Calcium in PDB 2r1d: Crystal Structure of Rat Neurexin 1BETA in the CA2+ Containing Form

The structure of Crystal Structure of Rat Neurexin 1BETA in the CA2+ Containing Form, PDB code: 2r1d was solved by G.Rudenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.683, 195.719, 103.867, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.4

The binding sites of Calcium atom in the Crystal Structure of Rat Neurexin 1BETA in the CA2+ Containing Form (pdb code 2r1d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Rat Neurexin 1BETA in the CA2+ Containing Form, PDB code: 2r1d:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Rat Neurexin 1BETA in the CA2+ Containing Form


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 Rat Neurexin 1BETA in the CA2+ Containing Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1000 b:50.9 occ:1.00 O B:ILE160 2.2 41.0 1.0 OD1 B:ASN162 2.3 36.0 1.0 O B:VAL108 2.3 38.9 1.0 O B:HOH1019 2.5 30.8 1.0 OD2 B:ASP91 2.7 41.0 1.0 C B:VAL108 3.4 38.3 1.0 C B:ILE160 3.4 39.2 1.0 CG B:ASN162 3.5 36.8 1.0 CG B:ASP91 3.6 41.7 1.0 OD1 B:ASP91 3.8 42.9 1.0 N B:ASN162 4.1 37.0 1.0 CA B:ILE160 4.2 39.4 1.0 CA B:VAL108 4.2 37.5 1.0 N B:GLY109 4.2 38.8 1.0 CA B:GLY109 4.3 39.5 1.0 CB B:ILE160 4.3 39.1 1.0 CB B:ASN162 4.3 37.0 1.0 N B:PHE161 4.4 37.5 1.0 CB B:VAL108 4.4 38.3 1.0 N B:ILE160 4.4 39.2 1.0 ND2 B:ASN162 4.5 38.3 1.0 CA B:PHE161 4.6 37.0 1.0 CG2 B:ILE160 4.6 39.7 1.0 C B:PHE161 4.8 37.0 1.0 CA B:ASN162 4.8 36.5 1.0 CD1 B:LEU158 5.0 37.4 1.0 CB B:LEU158 5.0 39.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Rat Neurexin 1BETA in the CA2+ Containing Form


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 Rat Neurexin 1BETA in the CA2+ Containing Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2000 b:46.8 occ:1.00 OD1 D:ASN162 2.3 38.9 1.0 O D:VAL108 2.3 45.6 1.0 OD2 D:ASP91 2.4 42.5 1.0 O D:ILE160 2.4 36.4 1.0 O D:HOH2007 2.5 32.4 1.0 O D:HOH2017 2.7 40.1 1.0 CG D:ASP91 3.4 41.1 1.0 C D:VAL108 3.4 44.4 1.0 CG D:ASN162 3.4 34.5 1.0 OD1 D:ASP91 3.5 40.7 1.0 C D:ILE160 3.6 36.0 1.0 N D:ASN162 4.2 35.2 1.0 CA D:VAL108 4.2 42.1 1.0 ND2 D:ASN162 4.3 31.4 1.0 N D:GLY109 4.3 46.1 1.0 CA D:GLY109 4.4 47.6 1.0 CB D:ASN162 4.4 34.6 1.0 CB D:VAL108 4.4 41.9 1.0 CA D:ILE160 4.5 35.9 1.0 N D:PHE161 4.6 35.9 1.0 CB D:ILE160 4.6 35.8 1.0 N D:ILE160 4.6 36.8 1.0 CA D:PHE161 4.7 35.9 1.0 CB D:ASP91 4.8 39.6 1.0 CA D:ASN162 4.9 35.0 1.0 C D:PHE161 4.9 35.5 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Rat Neurexin 1BETA in the CA2+ Containing Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Rat Neurexin 1BETA in the CA2+ Containing Form within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca3000 b:33.4 occ:1.00 O I:VAL108 2.3 37.8 1.0 O I:ILE160 2.4 35.3 1.0 OD1 I:ASN162 2.6 35.4 1.0 OD2 I:ASP91 2.8 40.6 1.0 O I:HOH230 3.1 60.6 1.0 C I:VAL108 3.4 38.0 1.0 C I:ILE160 3.5 35.4 1.0 OD1 I:ASP91 3.6 40.3 1.0 CG I:ASP91 3.6 40.1 1.0 CG I:ASN162 3.7 35.0 1.0 N I:ASN162 4.1 35.8 1.0 CB I:ASN162 4.1 35.5 1.0 CA I:VAL108 4.3 37.8 1.0 N I:GLY109 4.3 38.2 1.0 CA I:ILE160 4.3 35.1 1.0 CA I:GLY109 4.4 38.5 1.0 CB I:ILE160 4.5 35.0 1.0 N I:PHE161 4.6 35.6 1.0 N I:ILE160 4.6 35.3 1.0 CB I:VAL108 4.6 37.8 1.0 CA I:PHE161 4.8 35.8 1.0 CA I:ASN162 4.8 35.5 1.0 ND2 I:ASN162 4.8 33.8 1.0 O I:HOH229 4.9 57.0 1.0 C I:PHE161 4.9 36.0 1.0 CG2 I:ILE160 5.0 34.5 1.0

K.C.Shen, D.A.Kuczynska, I.J.Wu, B.H.Murray, L.R.Sheckler, G.Rudenko. Regulation of Neurexin 1BETA Tertiary Structure and Ligand Binding Through Alternative Splicing Structure V. 16 422 2008.
ISSN: ISSN 0969-2126
PubMed: 18334217
DOI: 10.1016/J.STR.2008.01.005