Calcium 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
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Netrin-1 in Complex with Sos (pdb code 7lrf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Netrin-1 in Complex with Sos, PDB code: 7lrf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Netrin-1 in Complex with Sos


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Netrin-1 in Complex with Sos within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:305.1 occ:1.00 OG1 A:THR120 2.3 79.2 1.0 O A:SER279 2.5 88.8 1.0 OD1 A:ASP112 2.6 107.4 1.0 O A:PHE109 2.9 69.2 1.0 OD1 A:ASP280 3.5 91.8 1.0 OD1 A:ASN114 3.5 89.1 1.0 C A:SER279 3.5 82.7 1.0 CA A:ASP280 3.6 80.0 1.0 CB A:THR120 3.6 99.6 1.0 CB A:ASP280 3.7 94.0 1.0 CB A:ASN114 3.7 104.1 1.0 O A:ASP112 3.7 103.5 1.0 CG A:ASP280 3.7 89.4 1.0 CG A:ASP112 3.8 98.8 1.0 CA A:ASN114 3.8 97.2 1.0 C A:PHE109 4.0 84.9 1.0 N A:ASN114 4.0 102.0 1.0 CG A:ASN114 4.0 95.7 1.0 N A:ASP280 4.0 74.1 1.0 CG2 A:THR120 4.0 103.0 1.0 O A:LEU110 4.1 97.5 1.0 C A:ASP112 4.2 92.9 1.0 N A:ASP112 4.3 76.4 1.0 C A:LEU110 4.3 91.3 1.0 O A:THR120 4.3 98.5 1.0 C A:LEU113 4.4 99.5 1.0 OD2 A:ASP112 4.5 88.4 1.0 OD2 A:ASP280 4.6 73.0 1.0 O A:LEU113 4.6 102.4 1.0 CA A:LEU110 4.7 80.1 1.0 CA A:ASP112 4.7 81.3 1.0 CA A:THR120 4.7 89.4 1.0 N A:THR111 4.8 93.1 1.0 N A:LEU110 4.8 76.0 1.0 CA A:SER279 4.8 81.2 1.0 N A:THR120 4.9 100.8 1.0 CB A:ASP112 4.9 96.0 1.0 CA A:PHE109 4.9 90.4 1.0 C A:ASP280 4.9 85.4 1.0 C A:THR120 5.0 94.4 1.0 N A:LEU113 5.0 88.8 1.0

Calcium binding site 2 out of 2 in the Netrin-1 in Complex with Sos


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Netrin-1 in Complex with Sos within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:137.7 occ:1.00 OG1 B:THR120 2.4 115.8 1.0 O B:PHE109 2.6 82.7 1.0 O B:SER279 2.7 96.6 1.0 OD1 B:ASN114 2.8 106.6 1.0 OD1 B:ASP112 2.8 116.6 1.0 O B:THR120 2.9 97.7 1.0 CG B:ASN114 3.6 116.7 1.0 C B:PHE109 3.7 88.2 1.0 CB B:ASN114 3.7 106.0 1.0 CB B:THR120 3.7 116.3 1.0 C B:THR120 3.8 120.0 1.0 CG B:ASP112 3.9 118.4 1.0 C B:SER279 3.9 93.4 1.0 CA B:ASN114 4.1 100.7 1.0 CA B:THR120 4.1 115.1 1.0 O B:ASP112 4.2 94.8 1.0 N B:THR120 4.2 108.8 1.0 OD1 B:ASP280 4.2 115.8 1.0 OD2 B:ASP112 4.2 108.2 1.0 CA B:PHE109 4.4 96.3 1.0 CG2 B:THR120 4.5 121.5 1.0 CA B:ASP280 4.6 92.9 1.0 CB B:ASP280 4.6 86.0 1.0 N B:ASP280 4.6 94.5 1.0 N B:LEU110 4.7 88.3 1.0 CB B:PHE109 4.7 106.9 1.0 O B:LEU113 4.7 113.8 1.0 N B:ASN114 4.7 94.8 1.0 CG B:ASP280 4.8 99.1 1.0 CA B:LEU110 4.8 90.5 1.0 C B:ASP112 4.8 101.3 1.0 CA B:SER279 4.9 85.7 1.0 C B:LEU110 4.9 96.4 1.0 N B:ASP112 4.9 90.6 1.0 ND2 B:ASN114 4.9 104.2 1.0 C B:LEU113 4.9 107.7 1.0 O B:LEU110 5.0 94.0 1.0

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