Sodium in PDB 7lrf: Netrin-1 in Complex with Sos

The structure of Netrin-1 in Complex with Sos, PDB code: 7lrf was solved by M.Gupta, M.Mcdougall, A.M.Torres, J.Stetefeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.36 / 3.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.105, 80.152, 241.702, 90, 90, 90
R / Rfree (%)	22.6 / 28.1

The structure of Netrin-1 in Complex with Sos also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Netrin-1 in Complex with Sos (pdb code 7lrf). 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 Netrin-1 in Complex with Sos, PDB code: 7lrf:

Sodium binding site 1 out of 1 in the Netrin-1 in Complex with Sos


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Netrin-1 in Complex with Sos within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:77.6 occ:1.00 OD1 A:ASP272 2.2 101.2 1.0 OE1 A:GLU268 2.8 101.8 1.0 CG A:ASP272 3.4 104.4 1.0 CD A:GLU268 3.5 103.5 1.0 O A:SER267 3.5 107.0 1.0 CB A:ASP261 3.9 127.9 1.0 OD2 A:ASP272 4.0 106.3 1.0 OG A:SER273 4.1 98.9 1.0 OE2 A:GLU268 4.1 88.3 1.0 CG A:GLU268 4.2 110.3 1.0 C A:SER267 4.3 123.9 1.0 CB A:GLU268 4.4 119.3 1.0 CA A:ASP272 4.4 119.8 1.0 N A:SER273 4.4 113.3 1.0 CB A:ASP272 4.5 110.2 1.0 CG A:ASP261 4.6 138.5 1.0 O A:ASP266 4.7 131.6 1.0 O A:ASP261 4.8 138.8 1.0 CA A:SER267 4.8 124.0 1.0 OD2 A:ASP261 4.9 154.1 1.0 C A:ASP261 4.9 126.9 1.0 CA A:ASP261 5.0 124.5 1.0 C A:ASP272 5.0 113.2 1.0

M.Gupta, M.Mcdougall, A.M.Torres, J.Stetefeld. Netrin-1 in Complex with Sos To Be Published.