Sodium in PDB 6y76: AP01 - A Redesigned Transferrin Receptor Apical Domain

The structure of AP01 - A Redesigned Transferrin Receptor Apical Domain, PDB code: 6y76 was solved by G.Oberdorfer, S.A.Berger, S.Bjelic, D.Sjorstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.70 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.122, 119.558, 33.167, 90.00, 112.25, 90.00
R / Rfree (%)	23.4 / 27.5

The binding sites of Sodium atom in the AP01 - A Redesigned Transferrin Receptor Apical Domain (pdb code 6y76). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the AP01 - A Redesigned Transferrin Receptor Apical Domain, PDB code: 6y76:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the AP01 - A Redesigned Transferrin Receptor Apical Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of AP01 - A Redesigned Transferrin Receptor Apical Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:28.0 occ:1.00 OG1 A:THR53 2.4 25.8 0.4 O A:HOH324 2.8 20.1 1.0 CG2 A:THR53 2.8 25.0 0.6 CE A:MET143 3.0 30.5 1.0 CE2 A:TYR52 3.3 29.9 1.0 CD2 A:TYR52 3.3 29.9 1.0 N A:TYR52 3.4 26.7 1.0 CZ A:TYR52 3.5 31.4 1.0 CG A:TYR52 3.5 24.9 1.0 N A:THR53 3.6 26.6 0.6 N A:THR53 3.6 26.7 0.4 CE1 A:TYR52 3.7 32.9 1.0 CB A:THR53 3.7 24.9 0.4 CD1 A:TYR52 3.7 30.8 1.0 CD2 A:LEU51 3.8 20.5 1.0 CB A:THR53 3.9 24.7 0.6 CA A:LEU51 4.0 22.8 1.0 OH A:TYR52 4.2 32.1 1.0 C A:LEU51 4.2 25.8 1.0 CA A:TYR52 4.2 24.7 1.0 CB A:MET143 4.2 17.0 1.0 CB A:LEU51 4.3 19.6 1.0 CA A:THR53 4.3 27.8 0.4 C A:TYR52 4.3 28.0 1.0 CA A:THR53 4.4 27.9 0.6 CB A:TYR52 4.4 21.8 1.0 CG A:LEU51 4.5 23.3 1.0 SD A:MET143 4.6 23.2 1.0 CG A:MET143 4.6 24.1 1.0 CG2 A:THR53 4.8 27.8 0.4 CG1 A:VAL38 5.0 16.9 1.0 CD1 A:LEU51 5.0 18.2 1.0

Sodium binding site 2 out of 3 in the AP01 - A Redesigned Transferrin Receptor Apical Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of AP01 - A Redesigned Transferrin Receptor Apical Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:32.8 occ:1.00 CD1 B:LEU14 3.7 25.0 1.0 CD2 B:LEU17 3.8 33.4 1.0 O B:HOH353 3.8 37.0 1.0 CB B:LEU17 4.3 25.2 1.0 CG B:LEU17 4.4 21.4 1.0 CD1 B:LEU17 4.4 21.3 1.0

Sodium binding site 3 out of 3 in the AP01 - A Redesigned Transferrin Receptor Apical Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of AP01 - A Redesigned Transferrin Receptor Apical Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:32.6 occ:1.00 O B:HOH316 3.4 29.7 1.0 O B:HOH353 4.1 37.0 1.0 O B:HOH376 4.2 39.4 1.0

D.J.Sjostrom, S.A.Berger, G.Oberdorfer, S.Bjelic. Computational Backbone Design Enables Soluble Engineering of Transferrin Receptor Apical Domain. Proteins V. 88 1569 2020.
ISSN: ESSN 1097-0134
PubMed: 32592192
DOI: 10.1002/PROT.25974