Sodium in PDB 6i9s: HROBO2 Extracellular Domains 2-3

The structure of HROBO2 Extracellular Domains 2-3, PDB code: 6i9s was solved by R.Barak, N.M.Isupov, Y.Opatowsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.66 / 2.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.220, 70.520, 97.280, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 29.3

The binding sites of Sodium atom in the HROBO2 Extracellular Domains 2-3 (pdb code 6i9s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the HROBO2 Extracellular Domains 2-3, PDB code: 6i9s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the HROBO2 Extracellular Domains 2-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of HROBO2 Extracellular Domains 2-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:71.6 occ:1.00 O A:GLU178 2.3 72.2 1.0 O A:HOH544 2.3 69.9 1.0 O A:ILE181 2.3 65.6 1.0 O A:ASP176 2.3 68.1 1.0 C A:GLU178 3.2 68.2 1.0 C A:ASP176 3.4 61.9 1.0 C A:ILE181 3.6 55.1 1.0 O A:GLU179 3.7 56.4 1.0 CA A:GLU179 3.7 71.5 1.0 O A:LYS177 3.8 55.4 1.0 N A:GLU179 3.8 67.8 1.0 C A:GLU179 3.9 61.6 1.0 CB A:ASP176 3.9 69.9 1.0 CA A:ASP176 4.1 67.3 1.0 C A:LYS177 4.1 67.9 1.0 N A:ILE181 4.3 55.0 1.0 OG A:SER182 4.3 57.1 1.0 N A:GLU178 4.4 73.7 1.0 CA A:GLU178 4.4 71.1 1.0 N A:LYS177 4.4 60.3 1.0 CA A:ILE181 4.5 55.9 1.0 N A:SER182 4.5 52.2 1.0 CG A:ASP176 4.5 71.2 1.0 CA A:SER182 4.6 53.4 1.0 N A:ARG180 4.7 55.6 1.0 CA A:LYS177 4.8 69.8 1.0 OD2 A:ASP176 4.8 72.8 1.0

Sodium binding site 2 out of 2 in the HROBO2 Extracellular Domains 2-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of HROBO2 Extracellular Domains 2-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:74.5 occ:1.00 O B:HOH516 2.3 66.6 1.0 O B:GLU178 2.3 66.5 1.0 O B:ILE181 2.3 64.3 1.0 O B:ASP176 2.3 67.6 1.0 C B:GLU178 3.3 66.3 1.0 C B:ASP176 3.5 63.0 1.0 C B:ILE181 3.5 58.1 1.0 O B:GLU179 3.6 63.4 1.0 CA B:GLU179 3.7 75.1 1.0 C B:GLU179 3.8 65.8 1.0 N B:GLU179 3.8 73.5 1.0 O B:LYS177 3.9 61.2 1.0 CB B:ASP176 4.1 76.4 1.0 N B:ILE181 4.1 66.0 1.0 CA B:ASP176 4.2 70.5 1.0 C B:LYS177 4.2 69.9 1.0 CA B:ILE181 4.3 64.1 1.0 OG B:SER182 4.4 52.0 1.0 N B:GLU178 4.4 73.7 1.0 N B:SER182 4.5 55.9 1.0 N B:LYS177 4.5 69.1 1.0 CA B:GLU178 4.5 73.0 1.0 CA B:SER182 4.7 56.1 1.0 N B:ARG180 4.7 66.0 1.0 CG B:ASP176 4.7 79.1 1.0 CA B:LYS177 4.9 81.1 1.0 O B:HOH507 4.9 66.8 1.0 OD2 B:ASP176 4.9 85.9 1.0 CB B:ILE181 5.0 60.3 1.0

R.Barak, G.Yom-Tov, J.Guez-Haddad, L.Gasri-Plotnitsky, R.Maimon, M.Cohen-Berkman, A.A.Mccarthy, E.Perlson, S.Henis-Korenblit, M.N.Isupov, Y.Opatowsky. Structural Principles in Robo Activation and Auto-Inhibition. Cell V. 177 272 2019.
ISSN: ISSN 1097-4172
PubMed: 30853216
DOI: 10.1016/J.CELL.2019.02.004