7 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