Sodium in PDB 6o3c: Crystal Structure of Active Smoothened Bound to SAG21K, Cholesterol, and NBSMO8

The structure of Crystal Structure of Active Smoothened Bound to SAG21K, Cholesterol, and NBSMO8, PDB code: 6o3c was solved by I.S.Deshpande, J.Liang, D.Hedeen, K.J.Roberts, Y.Zhang, B.Ha, N.R.Latorraca, B.Faust, R.O.Dror, P.A.Beachy, B.R.Myers, A.Manglik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.94 / 2.80
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	39.010, 121.090, 157.010, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 29.4

The structure of Crystal Structure of Active Smoothened Bound to SAG21K, Cholesterol, and NBSMO8 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Active Smoothened Bound to SAG21K, Cholesterol, and NBSMO8 (pdb code 6o3c). 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 Active Smoothened Bound to SAG21K, Cholesterol, and NBSMO8, PDB code: 6o3c:

Sodium binding site 1 out of 1 in the Crystal Structure of Active Smoothened Bound to SAG21K, Cholesterol, and NBSMO8


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 Active Smoothened Bound to SAG21K, Cholesterol, and NBSMO8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:72.1 occ:1.00 O A:SER100 2.4 71.5 1.0 O A:THR94 2.5 53.0 1.0 O A:ALA97 2.6 70.0 1.0 OD1 A:ASP101 3.0 82.1 1.0 C A:SER100 3.6 75.2 1.0 C A:ALA97 3.7 61.8 1.0 C A:THR94 3.7 64.0 1.0 CB A:THR94 4.0 73.1 1.0 CG A:ASP101 4.1 87.3 1.0 CA A:ASP101 4.1 78.2 1.0 OG1 A:THR94 4.1 73.4 1.0 CA A:GLY98 4.1 62.6 1.0 N A:ASP101 4.3 74.1 1.0 N A:GLY98 4.3 61.9 1.0 N A:SER100 4.4 65.4 1.0 C A:GLY98 4.4 59.3 1.0 CA A:THR94 4.5 68.8 1.0 O A:LEU95 4.6 79.5 1.0 N A:LEU95 4.6 67.0 1.0 CA A:SER100 4.6 78.2 1.0 CA A:LEU95 4.7 66.3 1.0 O A:GLY98 4.7 68.3 1.0 CB A:ASP101 4.7 79.5 1.0 CA A:ALA97 4.7 55.4 1.0 C A:LEU95 4.8 70.0 1.0 N A:ALA97 4.9 68.8 1.0 N A:ASP99 5.0 56.6 1.0

I.Deshpande, J.Liang, D.Hedeen, K.J.Roberts, Y.Zhang, B.Ha, N.R.Latorraca, B.Faust, R.O.Dror, P.A.Beachy, B.R.Myers, A.Manglik. Smoothened Stimulation By Membrane Sterols Drives Hedgehog Pathway Activity. Nature V. 571 284 2019.
ISSN: ESSN 1476-4687
PubMed: 31263273
DOI: 10.1038/S41586-019-1355-4