Calcium in PDB 7ne0: Structure of the Ternary Complex Between Netrin-1, Repulsive-Guidance Molecule-B (Rgmb) and Neogenin

The structure of Structure of the Ternary Complex Between Netrin-1, Repulsive-Guidance Molecule-B (Rgmb) and Neogenin, PDB code: 7ne0 was solved by R.A.Robinson, S.C.Griffiths, L.L.Van De Haar, T.Malinauskas, E.Y.Vanbattum, P.Zelina, R.A.Schwab, D.Karia, L.Malinauskaite, S.Brignani, M.Vanden Munkhof, O.Dudukcu, A.A.De Ruiter, D.M.A.Van Den Heuvel, B.Bishop, J.Elegheert, A.R.Aricescu, R.J.Pasterkamp, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.96 / 3.25
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	136.78, 136.78, 430.11, 90, 90, 120
R / Rfree (%)	24.9 / 26.3

The binding sites of Calcium atom in the Structure of the Ternary Complex Between Netrin-1, Repulsive-Guidance Molecule-B (Rgmb) and Neogenin (pdb code 7ne0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Structure of the Ternary Complex Between Netrin-1, Repulsive-Guidance Molecule-B (Rgmb) and Neogenin, PDB code: 7ne0:

Calcium binding site 1 out of 1 in the Structure of the Ternary Complex Between Netrin-1, Repulsive-Guidance Molecule-B (Rgmb) and Neogenin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Ternary Complex Between Netrin-1, Repulsive-Guidance Molecule-B (Rgmb) and Neogenin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:111.0 occ:1.00 OD1 A:ASP110 2.5 148.0 1.0 O A:SER277 2.5 123.6 1.0 O A:THR118 2.6 136.8 1.0 O A:PHE107 2.8 129.1 1.0 OG1 A:THR118 2.8 148.5 1.0 CG A:ASP110 3.5 150.0 1.0 C A:SER277 3.6 122.0 1.0 C A:THR118 3.6 140.2 1.0 CB A:THR118 3.9 150.3 1.0 OD2 A:ASP110 3.9 157.3 1.0 C A:PHE107 4.0 130.4 1.0 O A:ASP110 4.0 136.3 1.0 CA A:THR118 4.1 140.6 1.0 N A:THR118 4.1 140.5 1.0 O A:LEU111 4.2 142.8 1.0 CA A:SER277 4.2 119.6 1.0 CA A:ASN112 4.4 133.2 1.0 OD1 A:ASN112 4.5 154.5 1.0 CB A:SER277 4.5 124.0 1.0 C A:ASP110 4.5 138.9 1.0 O A:LEU108 4.5 124.7 1.0 C A:LEU111 4.6 140.6 1.0 N A:ASN112 4.7 133.9 1.0 N A:ASP278 4.7 115.3 1.0 CA A:PHE107 4.8 130.4 1.0 CB A:ASP110 4.8 140.8 1.0 N A:CYS119 4.8 136.6 1.0 CB A:ASN112 4.9 131.9 1.0 C A:LEU108 4.9 126.4 1.0 N A:LEU108 4.9 124.7 1.0 OD1 A:ASP278 4.9 134.2 1.0 N A:ASP110 4.9 132.8 1.0 CA A:ASP278 5.0 113.4 1.0 CA A:ASP110 5.0 135.6 1.0 CA A:LEU108 5.0 121.1 1.0

R.A.Robinson, S.C.Griffiths, L.L.Van De Haar, T.Malinauskas, E.Y.Van Battum, P.Zelina, R.A.Schwab, D.Karia, L.Malinauskaite, S.Brignani, M.H.Van Den Munkhof, O.Dudukcu, A.A.De Ruiter, D.M.A.Van Den Heuvel, B.Bishop, J.Elegheert, A.R.Aricescu, R.J.Pasterkamp, C.Siebold. Simultaneous Binding of Guidance Cues NET1 and Rgm Blocks Extracellular NEO1 Signaling. Cell 2021.
PubMed: 33740419
DOI: 10.1016/J.CELL.2021.02.045