Calcium in PDB 6fkq: The Crystal Structure of A Fragment of Netrin-1 in Complex with A Fragment of Draxin

The structure of The Crystal Structure of A Fragment of Netrin-1 in Complex with A Fragment of Draxin, PDB code: 6fkq was solved by T.Bhowmick, R.Meijers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.01 / 3.07
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	130.794, 130.794, 183.870, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 27.1

The binding sites of Calcium atom in the The Crystal Structure of A Fragment of Netrin-1 in Complex with A Fragment of Draxin (pdb code 6fkq). 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 The Crystal Structure of A Fragment of Netrin-1 in Complex with A Fragment of Draxin, PDB code: 6fkq:

Calcium binding site 1 out of 1 in the The Crystal Structure of A Fragment of Netrin-1 in Complex with A Fragment of Draxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of A Fragment of Netrin-1 in Complex with A Fragment of Draxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:51.3 occ:1.00 O A:SER277 2.3 48.4 1.0 OG1 A:THR118 2.3 56.3 1.0 O A:PHE107 2.3 43.0 1.0 OD1 A:ASP110 2.4 55.6 1.0 O A:THR118 2.4 55.5 1.0 OD1 A:ASN112 2.4 68.9 1.0 CG A:ASP110 3.4 48.7 1.0 C A:SER277 3.4 42.3 1.0 C A:THR118 3.5 56.6 1.0 C A:PHE107 3.6 43.2 1.0 CB A:THR118 3.7 53.6 1.0 CG A:ASN112 3.7 61.3 1.0 OD2 A:ASP110 3.8 49.6 1.0 N A:THR118 3.9 54.1 1.0 CA A:THR118 3.9 54.0 1.0 CA A:SER277 4.1 41.1 1.0 CA A:PHE107 4.3 45.9 1.0 OD1 A:ASP278 4.3 61.9 1.0 CB A:SER277 4.4 41.7 1.0 CB A:PHE107 4.5 48.3 1.0 N A:ASP278 4.5 42.9 1.0 O A:LEU111 4.5 52.7 1.0 ND2 A:ASN112 4.5 55.9 1.0 O A:ASP110 4.6 54.1 1.0 CG2 A:THR118 4.6 51.4 1.0 N A:LEU108 4.6 40.7 1.0 CA A:ASP278 4.7 47.1 1.0 N A:CYS119 4.7 58.1 1.0 CB A:ASN112 4.7 55.7 1.0 CB A:ASP110 4.8 45.5 1.0 CB A:ASP278 4.8 50.7 1.0 C A:LEU108 4.8 46.4 1.0 N A:ASP110 4.9 44.8 1.0 CA A:LEU108 4.9 42.7 1.0 O A:LEU108 4.9 51.7 1.0 CA A:ASN112 4.9 52.2 1.0 C A:ASP110 4.9 48.0 1.0

Y.Liu, T.Bhowmick, Y.Liu, X.Gao, H.D.T.Mertens, D.I.Svergun, J.Xiao, Y.Zhang, J.H.Wang, R.Meijers. Structural Basis For Draxin-Modulated Axon Guidance and Fasciculation By Netrin-1 Through Dcc. Neuron V. 97 1261 2018.
ISSN: ISSN 1097-4199
PubMed: 29503192
DOI: 10.1016/J.NEURON.2018.02.010