Sodium in PDB 8ig1: Crystal Structure of Wild-Type Transthyretin in Complex with Rafoxanide

The structure of Crystal Structure of Wild-Type Transthyretin in Complex with Rafoxanide, PDB code: 8ig1 was solved by T.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.41 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.71, 84.825, 64.326, 90, 90, 90
R / Rfree (%)	17 / 19.3

The structure of Crystal Structure of Wild-Type Transthyretin in Complex with Rafoxanide also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Iodine	(I)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of Wild-Type Transthyretin in Complex with Rafoxanide (pdb code 8ig1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Wild-Type Transthyretin in Complex with Rafoxanide, PDB code: 8ig1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Wild-Type Transthyretin in Complex with Rafoxanide


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 Wild-Type Transthyretin in Complex with Rafoxanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:38.0 occ:1.00 O A:HOH302 2.3 35.4 1.0 O A:ASP99 2.3 30.3 1.0 O A:HOH372 2.5 38.2 1.0 O A:HOH395 3.0 41.2 1.0 C A:ASP99 3.5 29.9 1.0 OE1 A:GLU66 4.0 26.1 1.0 CA A:ASP99 4.2 30.9 1.0 O A:HOH361 4.4 40.0 1.0 N A:SER100 4.5 31.1 1.0 CB A:ASP99 4.7 38.9 1.0 CD A:GLU66 4.7 22.7 1.0 OE2 A:GLU66 4.8 22.6 1.0 CA A:SER100 4.8 32.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Wild-Type Transthyretin in Complex with Rafoxanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Wild-Type Transthyretin in Complex with Rafoxanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:49.2 occ:1.00 O B:ASP99 2.4 42.4 0.5 O B:HOH308 2.5 51.6 1.0 C B:ASP99 3.6 34.6 0.5 OG B:SER100 4.2 30.6 0.5 O B:HOH345 4.4 30.5 1.0 OD1 B:ASN98 4.4 32.3 0.5 CB B:ASP99 4.4 31.9 0.5 N B:SER100 4.5 30.0 0.5 CA B:ASP99 4.5 31.1 0.5 CA B:SER100 4.6 28.6 0.5 OD2 B:ASP99 4.9 34.9 0.5 CG B:ASP99 4.9 33.7 0.5 CB B:SER100 5.0 29.2 0.5

T.Yokoyama, M.Mizuguchi, Y.Nabeshima, Y.Nakagawa, T.Okada, N.Toyooka, K.Kusaka. Rafoxanide, A Salicylanilide Anthelmintic, Interacts with Human Plasma Protein Transthyretin. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 37522420
DOI: 10.1111/FEBS.16915