Sodium in PDB 5uc6: Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III

The structure of Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III, PDB code: 5uc6 was solved by X.Ren, A.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.77 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.790, 74.790, 86.360, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 21.9

The structure of Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III (pdb code 5uc6). 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 Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III, PDB code: 5uc6:

Sodium binding site 1 out of 1 in the Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:27.8 occ:1.00 O B:HOH222 2.2 26.8 1.0 O A:ASP65 2.3 28.7 1.0 OD1 A:ASP64 2.4 31.8 1.0 O A:HOH333 2.4 33.2 1.0 O21 B:85Y7 2.5 23.8 1.0 O B:HOH245 2.6 43.1 1.0 C20 B:85Y7 3.3 21.7 1.0 C A:ASP65 3.5 28.9 1.0 CG A:ASP64 3.5 35.8 1.0 O A:ASP64 3.8 28.8 1.0 C A:ASP64 3.9 30.6 1.0 C6 B:85Y7 4.0 24.4 1.0 O2 B:85Y10 4.1 26.4 1.0 C5 B:85Y7 4.1 22.5 1.0 CA A:ALA66 4.2 24.2 1.0 N3 B:85Y10 4.2 20.9 1.0 N A:ASP65 4.2 28.0 1.0 OD2 A:ASP64 4.2 41.7 1.0 C23 B:85Y7 4.3 21.3 1.0 N A:ALA66 4.3 22.6 1.0 CA A:ASP64 4.3 30.1 1.0 N22 B:85Y7 4.4 22.7 1.0 CB A:ASP64 4.4 27.8 1.0 O A:ALA66 4.5 25.6 1.0 CA A:ASP65 4.5 28.8 1.0 O A:HOH328 4.5 46.5 1.0 C A:ALA66 4.6 23.5 1.0 C2 B:85Y10 4.6 29.3 1.0 C8 B:DA9 4.7 23.5 1.0 C24 B:85Y7 4.8 24.8 1.0 C29 B:85Y7 5.0 24.5 1.0

X.Ren, A.D.Gelinas, I.Von Carlowitz, N.Janjic, A.M.Pyle. Structural Basis For Il-1 Alpha Recognition By A Modified Dna Aptamer That Specifically Inhibits Il-1 Alpha Signaling. Nat Commun V. 8 810 2017.
ISSN: ESSN 2041-1723
PubMed: 28993621
DOI: 10.1038/S41467-017-00864-2