Calcium in PDB 2wqz: Crystal Structure of Synaptic Protein Neuroligin-4 in Complex with Neurexin-Beta 1: Alternative Refinement

The structure of Crystal Structure of Synaptic Protein Neuroligin-4 in Complex with Neurexin-Beta 1: Alternative Refinement, PDB code: 2wqz was solved by I.P.Fabrichny, P.Leone, G.Sulzenbacher, D.Comoletti, M.T.Miller, P.Taylor, Y.Bourne, P.Marchot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	158.520, 198.670, 85.740, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 27.6

The binding sites of Calcium atom in the Crystal Structure of Synaptic Protein Neuroligin-4 in Complex with Neurexin-Beta 1: Alternative Refinement (pdb code 2wqz). 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 Synaptic Protein Neuroligin-4 in Complex with Neurexin-Beta 1: Alternative Refinement, PDB code: 2wqz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Synaptic Protein Neuroligin-4 in Complex with Neurexin-Beta 1: Alternative Refinement


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 Synaptic Protein Neuroligin-4 in Complex with Neurexin-Beta 1: Alternative Refinement within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1289 b:0.0 occ:1.00 O C:VAL154 1.9 67.3 1.0 OD2 C:ASP137 2.4 67.1 1.0 O C:ILE236 2.6 59.4 1.0 OD1 C:ASN238 2.7 62.6 1.0 C C:VAL154 3.1 67.4 1.0 CG C:ASP137 3.2 67.1 1.0 OD1 C:ASP137 3.3 67.6 1.0 CG C:ASN238 3.6 62.0 1.0 CA C:GLY155 3.7 68.5 1.0 C C:ILE236 3.8 59.7 1.0 N C:GLY155 3.8 67.9 1.0 CD1 C:LEU234 4.0 61.0 1.0 N C:ASN238 4.1 61.1 1.0 O B:GLN359 4.1 75.6 1.0 CA C:VAL154 4.2 67.1 1.0 CB C:ASN238 4.2 61.7 1.0 CB C:VAL154 4.5 66.9 1.0 ND2 C:ASN238 4.6 62.2 1.0 CB C:ASP137 4.7 66.7 1.0 CA C:ILE236 4.7 59.5 1.0 CA B:GLY360 4.7 75.8 1.0 N C:PHE237 4.7 60.1 1.0 CA C:ASN238 4.8 61.6 1.0 N C:ILE236 4.9 59.6 1.0 CA C:PHE237 4.9 60.4 1.0 CD2 C:LEU234 5.0 60.3 1.0 CB C:ILE236 5.0 59.3 1.0 CG C:LEU234 5.0 60.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Synaptic Protein Neuroligin-4 in Complex with Neurexin-Beta 1: Alternative Refinement


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 Synaptic Protein Neuroligin-4 in Complex with Neurexin-Beta 1: Alternative Refinement within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1289 b:0.4 occ:1.00 OD1 D:ASN238 2.0 59.7 1.0 O D:VAL154 2.4 70.4 1.0 OD2 D:ASP137 2.4 68.6 1.0 O D:ILE236 2.6 62.7 1.0 CG D:ASN238 3.2 60.5 1.0 CG D:ASP137 3.5 69.2 1.0 CD1 D:ILE236 3.5 63.4 1.0 C D:VAL154 3.6 70.5 1.0 C D:ILE236 3.8 63.0 1.0 OD1 D:ASP137 3.8 69.0 1.0 ND2 D:ASN238 3.8 60.0 1.0 CA D:GLY155 4.0 71.2 1.0 CA A:GLY360 4.1 75.1 1.0 O D:PHE237 4.2 61.8 1.0 N D:GLY155 4.3 70.8 1.0 C D:PHE237 4.3 61.7 1.0 CB D:ASN238 4.3 61.1 1.0 N D:ASN238 4.6 61.4 1.0 N D:PHE237 4.6 62.4 1.0 CA D:PHE237 4.6 62.0 1.0 CA D:VAL154 4.7 70.3 1.0 CB D:ASP137 4.8 69.4 1.0 CA D:ILE236 4.9 63.4 1.0 CG1 D:ILE236 4.9 63.2 1.0 N A:GLY360 4.9 75.0 1.0 CD1 D:LEU234 5.0 66.8 1.0

I.P.Fabrichny, P.Leone, G.Sulzenbacher, D.Comoletti, M.T.Miller, P.Taylor, Y.Bourne, P.Marchot. Structural Analysis of the Synaptic Protein Neuroligin and Its Beta-Neurexin Complex: Determinants For Folding and Cell Adhesion. Neuron V. 56 979 2007.
ISSN: ISSN 0896-6273
PubMed: 18093521
DOI: 10.1016/J.NEURON.2007.11.013