Atomistry » Calcium » PDB 4q1o-4qn4 » 4qd2
Atomistry »
  Calcium »
    PDB 4q1o-4qn4 »
      4qd2 »

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: Sun Jul 14 12:24:38 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy