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Calcium in PDB 4qd2: Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex

Protein crystallography data

The structure of Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex, PDB code: 4qd2 was solved by K.Lee, X.Zhong, S.Gu, A.Kruel, M.B.Dorner, K.Perry, A.Rummel, M.Dong, R.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.73 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 86.990, 95.730, 96.140, 116.89, 96.34, 93.70
R / Rfree (%) 20.8 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex (pdb code 4qd2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex, PDB code: 4qd2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4qd2

Go back to Calcium Binding Sites List in 4qd2
Calcium binding site 1 out of 6 in the Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:44.0
occ:1.00
 OE1 E:GLU69 2.3 51.3 1.0
OD1 E:ASP67 2.3 46.3 1.0
OD2 E:ASP103 2.3 42.2 1.0
OE1 E:GLU11 2.4 32.9 1.0
O E:HOH430 3.0 40.2 1.0
O E:HOH417 3.1 40.7 1.0
CG E:ASP103 3.1 40.8 1.0
OD1 E:ASP103 3.3 41.6 1.0
CG E:ASP67 3.3 47.3 1.0
CD E:GLU11 3.4 34.8 1.0
CD E:GLU69 3.4 47.5 1.0
CA E:CA302 3.8 36.2 1.0
OE2 E:GLU11 3.9 36.4 1.0
OD2 E:ASP67 4.0 49.2 1.0
ND2 E:ASN104 4.1 39.7 1.0
OE2 E:GLU69 4.1 48.0 1.0
N E:ARG68 4.2 39.5 1.0
OD1 E:ASN12 4.3 35.4 1.0
CB E:ASP67 4.3 43.8 1.0
CA E:ASP67 4.3 41.8 1.0
N E:GLU69 4.4 42.6 1.0
O E:HOH429 4.4 42.7 1.0
CG E:GLU69 4.4 46.7 1.0
CB E:GLU69 4.5 46.2 1.0
C E:ASP67 4.5 39.1 1.0
CG E:GLU11 4.6 34.8 1.0
CB E:ASP103 4.6 38.6 1.0
ND2 E:ASN12 4.6 33.0 1.0
O E:HOH434 4.8 47.8 1.0
CB E:GLU11 4.9 36.9 1.0
CG E:ASN12 4.9 33.7 1.0

Calcium binding site 2 out of 6 in 4qd2

Go back to Calcium Binding Sites List in 4qd2
Calcium binding site 2 out of 6 in the Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:36.2
occ:1.00
 OD1 E:ASP100 2.3 38.6 1.0
OE2 E:GLU69 2.3 48.0 1.0
OD1 E:ASP103 2.3 41.6 1.0
O E:GLN101 2.4 31.7 1.0
OD1 E:ASP136 2.5 47.3 1.0
OE2 E:GLU11 2.5 36.4 1.0
CD E:GLU69 3.0 47.5 1.0
OE1 E:GLU69 3.2 51.3 1.0
CG E:ASP103 3.3 40.8 1.0
CD E:GLU11 3.4 34.8 1.0
CG E:ASP136 3.4 44.8 1.0
CG E:ASP100 3.4 41.8 1.0
OE1 E:GLU11 3.6 32.9 1.0
C E:GLN101 3.6 34.1 1.0
ND2 E:ASN104 3.8 39.7 1.0
CA E:CA301 3.8 44.0 1.0
N E:GLN101 3.9 36.6 1.0
OD2 E:ASP103 3.9 42.2 1.0
OD2 E:ASP100 4.0 41.2 1.0
N E:ASP103 4.0 33.7 1.0
CB E:ASP136 4.1 43.5 1.0
OD2 E:ASP136 4.2 45.1 1.0
CA E:ASP136 4.3 43.1 1.0
CA E:GLN101 4.3 35.8 1.0
CG E:GLU69 4.4 46.7 1.0
NE E:ARG68 4.4 43.6 1.0
CB E:ASP103 4.5 38.6 1.0
CB E:ASP100 4.6 44.2 1.0
N E:ASN102 4.7 34.4 1.0
CA E:ASP100 4.7 43.4 1.0
CA E:ASP103 4.7 36.4 1.0
C E:ASP100 4.7 41.2 1.0
NH2 E:ARG68 4.8 45.6 1.0
CG E:GLU11 4.8 34.8 1.0
CA E:ASN102 4.8 34.0 1.0
N E:ASN104 4.9 40.6 1.0
CB E:GLN101 4.9 35.7 1.0
C E:ASN102 4.9 35.0 1.0
CG E:ASN104 5.0 40.6 1.0

Calcium binding site 3 out of 6 in 4qd2

Go back to Calcium Binding Sites List in 4qd2
Calcium binding site 3 out of 6 in the Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca303

b:42.0
occ:1.00
 OD2 E:ASP134 2.3 42.1 1.0
O E:ASN143 2.4 37.6 1.0
OD2 E:ASP136 2.4 45.1 1.0
O E:ASN104 2.4 45.6 1.0
OD2 E:ASP195 2.4 34.4 1.0
OD1 E:ASN102 2.4 31.9 1.0
OD1 E:ASP134 2.5 41.5 1.0
CG E:ASP134 2.7 42.1 1.0
CG E:ASP195 3.3 33.0 1.0
CG E:ASP136 3.4 44.8 1.0
C E:ASN143 3.5 37.9 1.0
C E:ASN104 3.6 44.4 1.0
CG E:ASN102 3.6 36.0 1.0
CB E:ASP136 3.8 43.5 1.0
CB E:ASP195 3.8 29.4 1.0
CB E:ASP134 4.2 42.0 1.0
N E:ASN104 4.3 40.6 1.0
CA E:ASN104 4.3 41.2 1.0
ND2 E:ASN102 4.3 28.6 1.0
OD1 E:ASP195 4.3 33.7 1.0
CB E:ASN104 4.4 40.3 1.0
OD1 E:ASP136 4.4 47.3 1.0
CA E:ASN143 4.4 39.6 1.0
CB E:ASN143 4.4 39.1 1.0
N E:ALA144 4.5 37.3 1.0
CA E:ALA144 4.6 34.4 1.0
CD E:PRO106 4.6 43.3 1.0
N E:ARG105 4.6 44.8 1.0
N E:ASP136 4.8 40.0 1.0
CB E:ASN102 4.8 34.7 1.0
CA E:ASN102 4.8 34.0 1.0
N E:PRO106 4.9 43.7 1.0
CA E:ARG105 4.9 44.2 1.0
C E:ASN102 4.9 35.0 1.0
C E:ARG105 4.9 42.0 1.0
CA E:ASP136 4.9 43.1 1.0

Calcium binding site 4 out of 6 in 4qd2

Go back to Calcium Binding Sites List in 4qd2
Calcium binding site 4 out of 6 in the Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca301

b:45.5
occ:1.00
 OD2 J:ASP103 2.3 46.0 1.0
OD1 J:ASP67 2.3 47.3 1.0
OE1 J:GLU69 2.3 36.1 1.0
OE1 J:GLU11 2.4 41.2 1.0
CG J:ASP103 3.1 43.3 1.0
OD1 J:ASP103 3.2 43.0 1.0
CG J:ASP67 3.4 47.8 1.0
CD J:GLU11 3.4 43.3 1.0
CD J:GLU69 3.5 37.1 1.0
CA J:CA302 3.8 39.0 1.0
OE2 J:GLU11 3.9 45.2 1.0
OD2 J:ASP67 4.2 49.6 1.0
ND2 J:ASN104 4.2 40.5 1.0
CB J:GLU69 4.3 41.5 1.0
CG J:GLU69 4.3 38.5 1.0
OD1 J:ASN12 4.3 40.8 1.0
CB J:ASP67 4.4 46.9 1.0
N J:GLU69 4.4 45.0 1.0
N J:ARG68 4.4 46.1 1.0
ND2 J:ASN12 4.4 40.7 1.0
CB J:ASP103 4.4 40.0 1.0
OE2 J:GLU69 4.5 39.1 1.0
CA J:ASP67 4.5 47.9 1.0
CG J:GLU11 4.7 44.3 1.0
C J:ASP67 4.8 48.1 1.0
CG J:ASN12 4.8 40.2 1.0

Calcium binding site 5 out of 6 in 4qd2

Go back to Calcium Binding Sites List in 4qd2
Calcium binding site 5 out of 6 in the Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca302

b:39.0
occ:1.00
 OD1 J:ASP100 2.3 48.4 1.0
OD1 J:ASP136 2.4 46.2 1.0
OD1 J:ASP103 2.4 43.0 1.0
OE2 J:GLU69 2.4 39.1 1.0
OE2 J:GLU11 2.4 45.2 1.0
OE1 J:GLU69 2.5 36.1 1.0
O J:GLN101 2.5 47.2 1.0
CD J:GLU69 2.8 37.1 1.0
CD J:GLU11 3.4 43.3 1.0
CG J:ASP103 3.4 43.3 1.0
CG J:ASP136 3.5 45.1 1.0
CG J:ASP100 3.5 48.2 1.0
OE1 J:GLU11 3.6 41.2 1.0
ND2 J:ASN104 3.7 40.5 1.0
C J:GLN101 3.7 46.6 1.0
CA J:CA301 3.8 45.5 1.0
OD2 J:ASP103 3.8 46.0 1.0
N J:GLN101 4.0 44.9 1.0
OD2 J:ASP100 4.0 47.9 1.0
N J:ASP103 4.1 39.6 1.0
CG J:GLU69 4.2 38.5 1.0
CB J:ASP136 4.2 43.0 1.0
CA J:ASP136 4.3 45.5 1.0
OD2 J:ASP136 4.3 49.1 1.0
NE J:ARG68 4.4 47.1 1.0
CA J:GLN101 4.4 47.5 1.0
CB J:ASP103 4.6 40.0 1.0
CB J:ASP100 4.7 46.4 1.0
CG J:GLU11 4.7 44.3 1.0
CA J:ASP100 4.8 46.2 1.0
N J:ASN102 4.8 43.7 1.0
C J:ASP100 4.8 46.6 1.0
CB J:ARG68 4.8 43.9 1.0
CA J:ASP103 4.8 39.3 1.0
CB J:GLN101 4.9 48.8 1.0
CG J:ASN104 4.9 42.5 1.0
CA J:ASN102 5.0 41.7 1.0
NH2 J:ARG68 5.0 45.9 1.0
N J:ASN104 5.0 37.4 1.0

Calcium binding site 6 out of 6 in 4qd2

Go back to Calcium Binding Sites List in 4qd2
Calcium binding site 6 out of 6 in the Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca303

b:45.9
occ:1.00
 O J:ASN143 2.3 49.8 1.0
OD2 J:ASP134 2.4 46.3 1.0
O J:ASN104 2.4 44.3 1.0
OD1 J:ASP134 2.4 46.4 1.0
OD2 J:ASP136 2.4 49.1 1.0
OD2 J:ASP195 2.4 42.4 1.0
OD1 J:ASN102 2.4 40.3 1.0
CG J:ASP134 2.7 46.6 1.0
CG J:ASP136 3.4 45.1 1.0
CG J:ASP195 3.4 43.8 1.0
C J:ASN104 3.5 44.5 1.0
C J:ASN143 3.5 52.0 1.0
CG J:ASN102 3.6 39.7 1.0
CB J:ASP136 3.7 43.0 1.0
CB J:ASP195 3.8 43.4 1.0
CA J:ASN104 4.2 40.4 1.0
CB J:ASP134 4.2 47.3 1.0
N J:ASN104 4.2 37.4 1.0
CB J:ASN104 4.3 41.3 1.0
ND2 J:ASN102 4.3 39.3 1.0
OD1 J:ASP195 4.4 45.4 1.0
N J:ALA144 4.4 53.5 1.0
CA J:ASN143 4.5 51.5 1.0
OD1 J:ASP136 4.5 46.2 1.0
CA J:ALA144 4.5 52.6 1.0
CB J:ASN143 4.5 50.0 1.0
N J:ARG105 4.6 48.3 1.0
CD J:PRO106 4.7 52.4 1.0
CB J:ASN102 4.8 40.1 1.0
CA J:ASN102 4.8 41.7 1.0
N J:ASP136 4.8 46.1 1.0
CD1 J:LEU201 4.9 38.4 1.0
CA J:ASP136 4.9 45.5 1.0
CA J:ARG105 4.9 50.9 1.0
C J:ASN102 4.9 41.9 1.0
N J:PRO106 5.0 52.8 1.0
C J:ARG105 5.0 51.6 1.0

Reference:

K.Lee, X.Zhong, S.Gu, A.M.Kruel, M.B.Dorner, K.Perry, A.Rummel, M.Dong, R.Jin. Molecular Basis For Disruption of E-Cadherin Adhesion By Botulinum Neurotoxin A Complex. Science V. 344 1405 2014.
ISSN: ISSN 0036-8075
PubMed: 24948737
DOI: 10.1126/SCIENCE.1253823
Page generated: Sat Dec 12 05:05:48 2020

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