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Calcium in PDB 1ncj: N-Cadherin, Two-Domain Fragment

Protein crystallography data

The structure of N-Cadherin, Two-Domain Fragment, PDB code: 1ncj was solved by K.Tamura, W.-S.Shan, W.A.Hendrickson, D.R.Colman, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 3.40
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 99.000, 99.000, 136.100, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 32.1

Other elements in 1ncj:

The structure of N-Cadherin, Two-Domain Fragment also contains other interesting chemical elements:

Uranium (U) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the N-Cadherin, Two-Domain Fragment (pdb code 1ncj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the N-Cadherin, Two-Domain Fragment, PDB code: 1ncj:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1ncj

Go back to Calcium Binding Sites List in 1ncj
Calcium binding site 1 out of 3 in the N-Cadherin, Two-Domain Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of N-Cadherin, Two-Domain Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:25.3
occ:1.00
OD2 A:ASP134 1.6 14.0 1.0
OD2 A:ASP194 1.8 27.1 1.0
O A:ASN104 2.4 9.4 1.0
O A:ASN142 2.4 8.8 1.0
CG A:ASP134 2.5 14.0 1.0
OD1 A:ASN102 2.6 27.2 1.0
OD1 A:ASP134 2.7 10.1 1.0
CG A:ASP194 2.9 21.9 1.0
CB A:ASP194 3.5 19.8 1.0
C A:ASN104 3.6 13.2 1.0
C A:ASN142 3.7 8.4 1.0
CG A:ASN102 3.7 21.8 1.0
HD21 A:ASN102 3.8 0.0 0.0
H A:ASN104 3.8 0.0 0.0
CB A:ASP134 3.9 14.3 1.0
OD1 A:ASP194 4.0 15.4 1.0
O A:ARG105 4.0 19.8 1.0
OD1 A:ASN104 4.1 16.6 1.0
CD1 A:LEU203 4.1 2.0 1.0
ND2 A:ASN102 4.2 14.9 1.0
C A:ARG105 4.2 15.5 1.0
N A:ARG105 4.4 12.5 1.0
CA A:ARG105 4.5 14.7 1.0
CA A:GLY143 4.5 2.2 1.0
N A:ASN104 4.6 14.0 1.0
N A:GLY143 4.6 4.7 1.0
N A:PRO106 4.6 16.2 1.0
CA A:ASN104 4.6 14.2 1.0
CA A:ASN142 4.7 10.4 1.0
H A:ASP136 4.7 0.0 0.0
H A:ASP103 4.7 0.0 0.0
CG A:PRO106 4.7 14.4 1.0
CA A:ASP134 4.8 19.8 1.0
CD A:PRO106 4.8 15.4 1.0
H A:ALA135 4.8 0.0 0.0
CG A:ASN104 5.0 14.2 1.0
CB A:ASP136 5.0 30.2 1.0

Calcium binding site 2 out of 3 in 1ncj

Go back to Calcium Binding Sites List in 1ncj
Calcium binding site 2 out of 3 in the N-Cadherin, Two-Domain Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of N-Cadherin, Two-Domain Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:48.9
occ:1.00
O A:MET101 1.7 17.2 1.0
OD1 A:ASP103 1.7 29.5 1.0
OD1 A:ASP100 2.1 6.9 1.0
OE1 A:GLU11 2.2 32.6 1.0
H A:MET101 2.5 0.0 0.0
C A:MET101 2.9 13.5 1.0
CG A:ASP103 2.9 25.4 1.0
H A:ASP103 3.2 0.0 0.0
CG A:ASP100 3.2 2.0 1.0
CD A:GLU11 3.2 33.0 1.0
N A:MET101 3.3 2.0 1.0
OE2 A:GLU11 3.5 38.3 1.0
N A:ASP103 3.6 15.7 1.0
OD2 A:ASP103 3.7 26.6 1.0
CA A:MET101 3.7 12.1 1.0
OD2 A:ASP100 3.8 2.0 1.0
N A:ASN102 3.9 13.9 1.0
CB A:ASP103 3.9 18.6 1.0
C A:ASN102 4.0 14.9 1.0
CA A:ASN102 4.1 15.0 1.0
CA A:ASP103 4.3 15.0 1.0
CB A:MET101 4.3 16.0 1.0
CB A:ASP100 4.4 5.7 1.0
C A:ASP100 4.4 2.7 1.0
CA A:CA303 4.5 77.5 1.0
CA A:ASP100 4.5 7.8 1.0
CG A:GLU11 4.6 28.2 1.0
H A:ASN102 4.8 0.0 0.0
O A:ASN102 4.8 15.5 1.0
CB A:GLU11 4.9 28.3 1.0
HD22 A:ASN142 5.0 0.0 0.0

Calcium binding site 3 out of 3 in 1ncj

Go back to Calcium Binding Sites List in 1ncj
Calcium binding site 3 out of 3 in the N-Cadherin, Two-Domain Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of N-Cadherin, Two-Domain Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:77.5
occ:1.00
OD1 A:ASP67 1.7 20.8 1.0
OD2 A:ASP103 1.7 26.6 1.0
OE2 A:GLU11 1.8 38.3 1.0
CD A:GLU11 2.8 33.0 1.0
CG A:ASP67 2.9 20.6 1.0
CG A:ASP103 2.9 25.4 1.0
OD1 A:ASN12 3.0 45.8 1.0
OD1 A:ASP103 3.5 29.5 1.0
CG A:GLU11 3.5 28.2 1.0
OE1 A:GLU11 3.7 32.6 1.0
CB A:ASP67 3.7 19.0 1.0
H A:GLU69 3.7 0.0 0.0
H A:ARG68 3.9 0.0 0.0
OD2 A:ASP67 3.9 19.8 1.0
CB A:ASP103 4.0 18.6 1.0
CA A:ASP67 4.1 16.7 1.0
CG A:ASN12 4.2 44.2 1.0
N A:ARG68 4.3 14.2 1.0
HD21 A:ASN12 4.5 0.0 0.0
C A:ASP67 4.5 14.1 1.0
CA A:CA302 4.5 48.9 1.0
N A:GLU69 4.7 6.8 1.0
H A:ASN12 4.8 0.0 0.0
ND2 A:ASN12 4.8 46.1 1.0
CB A:GLU11 4.9 28.3 1.0
CB A:GLU69 4.9 8.8 1.0

Reference:

K.Tamura, W.S.Shan, W.A.Hendrickson, D.R.Colman, L.Shapiro. Structure-Function Analysis of Cell Adhesion By Neural (N-) Cadherin. Neuron V. 20 1153 1998.
ISSN: ISSN 0896-6273
PubMed: 9655503
DOI: 10.1016/S0896-6273(00)80496-1
Page generated: Wed Oct 28 07:17:03 2020

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