Calcium in PDB 3zyj: NETRING1 in Complex with NGL1

The structure of NETRING1 in Complex with NGL1, PDB code: 3zyj was solved by E.Seiradake, C.H.Coles, P.V.Perestenko, K.Harlos, R.A.J.Mcilhinney, A.R.Aricescu, E.Y.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.44 / 3.25
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	184.420, 204.430, 288.070, 90.00, 90.00, 90.00
R / Rfree (%)	25.61 / 26.83

The binding sites of Calcium atom in the NETRING1 in Complex with NGL1 (pdb code 3zyj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the NETRING1 in Complex with NGL1, PDB code: 3zyj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the NETRING1 in Complex with NGL1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of NETRING1 in Complex with NGL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1373 b:1.0 occ:1.00 O B:LEU105 2.2 0.1 1.0 OG1 B:THR126 2.8 0.6 1.0 O B:THR126 2.8 0.9 1.0 O B:SER299 2.8 88.5 1.0 OE2 B:GLU110 3.2 0.7 1.0 C B:LEU105 3.4 0.1 1.0 CB B:ASP108 3.4 0.7 1.0 C B:THR126 3.6 0.1 1.0 O B:ASP108 3.7 0.4 1.0 CG B:GLU110 3.7 0.2 1.0 CD B:GLU110 3.8 0.2 1.0 CB B:THR126 3.9 0.0 1.0 OD2 B:ASP300 3.9 0.9 1.0 C B:SER299 4.0 88.3 1.0 N B:ASP108 4.0 99.5 1.0 CA B:ASP108 4.1 0.1 1.0 CA B:THR126 4.1 0.2 1.0 C B:ASP108 4.2 0.7 1.0 CA B:LEU105 4.2 97.3 1.0 N B:THR126 4.2 0.2 1.0 OD2 B:ASP108 4.3 0.1 1.0 CG B:ASP108 4.3 0.7 1.0 N B:MET106 4.4 95.4 1.0 CB B:LEU105 4.5 97.9 1.0 CA B:MET106 4.6 94.2 1.0 CB B:ASP300 4.6 87.4 1.0 C B:MET106 4.6 98.4 1.0 N B:PHE127 4.6 0.0 1.0 CG B:ASP300 4.7 99.3 1.0 CA B:ASP300 4.8 84.4 1.0 N B:ASP300 4.8 84.6 1.0 N B:PHE107 4.9 95.7 1.0 OE1 B:GLU110 4.9 0.8 1.0 O B:MET106 5.0 97.6 1.0 CA B:SER299 5.0 84.0 1.0

Calcium binding site 2 out of 2 in the NETRING1 in Complex with NGL1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of NETRING1 in Complex with NGL1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1375 b:88.2 occ:1.00 O D:LEU105 2.2 83.3 1.0 OE2 D:GLU110 2.2 0.3 1.0 OG1 D:THR126 2.6 0.8 1.0 OD1 D:ASP300 2.7 88.0 1.0 O D:THR126 2.9 92.8 1.0 O D:SER299 3.0 75.5 1.0 CD D:GLU110 3.1 0.5 1.0 C D:LEU105 3.4 82.9 1.0 CB D:ASP108 3.4 90.4 1.0 C D:THR126 3.6 94.0 1.0 OE1 D:GLU110 3.7 0.3 1.0 CB D:THR126 3.7 0.9 1.0 O D:ASP108 3.7 91.9 1.0 CG D:ASP300 3.9 87.2 1.0 CA D:THR126 4.0 92.9 1.0 N D:ASP108 4.1 85.5 1.0 OD2 D:ASP108 4.1 0.8 1.0 N D:THR126 4.1 94.4 1.0 CA D:ASP108 4.1 87.6 1.0 CG D:GLU110 4.1 0.1 1.0 CA D:LEU105 4.2 79.3 1.0 C D:SER299 4.2 75.5 1.0 C D:ASP108 4.2 93.0 1.0 CG D:ASP108 4.3 0.8 1.0 N D:MET106 4.4 78.3 1.0 CB D:LEU105 4.4 79.9 1.0 N D:PHE127 4.5 89.2 1.0 CB D:ASP300 4.6 75.5 1.0 CA D:MET106 4.6 77.3 1.0 C D:MET106 4.7 81.8 1.0 OD2 D:ASP300 4.7 93.9 1.0 N D:PHE107 4.9 79.6 1.0 CA D:ASP300 4.9 72.1 1.0 CG2 D:THR126 5.0 0.6 1.0 N D:ASP300 5.0 72.2 1.0

E.Seiradake, C.H.Coles, P.V.Perestenko, K.Harlos, R.A.J.Mcilhinney, A.R.Aricescu, E.Y.Jones. Structural Basis For Cell Surface Patterning Through Netring-Ngl Interactions. Embo J. V. 30 4479 2011.
ISSN: ISSN 0261-4189
PubMed: 21946559
DOI: 10.1038/EMBOJ.2011.346