Calcium in PDB 4plm: Crystal Structure of Chicken Netrin-1 (Ln-LE3)

The structure of Crystal Structure of Chicken Netrin-1 (Ln-LE3), PDB code: 4plm 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)	28.64 / 2.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	62.627, 62.627, 269.788, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 25.7

The structure of Crystal Structure of Chicken Netrin-1 (Ln-LE3) also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Chicken Netrin-1 (Ln-LE3) (pdb code 4plm). 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 Crystal Structure of Chicken Netrin-1 (Ln-LE3), PDB code: 4plm:

Calcium binding site 1 out of 1 in the Crystal Structure of Chicken Netrin-1 (Ln-LE3)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:69.5 occ:1.00 O A:SER279 2.3 75.6 1.0 O A:HOH656 2.4 64.4 1.0 O A:PHE109 2.4 60.2 1.0 OD1 A:ASP112 2.4 83.6 1.0 O A:THR120 2.6 70.3 1.0 OG1 A:THR120 2.9 71.1 1.0 C A:SER279 3.4 69.3 1.0 CB A:THR120 3.5 64.3 1.0 CG A:ASP112 3.5 84.4 1.0 C A:THR120 3.5 68.0 1.0 C A:PHE109 3.5 64.2 1.0 CA A:THR120 3.9 64.1 1.0 OD2 A:ASP112 3.9 87.3 1.0 N A:THR120 4.0 65.3 1.0 CA A:SER279 4.1 66.6 1.0 CA A:PHE109 4.2 71.0 1.0 OD1 A:ASN114 4.3 76.8 1.0 O A:ASP112 4.4 73.3 1.0 CB A:PHE109 4.4 77.2 1.0 CB A:SER279 4.4 66.3 1.0 N A:ASP280 4.5 64.2 1.0 N A:LEU110 4.6 57.9 1.0 O A:LEU110 4.6 64.7 1.0 N A:ASP112 4.7 72.7 1.0 C A:LEU110 4.7 62.6 1.0 N A:CYS121 4.7 69.5 1.0 CA A:ASP280 4.8 63.5 1.0 CB A:ASP112 4.8 80.2 1.0 CA A:LEU110 4.8 56.9 1.0 CG2 A:THR120 4.8 63.2 1.0 C A:ASP112 4.8 66.3 1.0 OD1 A:ASP280 4.9 67.8 1.0 O A:LEU113 5.0 79.7 1.0 CA A:ASP112 5.0 73.9 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