Sodium in PDB 5l7d: Structure of Human Smoothened in Complex with Cholesterol

The structure of Structure of Human Smoothened in Complex with Cholesterol, PDB code: 5l7d was solved by E.F.X.Byrne, R.Sircar, P.S.Miller, G.Hedger, G.Luchetti, S.Nachtergaele, M.D.Tully, L.Mydock-Mcgrane, D.F.Covey, R.P.Rambo, M.S.P.Sansom, S.Newstead, R.Rohatgi, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.33 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.900, 63.020, 208.590, 90.00, 96.64, 90.00
R / Rfree (%)	23 / 26.4

The binding sites of Sodium atom in the Structure of Human Smoothened in Complex with Cholesterol (pdb code 5l7d). 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, PDB code: 5l7d:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1204 b:0.5 occ:1.00 O A:ALA93 2.3 97.1 1.0 O A:SER96 2.5 0.0 1.0 O A:THR90 2.9 95.0 1.0 C A:ALA93 3.4 95.1 1.0 CA A:GLY94 3.6 98.2 1.0 O A:GLY94 3.6 0.9 1.0 C A:SER96 3.7 0.7 1.0 C A:GLY94 3.8 0.1 1.0 OD1 A:ASP97 3.8 0.4 1.0 N A:GLY94 3.9 94.0 1.0 C A:THR90 4.0 93.8 1.0 O A:LEU91 4.3 92.1 1.0 N A:SER96 4.4 99.9 1.0 CA A:LEU91 4.5 89.6 1.0 C A:LEU91 4.5 91.0 1.0 CA A:SER96 4.6 0.7 1.0 N A:ASP97 4.6 0.7 1.0 CA A:ALA93 4.7 85.3 1.0 N A:ASP95 4.7 98.3 1.0 N A:LEU91 4.7 88.8 1.0 CA A:ASP97 4.7 0.4 1.0 N A:ALA93 4.8 84.6 1.0 CG A:ASP97 5.0 0.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1205 b:71.2 occ:1.00 O A:PRO306 2.8 0.2 1.0 O A:GLU310 3.2 0.6 1.0 OE2 A:GLU305 3.6 0.4 1.0 CD2 A:LEU312 3.6 0.0 1.0 O A:THR311 3.6 1.0 1.0 C A:PRO306 3.8 0.6 1.0 C A:GLU310 4.0 0.9 1.0 C A:THR311 4.0 0.4 1.0 CA A:PRO306 4.1 0.3 1.0 N A:LEU312 4.3 0.1 1.0 CA A:LEU312 4.3 0.6 1.0 CB A:PRO306 4.4 0.6 1.0 CD A:GLU305 4.6 0.6 1.0 CG A:LEU312 4.6 0.4 1.0 CB A:GLU310 4.6 1.0 1.0 N A:THR311 4.7 0.7 1.0 CA A:GLU310 4.7 0.3 1.0 O A:SER308 4.7 0.3 1.0 OG1 A:THR307 4.7 0.7 1.0 CA A:THR311 4.8 0.0 1.0 N A:GLU310 4.8 0.3 1.0 CG2 A:VAL315 4.9 0.7 1.0 OE1 A:GLU305 4.9 0.3 1.0 N A:THR307 5.0 0.5 1.0 CB A:LEU312 5.0 0.9 1.0

E.F.Byrne, R.Sircar, P.S.Miller, G.Hedger, G.Luchetti, S.Nachtergaele, M.D.Tully, L.Mydock-Mcgrane, D.F.Covey, R.P.Rambo, M.S.Sansom, S.Newstead, R.Rohatgi, C.Siebold. Structural Basis of Smoothened Regulation By Its Extracellular Domains. Nature V. 535 517 2016.
ISSN: ESSN 1476-4687
PubMed: 27437577
DOI: 10.1038/NATURE18934