Calcium in PDB 3vkf: Crystal Structure of Neurexin 1BETA/Neuroligin 1 Complex

The structure of Crystal Structure of Neurexin 1BETA/Neuroligin 1 Complex, PDB code: 3vkf was solved by H.Tanaka, N.Miyazaki, T.Nogi, K.Iwasaki, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.91 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.261, 95.186, 120.396, 90.00, 108.62, 90.00
R / Rfree (%)	20.5 / 28.7

The binding sites of Calcium atom in the Crystal Structure of Neurexin 1BETA/Neuroligin 1 Complex (pdb code 3vkf). 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 Neurexin 1BETA/Neuroligin 1 Complex, PDB code: 3vkf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Neurexin 1BETA/Neuroligin 1 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 Neurexin 1BETA/Neuroligin 1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2001 b:68.5 occ:1.00 OD1 C:ASN237 2.3 57.0 1.0 O C:VAL153 2.4 51.4 1.0 OD2 C:ASP136 2.5 54.0 1.0 O C:ILE235 2.7 54.3 1.0 CG C:ASP136 3.4 54.0 1.0 OD1 C:ASP136 3.5 56.1 1.0 CG C:ASN237 3.5 58.1 1.0 C C:VAL153 3.5 51.1 1.0 C C:ILE235 3.9 54.0 1.0 O A:GLY396 4.0 59.6 1.0 CA C:GLY154 4.1 54.5 1.0 ND2 C:ASN237 4.2 59.4 1.0 N C:GLY154 4.2 52.5 1.0 O A:GLN395 4.3 62.5 1.0 CA C:VAL153 4.5 49.5 1.0 OE1 A:GLU397 4.6 62.6 1.0 N C:ASN237 4.6 54.8 1.0 CB C:ASN237 4.6 58.0 1.0 CD1 C:LEU233 4.6 59.1 1.0 CE2 A:PHE499 4.7 62.6 1.0 CB C:ILE235 4.8 56.8 1.0 CA C:ILE235 4.8 55.2 1.0 CB C:ASP136 4.8 52.0 1.0 N C:PHE236 4.9 53.4 1.0 CB C:VAL153 4.9 48.8 1.0 N C:ILE235 5.0 55.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Neurexin 1BETA/Neuroligin 1 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 Neurexin 1BETA/Neuroligin 1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2001 b:70.6 occ:1.00 O D:VAL153 2.1 68.7 1.0 O D:ILE235 2.3 67.5 1.0 OD1 D:ASN237 2.4 71.7 1.0 OD2 D:ASP136 2.5 68.0 1.0 C D:VAL153 3.3 68.2 1.0 CG D:ASN237 3.4 71.4 1.0 CG D:ASP136 3.5 68.1 1.0 C D:ILE235 3.5 66.7 1.0 OD1 D:ASP136 3.9 70.9 1.0 N D:ASN237 4.1 66.6 1.0 CA D:VAL153 4.1 65.1 1.0 CB D:VAL153 4.2 64.1 1.0 O B:GLN395 4.2 77.5 1.0 ND2 D:ASN237 4.3 71.6 1.0 N D:GLY154 4.3 70.8 1.0 CB D:ASN237 4.3 70.8 1.0 N D:PHE236 4.4 65.0 1.0 CA D:ILE235 4.4 68.0 1.0 CA D:GLY154 4.5 74.5 1.0 CB D:ILE235 4.5 70.2 1.0 CA D:PHE236 4.5 64.0 1.0 CD1 D:LEU233 4.7 79.0 1.0 N D:ILE235 4.7 68.7 1.0 CB D:ASP136 4.8 65.7 1.0 C D:PHE236 4.8 65.1 1.0 CA D:ASN237 4.8 68.5 1.0 O B:GLY396 4.9 74.0 1.0 CG2 D:ILE235 4.9 70.2 1.0

H.Tanaka, N.Miyazaki, K.Matoba, T.Nogi, K.Iwasaki, J.Takagi. Higher-Order Architecture of Cell Adhesion Mediated By Polymorphic Synaptic Adhesion Molecules Neurexin and Neuroligin. Cell Rep V. 2 101 2012.
ISSN: ESSN 2211-1247
PubMed: 22840401
DOI: 10.1016/J.CELREP.2012.06.009