Atomistry » Calcium » PDB 2qwd-2rex » 2r1d
Atomistry »
  Calcium »
    PDB 2qwd-2rex »
      2r1d »

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

Protein crystallography data

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

Calcium Binding Sites:

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 2r1d

Go back to Calcium Binding Sites List in 2r1d
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 2r1d

Go back to Calcium Binding Sites List in 2r1d
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 2r1d

Go back to Calcium Binding Sites List in 2r1d
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

Reference:

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
Page generated: Sat Dec 12 03:51:39 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy