Calcium in PDB 4nuq: Crystal Structure of Mouse N-Cadherin EC1-2 W2F
Protein crystallography data
The structure of Crystal Structure of Mouse N-Cadherin EC1-2 W2F, PDB code: 4nuq
was solved by
X.Jin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.91 /
2.12
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.587,
86.245,
46.722,
90.00,
98.52,
90.00
|
R / Rfree (%)
|
21.2 /
25.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Mouse N-Cadherin EC1-2 W2F
(pdb code 4nuq). 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 Mouse N-Cadherin EC1-2 W2F, PDB code: 4nuq:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 4nuq
Go back to
Calcium Binding Sites List in 4nuq
Calcium binding site 1 out
of 3 in the Crystal Structure of Mouse N-Cadherin EC1-2 W2F
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 Mouse N-Cadherin EC1-2 W2F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:49.2
occ:1.00
|
OE1
|
A:GLU11
|
2.2
|
48.0
|
1.0
|
OD1
|
A:ASP67
|
2.3
|
47.0
|
1.0
|
OD2
|
A:ASP103
|
2.3
|
51.4
|
1.0
|
O
|
A:HOH413
|
2.4
|
51.1
|
1.0
|
OE1
|
A:GLU69
|
2.4
|
46.0
|
1.0
|
O
|
A:HOH448
|
2.4
|
51.7
|
1.0
|
CG
|
A:ASP103
|
3.0
|
52.9
|
1.0
|
OD1
|
A:ASP103
|
3.1
|
46.7
|
1.0
|
CG
|
A:ASP67
|
3.3
|
51.0
|
1.0
|
CD
|
A:GLU11
|
3.3
|
53.7
|
1.0
|
CD
|
A:GLU69
|
3.6
|
46.2
|
1.0
|
OE2
|
A:GLU11
|
3.7
|
54.0
|
1.0
|
CA
|
A:CA302
|
3.9
|
47.1
|
1.0
|
N
|
A:ARG68
|
4.0
|
47.1
|
1.0
|
CB
|
A:ASP67
|
4.1
|
47.4
|
1.0
|
CA
|
A:ASP67
|
4.1
|
51.0
|
1.0
|
OD2
|
A:ASP67
|
4.1
|
47.4
|
1.0
|
N
|
A:GLU69
|
4.3
|
43.5
|
1.0
|
O
|
A:HOH479
|
4.3
|
58.8
|
1.0
|
OD1
|
A:ASN104
|
4.4
|
46.1
|
1.0
|
C
|
A:ASP67
|
4.4
|
48.0
|
1.0
|
CB
|
A:GLU69
|
4.4
|
47.5
|
1.0
|
ND2
|
A:ASN12
|
4.4
|
57.3
|
1.0
|
OE2
|
A:GLU69
|
4.4
|
44.8
|
1.0
|
CG
|
A:GLU69
|
4.5
|
44.4
|
1.0
|
CB
|
A:ASP103
|
4.5
|
46.0
|
1.0
|
OD1
|
A:ASN12
|
4.6
|
64.3
|
1.0
|
CG
|
A:GLU11
|
4.6
|
47.2
|
1.0
|
CG
|
A:ASN12
|
4.9
|
57.8
|
1.0
|
CA
|
A:GLU69
|
5.0
|
46.2
|
1.0
|
|
Calcium binding site 2 out
of 3 in 4nuq
Go back to
Calcium Binding Sites List in 4nuq
Calcium binding site 2 out
of 3 in the Crystal Structure of Mouse N-Cadherin EC1-2 W2F
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 Mouse N-Cadherin EC1-2 W2F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:47.1
occ:1.00
|
OD1
|
A:ASP100
|
2.3
|
52.9
|
1.0
|
OE2
|
A:GLU69
|
2.4
|
44.8
|
1.0
|
OD1
|
A:ASP103
|
2.4
|
46.7
|
1.0
|
OD1
|
A:ASP136
|
2.5
|
48.5
|
1.0
|
OE2
|
A:GLU11
|
2.5
|
54.0
|
1.0
|
O
|
A:MET101
|
2.5
|
49.8
|
1.0
|
OE1
|
A:GLU69
|
2.5
|
46.0
|
1.0
|
CD
|
A:GLU69
|
2.8
|
46.2
|
1.0
|
CG
|
A:ASP100
|
3.4
|
58.0
|
1.0
|
CD
|
A:GLU11
|
3.5
|
53.7
|
1.0
|
CG
|
A:ASP136
|
3.5
|
52.4
|
1.0
|
CG
|
A:ASP103
|
3.5
|
52.9
|
1.0
|
C
|
A:MET101
|
3.7
|
52.1
|
1.0
|
OE1
|
A:GLU11
|
3.8
|
48.0
|
1.0
|
N
|
A:MET101
|
3.9
|
42.6
|
1.0
|
CA
|
A:CA301
|
3.9
|
49.2
|
1.0
|
OD1
|
A:ASN104
|
4.0
|
46.1
|
1.0
|
OD2
|
A:ASP100
|
4.0
|
56.2
|
1.0
|
CB
|
A:ASP136
|
4.1
|
49.6
|
1.0
|
OD2
|
A:ASP103
|
4.1
|
51.4
|
1.0
|
N
|
A:ASP103
|
4.1
|
59.5
|
1.0
|
NE
|
A:ARG68
|
4.2
|
54.2
|
1.0
|
CA
|
A:ASP136
|
4.2
|
50.3
|
1.0
|
CG
|
A:GLU69
|
4.2
|
44.4
|
1.0
|
CA
|
A:MET101
|
4.4
|
50.6
|
1.0
|
OD2
|
A:ASP136
|
4.5
|
50.4
|
1.0
|
NH2
|
A:ARG68
|
4.6
|
47.2
|
1.0
|
CB
|
A:ASP100
|
4.6
|
50.3
|
1.0
|
CA
|
A:ASP100
|
4.7
|
52.3
|
1.0
|
CB
|
A:ASP103
|
4.7
|
46.0
|
1.0
|
C
|
A:ASP100
|
4.7
|
51.0
|
1.0
|
N
|
A:ASN102
|
4.8
|
51.5
|
1.0
|
CB
|
A:ARG68
|
4.8
|
43.5
|
1.0
|
CA
|
A:ASP103
|
4.8
|
53.6
|
1.0
|
CG
|
A:GLU11
|
4.8
|
47.2
|
1.0
|
CZ
|
A:ARG68
|
4.9
|
52.9
|
1.0
|
CA
|
A:ASN102
|
4.9
|
52.8
|
1.0
|
|
Calcium binding site 3 out
of 3 in 4nuq
Go back to
Calcium Binding Sites List in 4nuq
Calcium binding site 3 out
of 3 in the Crystal Structure of Mouse N-Cadherin EC1-2 W2F
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 Mouse N-Cadherin EC1-2 W2F within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:50.5
occ:1.00
|
O
|
A:ASN142
|
2.3
|
54.8
|
1.0
|
O
|
A:ASN104
|
2.3
|
56.9
|
1.0
|
OD1
|
A:ASN102
|
2.3
|
56.5
|
1.0
|
OD2
|
A:ASP136
|
2.4
|
50.4
|
1.0
|
OD2
|
A:ASP194
|
2.5
|
54.3
|
1.0
|
OD2
|
A:ASP134
|
2.5
|
58.1
|
1.0
|
OD1
|
A:ASP134
|
2.6
|
50.3
|
1.0
|
CG
|
A:ASP134
|
2.9
|
63.3
|
1.0
|
CG
|
A:ASP194
|
3.4
|
55.1
|
1.0
|
CG
|
A:ASP136
|
3.5
|
52.4
|
1.0
|
C
|
A:ASN142
|
3.5
|
50.1
|
1.0
|
CG
|
A:ASN102
|
3.5
|
60.0
|
1.0
|
C
|
A:ASN104
|
3.5
|
57.9
|
1.0
|
CB
|
A:ASP194
|
3.9
|
52.4
|
1.0
|
CB
|
A:ASP136
|
3.9
|
49.6
|
1.0
|
ND2
|
A:ASN102
|
4.1
|
52.5
|
1.0
|
N
|
A:ASN104
|
4.3
|
54.3
|
1.0
|
CA
|
A:ASN142
|
4.3
|
61.5
|
1.0
|
OD1
|
A:ASP194
|
4.3
|
54.2
|
1.0
|
CA
|
A:ASN104
|
4.3
|
49.0
|
1.0
|
CB
|
A:ASP134
|
4.4
|
55.2
|
1.0
|
N
|
A:GLY143
|
4.5
|
56.5
|
1.0
|
CD1
|
A:LEU203
|
4.5
|
53.1
|
1.0
|
N
|
A:ARG105
|
4.5
|
54.2
|
1.0
|
CB
|
A:ASN142
|
4.6
|
54.5
|
1.0
|
OD1
|
A:ASP136
|
4.6
|
48.5
|
1.0
|
CA
|
A:GLY143
|
4.6
|
59.3
|
1.0
|
CA
|
A:ARG105
|
4.6
|
59.3
|
1.0
|
CB
|
A:ASN104
|
4.6
|
52.5
|
1.0
|
CB
|
A:ASN102
|
4.7
|
54.1
|
1.0
|
CA
|
A:ASN102
|
4.8
|
52.8
|
1.0
|
N
|
A:ASP136
|
4.9
|
51.2
|
1.0
|
C
|
A:ARG105
|
4.9
|
54.8
|
1.0
|
|
Reference:
J.Vendome,
K.Felsovalyi,
H.Song,
Z.Yang,
X.Jin,
J.Brasch,
O.J.Harrison,
G.Ahlsen,
F.Bahna,
A.Kaczynska,
P.S.Katsamba,
D.Edmond,
W.L.Hubbell,
L.Shapiro,
B.Honig.
Structural and Energetic Determinants of Adhesive Binding Specificity in Type I Cadherins. Proc.Natl.Acad.Sci.Usa V. 111 E4175 2014.
ISSN: ISSN 0027-8424
PubMed: 25253890
DOI: 10.1073/PNAS.1416737111
Page generated: Sun Jul 14 11:10:16 2024
|