Sodium in PDB 3be8: Crystal Structure of the Synaptic Protein Neuroligin 4

The structure of Crystal Structure of the Synaptic Protein Neuroligin 4, PDB code: 3be8 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)	29.68 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	139.730, 154.050, 81.300, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.1

The structure of Crystal Structure of the Synaptic Protein Neuroligin 4 also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of the Synaptic Protein Neuroligin 4 (pdb code 3be8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Synaptic Protein Neuroligin 4, PDB code: 3be8:

Sodium binding site 1 out of 1 in the Crystal Structure of the Synaptic Protein Neuroligin 4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Synaptic Protein Neuroligin 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na626 b:43.3 occ:1.00 O A:LEU62 2.3 42.0 1.0 O A:LEU67 2.4 37.7 1.0 O A:HOH843 2.4 45.9 1.0 O A:ASN64 2.5 43.1 1.0 O A:HOH790 2.5 34.5 1.0 O A:HOH854 2.7 45.8 1.0 C A:LEU62 3.4 41.6 1.0 C A:ASN64 3.5 43.7 1.0 C A:LEU67 3.6 37.1 1.0 N A:LEU62 3.9 39.9 1.0 CA A:LEU62 4.0 40.0 1.0 CB A:LEU62 4.1 38.9 1.0 O A:GLU65 4.1 45.1 1.0 C A:GLU65 4.1 44.8 1.0 CA A:GLU65 4.1 46.2 1.0 N A:LEU67 4.2 39.6 1.0 N A:GLU65 4.3 44.8 1.0 C A:PRO63 4.3 44.6 1.0 O A:PRO63 4.3 46.1 1.0 CA A:LEU67 4.4 37.7 1.0 N A:ASN64 4.4 42.8 1.0 N A:PRO63 4.5 42.2 1.0 CA A:ASN64 4.5 43.5 1.0 N A:GLY68 4.6 35.2 1.0 CB A:LEU67 4.7 37.4 1.0 N A:ILE66 4.8 43.2 1.0 CA A:PRO63 4.8 44.3 1.0 CA A:GLY68 4.8 34.7 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