Calcium in PDB 3b3q: Crystal Structure of A Synaptic Adhesion Complex

The structure of Crystal Structure of A Synaptic Adhesion Complex, PDB code: 3b3q was solved by X.Chen, H.Liu, A.Shim, P.Focia, X.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.64 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.590, 125.400, 131.860, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 26.1

The binding sites of Calcium atom in the Crystal Structure of A Synaptic Adhesion Complex (pdb code 3b3q). 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 A Synaptic Adhesion Complex, PDB code: 3b3q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Synaptic Adhesion Complex


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 A Synaptic Adhesion Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1 b:30.8 occ:0.25 OD1 E:ASN238 2.0 48.9 1.0 O E:HOH300 2.3 46.4 0.2 OD1 E:ASP137 2.3 52.8 1.0 O A:HOH638 2.4 50.0 0.2 O E:VAL154 2.4 62.4 1.0 O E:ILE236 2.6 45.7 1.0 CG E:ASN238 3.1 48.7 1.0 CG E:ASP137 3.3 51.9 1.0 C E:VAL154 3.5 62.4 1.0 OD2 E:ASP137 3.5 51.1 1.0 CB E:ASN238 3.8 49.1 1.0 C E:ILE236 3.8 45.6 1.0 N E:ASN238 3.9 46.1 1.0 ND2 E:ASN238 4.2 48.5 1.0 CA E:VAL154 4.3 59.6 1.0 N E:GLY155 4.4 64.4 1.0 CA E:ASN238 4.5 47.2 1.0 CA E:GLY155 4.6 67.1 1.0 CB E:VAL154 4.6 58.2 1.0 CA E:PHE237 4.6 46.1 1.0 N E:PHE237 4.6 45.1 1.0 O A:GLN395 4.6 54.4 1.0 O A:GLY396 4.6 47.7 1.0 CB E:ASP137 4.6 50.5 1.0 C E:PHE237 4.7 45.5 1.0 CG2 E:ILE236 4.7 39.7 1.0 CA E:ILE236 4.7 45.9 1.0 CE2 A:PHE499 4.9 50.6 1.0 CB E:ILE236 4.9 44.9 1.0 OE1 A:GLU397 5.0 52.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Synaptic Adhesion Complex


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 A Synaptic Adhesion Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca2 b:33.4 occ:0.25 O F:ILE236 2.0 47.5 1.0 O F:VAL154 2.1 61.5 1.0 OD1 F:ASP137 2.3 46.9 1.0 O F:HOH716 2.3 53.1 0.2 OD1 F:ASN238 2.5 47.9 1.0 O B:HOH656 2.6 53.7 0.2 C F:VAL154 3.2 63.5 1.0 C F:ILE236 3.3 49.5 1.0 CG F:ASP137 3.3 49.9 1.0 CG F:ASN238 3.5 47.0 1.0 OD2 F:ASP137 3.7 46.1 1.0 CA F:VAL154 3.8 61.4 1.0 N F:ASN238 3.8 49.5 1.0 CB F:VAL154 4.0 59.3 1.0 N F:PHE237 4.1 50.4 1.0 CA F:PHE237 4.2 51.3 1.0 N F:GLY155 4.2 65.0 1.0 CB F:ASN238 4.2 48.2 1.0 CA F:ILE236 4.3 49.1 1.0 ND2 F:ASN238 4.4 44.2 1.0 C F:PHE237 4.5 50.7 1.0 CA F:GLY155 4.5 68.3 1.0 CB F:ILE236 4.6 49.6 1.0 CB F:ASP137 4.6 52.5 1.0 N F:ILE236 4.6 50.2 1.0 CA F:ASN238 4.6 50.7 1.0 CG1 F:VAL154 4.7 59.2 1.0 CG2 F:ILE236 4.8 49.6 1.0 OE1 B:GLU397 4.8 46.7 1.0 O B:GLY396 4.9 43.8 1.0

X.Chen, H.Liu, A.H.Shim, P.J.Focia, X.He. Structural Basis For Synaptic Adhesion Mediated By Neuroligin-Neurexin Interactions. Nat.Struct.Mol.Biol. V. 15 50 2008.
ISSN: ISSN 1545-9993
PubMed: 18084303
DOI: 10.1038/NSMB1350