Sodium in PDB 8p0z: AP01-S2.3 - A Variant of A Redesigned Transferrin Receptor Apical Domain

The structure of AP01-S2.3 - A Variant of A Redesigned Transferrin Receptor Apical Domain, PDB code: 8p0z was solved by G.Oberdorfer, B.Grill, S.Bjelic, D.Stoll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.95 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.99, 57.37, 39.1, 90, 113.15, 90
R / Rfree (%)	21.3 / 23.6

The binding sites of Sodium atom in the AP01-S2.3 - A Variant of A Redesigned Transferrin Receptor Apical Domain (pdb code 8p0z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the AP01-S2.3 - A Variant of A Redesigned Transferrin Receptor Apical Domain, PDB code: 8p0z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the AP01-S2.3 - A Variant of 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-S2.3 - A Variant of A Redesigned Transferrin Receptor Apical Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:35.3 occ:1.00 OE1 A:GLU71 2.4 32.8 1.0 N A:THR68 3.2 28.2 1.0 CG2 A:THR68 3.2 33.6 1.0 O A:HOH384 3.3 36.8 1.0 OG1 A:THR68 3.4 28.9 1.0 CD A:GLU71 3.5 33.3 1.0 CB A:THR68 3.7 31.9 1.0 CB A:GLU71 3.7 29.7 1.0 CB A:ILE67 3.8 27.5 1.0 CA A:ILE67 3.9 25.1 1.0 C A:ILE67 4.0 28.4 1.0 CA A:THR68 4.0 30.5 1.0 O A:HOH400 4.2 44.8 1.0 CG A:GLU71 4.2 34.0 1.0 CG2 A:ILE67 4.3 29.6 1.0 OE2 A:GLU71 4.5 35.8 1.0 O A:HOH358 4.5 39.8 1.0 O A:THR68 5.0 31.1 1.0 C A:THR68 5.0 31.0 1.0

Sodium binding site 2 out of 2 in the AP01-S2.3 - A Variant of 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-S2.3 - A Variant of A Redesigned Transferrin Receptor Apical Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:42.4 occ:1.00 OG1 A:THR145 2.5 34.5 1.0 O A:SER146 3.1 34.4 1.0 O A:LYS149 3.1 37.8 1.0 CG A:LYS36 3.1 32.7 0.4 CD A:LYS36 3.3 33.6 0.4 O A:HOH380 3.4 44.1 1.0 O A:THR145 3.5 31.9 1.0 CG A:LYS36 3.5 31.6 0.6 CB A:LYS36 3.6 30.9 0.6 CB A:THR145 3.7 36.1 1.0 CB A:LYS36 3.7 30.9 0.4 OD1 A:ASN150 3.8 33.7 1.0 C A:THR145 3.9 32.7 1.0 C A:SER146 4.0 35.1 1.0 CA A:LYS36 4.0 31.5 0.6 CA A:LYS36 4.0 31.5 0.4 CE A:LYS36 4.1 32.6 0.6 CA A:THR145 4.3 34.2 1.0 CD A:LYS36 4.3 33.1 0.6 C A:LYS149 4.3 35.6 1.0 CA A:GLU147 4.4 41.3 1.0 NZ A:LYS10 4.5 39.7 1.0 CE A:LYS36 4.5 33.2 0.4 N A:GLU147 4.6 39.9 1.0 N A:SER146 4.6 37.5 1.0 CE A:LYS10 4.7 36.5 1.0 N A:THR145 4.7 30.2 1.0 O A:GLU147 4.8 42.3 1.0 C A:GLU147 4.8 38.0 1.0 N A:LYS36 4.9 31.2 0.4 N A:LYS36 4.9 31.2 0.6 CG2 A:THR145 4.9 34.3 1.0 CA A:SER146 4.9 35.2 1.0 O A:HOH398 4.9 38.7 1.0

D.J.Sjostrom, B.Grill, E.Ambrosetti, A.A.Veetil, C.Mohlin, A.I.Teixeira, G.Oberdofer, S.Bjelic. Affinity Maturated Transferrin Receptor Apical Domain Blocks Machupo Virus Glycoprotein Binding. J.Mol.Biol. V. 435 68262 2023.
ISSN: ESSN 1089-8638
PubMed: 37678707
DOI: 10.1016/J.JMB.2023.168262