Calcium in PDB 4pln: Crystal Structure of Chicken Netrin-1 (Ln-LE3) Complexed with Mouse Neogenin (FN4-5)

The structure of Crystal Structure of Chicken Netrin-1 (Ln-LE3) Complexed with Mouse Neogenin (FN4-5), PDB code: 4pln was solved by K.Xu, D.B.Nikolov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.95 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.070, 130.211, 126.037, 90.00, 99.98, 90.00
R / Rfree (%)	19.6 / 24

The binding sites of Calcium atom in the Crystal Structure of Chicken Netrin-1 (Ln-LE3) Complexed with Mouse Neogenin (FN4-5) (pdb code 4pln). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Chicken Netrin-1 (Ln-LE3) Complexed with Mouse Neogenin (FN4-5), PDB code: 4pln:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Chicken Netrin-1 (Ln-LE3) Complexed with Mouse Neogenin (FN4-5)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Chicken Netrin-1 (Ln-LE3) Complexed with Mouse Neogenin (FN4-5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:47.0 occ:1.00 O A:SER279 2.3 34.2 1.0 OD1 A:ASP112 2.4 53.6 1.0 O A:THR120 2.9 38.1 1.0 OG1 A:THR120 2.9 36.9 1.0 O A:PHE109 2.9 44.7 1.0 C A:SER279 3.5 30.7 1.0 CG A:ASP112 3.5 50.9 1.0 C A:PHE109 3.7 45.6 1.0 C A:THR120 3.8 46.8 1.0 OD2 A:ASP112 3.9 42.6 1.0 O A:LEU113 4.0 41.4 1.0 OD1 A:ASP280 4.1 42.4 1.0 CB A:THR120 4.1 39.9 1.0 N A:THR120 4.2 48.8 1.0 O A:ASP112 4.2 52.1 1.0 CA A:SER279 4.2 29.0 1.0 CA A:THR120 4.2 42.7 1.0 CA A:PHE109 4.4 35.6 1.0 N A:ASP280 4.4 27.7 1.0 CA A:ASP280 4.5 24.7 1.0 O A:LEU110 4.5 54.7 1.0 CB A:SER279 4.6 36.0 1.0 OD1 A:ASN114 4.6 45.9 1.0 CB A:ASP280 4.6 39.9 1.0 C A:ASP112 4.6 44.9 1.0 N A:LEU110 4.6 35.7 1.0 CA A:ASN114 4.7 43.8 1.0 C A:LEU113 4.7 49.1 1.0 C A:LEU110 4.7 38.5 1.0 CG A:ASP280 4.7 54.7 1.0 N A:ASP112 4.7 34.8 1.0 CB A:ASP112 4.8 47.8 1.0 CA A:LEU110 4.8 32.1 1.0 CB A:PHE109 4.9 35.5 1.0 CA A:ASP112 5.0 37.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Chicken Netrin-1 (Ln-LE3) Complexed with Mouse Neogenin (FN4-5)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Chicken Netrin-1 (Ln-LE3) Complexed with Mouse Neogenin (FN4-5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:40.1 occ:1.00 OD1 B:ASP112 2.4 52.4 1.0 O B:SER279 2.4 38.5 1.0 OG1 B:THR120 2.4 39.7 1.0 O B:PHE109 2.6 42.2 1.0 O B:THR120 2.7 39.2 1.0 CG B:ASP112 3.5 49.7 1.0 C B:SER279 3.6 35.5 1.0 C B:THR120 3.7 43.3 1.0 CB B:THR120 3.7 42.8 1.0 C B:PHE109 3.7 38.1 1.0 OD2 B:ASP112 3.8 51.4 1.0 O B:LEU113 4.1 52.4 1.0 CA B:THR120 4.1 40.3 1.0 OD1 B:ASP280 4.1 49.4 1.0 O B:ASP112 4.2 45.5 1.0 N B:THR120 4.2 49.6 1.0 CA B:SER279 4.4 33.9 1.0 CA B:PHE109 4.5 32.4 1.0 N B:ASP280 4.5 34.9 1.0 CA B:ASP280 4.6 26.4 1.0 O B:LEU110 4.6 45.5 1.0 OD1 B:ASN114 4.6 51.0 1.0 C B:ASP112 4.6 49.8 1.0 N B:ASP112 4.7 40.0 1.0 C B:LEU113 4.7 53.2 1.0 C B:LEU110 4.7 31.5 1.0 N B:LEU110 4.7 36.0 1.0 CA B:ASN114 4.7 48.4 1.0 CB B:ASP112 4.8 49.3 1.0 CG2 B:THR120 4.8 65.1 1.0 CB B:ASP280 4.8 36.9 1.0 CA B:LEU110 4.9 35.9 1.0 CG B:ASP280 4.9 50.5 1.0 CB B:SER279 4.9 40.3 1.0 CB B:PHE109 4.9 33.8 1.0 CA B:ASP112 4.9 46.0 1.0 N B:CYS121 4.9 52.7 1.0

K.Xu, Z.Wu, N.Renier, A.Antipenko, D.Tzvetkova-Robev, Y.Xu, M.Minchenko, V.Nardi-Dei, K.R.Rajashankar, J.Himanen, M.Tessier-Lavigne, D.B.Nikolov. Neural Migration. Structures of Netrin-1 Bound to Two Receptors Provide Insight Into Its Axon Guidance Mechanism. Science V. 344 1275 2014.
ISSN: ESSN 1095-9203
PubMed: 24876346
DOI: 10.1126/SCIENCE.1255149