Sodium in PDB 7zi0: Structure of Human Smoothened in Complex with Cholesterol and Sag

The structure of Structure of Human Smoothened in Complex with Cholesterol and Sag, PDB code: 7zi0 was solved by E.F.X.Byrne, R.E.Woolley, B.Ansell, M.S.P.Sansom, S.Newstead, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.00 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.86, 63.15, 208.06, 90, 96.29, 90
R / Rfree (%)	23.1 / 27.5

The structure of Structure of Human Smoothened in Complex with Cholesterol and Sag also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Structure of Human Smoothened in Complex with Cholesterol and Sag (pdb code 7zi0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Smoothened in Complex with Cholesterol and Sag, PDB code: 7zi0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human Smoothened in Complex with Cholesterol and Sag


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Smoothened in Complex with Cholesterol and Sag within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:91.2 occ:1.00 O A:ALA93 2.3 108.6 1.0 O A:THR90 2.3 98.2 1.0 O A:SER96 2.7 95.0 1.0 C A:ALA93 3.4 100.4 1.0 C A:THR90 3.5 96.4 1.0 O A:LEU91 3.7 97.5 1.0 CA A:GLY94 3.8 98.6 1.0 C A:SER96 3.9 98.3 1.0 O A:GLY94 3.9 101.2 1.0 CA A:LEU91 4.0 93.2 1.0 N A:GLY94 4.0 98.6 1.0 C A:LEU91 4.0 92.5 1.0 C A:GLY94 4.1 98.3 1.0 OD1 A:ASP97 4.1 107.5 1.0 N A:LEU91 4.2 93.7 1.0 CA A:ALA93 4.5 94.8 1.0 N A:ALA93 4.5 92.8 1.0 N A:SER96 4.6 97.4 1.0 CA A:THR90 4.7 93.0 1.0 N A:ASP97 4.8 103.0 1.0 CA A:SER96 4.8 97.2 1.0 CB A:THR90 4.8 95.6 1.0 CA A:ASP97 4.9 104.7 1.0 N A:LEU92 4.9 88.0 1.0

Sodium binding site 2 out of 2 in the Structure of Human Smoothened in Complex with Cholesterol and Sag


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Smoothened in Complex with Cholesterol and Sag within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:85.5 occ:1.00 O A:THR307 3.0 151.3 1.0 OE2 A:GLU305 3.0 127.7 1.0 O A:GLU310 3.4 130.4 1.0 O A:THR311 3.7 124.3 1.0 N A:THR307 3.8 130.9 1.0 CB A:PRO306 3.8 123.3 1.0 CD2 A:LEU312 3.8 125.5 1.0 CA A:PRO306 3.9 121.6 1.0 C A:THR307 4.1 145.7 1.0 C A:PRO306 4.2 123.7 1.0 C A:GLU310 4.2 132.4 1.0 CD A:GLU305 4.2 123.7 1.0 C A:THR311 4.3 125.4 1.0 CA A:THR307 4.6 140.7 1.0 OE1 A:GLU305 4.7 125.2 1.0 CA A:LEU312 4.7 127.3 1.0 CG2 A:VAL315 4.8 125.1 1.0 N A:LEU312 4.8 128.5 1.0 CG1 A:VAL315 4.8 124.2 1.0 CB A:GLU310 4.8 137.2 1.0 CA A:GLU310 4.9 137.2 1.0 N A:THR311 4.9 128.4 1.0

M.Kinnebrew, R.E.Woolley, T.B.Ansell, E.F.X.Byrne, S.Frigui, G.Luchetti, R.Sircar, S.Nachtergaele, L.Mydock-Mcgrane, K.Krishnan, S.Newstead, M.S.P.Sansom, D.F.Covey, C.Siebold, R.Rohatgi. Patched 1 Regulates Smoothened By Controlling Sterol Binding to Its Extracellular Cysteine-Rich Domain. Sci Adv V. 8 M5563 2022.
ISSN: ESSN 2375-2548
PubMed: 35658032
DOI: 10.1126/SCIADV.ABM5563