Sodium in PDB 5l4i: Crystal Structure of Human Transthyretin in Complex with Clonixin

The structure of Crystal Structure of Human Transthyretin in Complex with Clonixin, PDB code: 5l4i was solved by C.Grundstrom, M.Hall, J.Zhang, A.Olofsson, P.Andersson, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.54 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.083, 86.275, 64.297, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 17.9

The structure of Crystal Structure of Human Transthyretin in Complex with Clonixin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Transthyretin in Complex with Clonixin (pdb code 5l4i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human Transthyretin in Complex with Clonixin, PDB code: 5l4i:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Transthyretin in Complex with Clonixin


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 Human Transthyretin in Complex with Clonixin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:54.1 occ:1.00 O A:ASP99 2.2 26.4 0.5 O A:ASP99 2.2 27.1 0.5 O A:HOH301 2.4 35.8 1.0 O A:HOH410 2.7 51.7 0.5 C A:ASP99 3.4 27.7 0.5 C A:ASP99 3.4 27.4 0.5 OD1 A:ASP99 3.7 40.1 0.5 HA A:SER100 3.9 36.5 1.0 HB2 A:ASP99 3.9 41.4 0.5 HA A:ASP99 3.9 34.4 0.5 HA A:ASP99 3.9 33.9 0.5 O A:HOH374 4.0 35.9 1.0 CG A:ASP99 4.1 38.8 0.5 OE2 A:GLU66 4.1 27.5 1.0 O A:HOH382 4.2 47.7 0.5 CA A:ASP99 4.2 28.7 0.5 CA A:ASP99 4.2 28.2 0.5 N A:SER100 4.4 27.8 1.0 CB A:ASP99 4.5 34.5 0.5 OD2 A:ASP99 4.6 41.1 0.5 CA A:SER100 4.6 30.4 1.0 CB A:ASP99 4.7 33.6 0.5 CD A:GLU66 4.7 24.4 1.0 OE1 A:GLU66 4.8 23.4 1.0 HB3 A:ASP99 4.9 40.3 0.5

J.Zhang, A.Begum, K.Brannstrom, C.Grundstrom, I.Iakovleva, A.Olofsson, A.E.Sauer-Eriksson, P.L.Andersson. Structure-Based Virtual Screening Protocol For in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin. Environ. Sci. Technol. V. 50 11984 2016.
ISSN: ISSN 1520-5851
PubMed: 27668830
DOI: 10.1021/ACS.EST.6B02771