Calcium in PDB 5eqx: Crystal Structure of Human Desmoglein-3 Ectodomain
Protein crystallography data
The structure of Crystal Structure of Human Desmoglein-3 Ectodomain, PDB code: 5eqx
was solved by
O.J.Harrison,
J.Brasch,
L.Shapiro,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.92 /
3.05
|
Space group
|
P 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.909,
44.862,
106.699,
90.00,
102.92,
90.00
|
R / Rfree (%)
|
23.6 /
27.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Desmoglein-3 Ectodomain
(pdb code 5eqx). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of Human Desmoglein-3 Ectodomain, PDB code: 5eqx:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 5eqx
Go back to
Calcium Binding Sites List in 5eqx
Calcium binding site 1 out
of 8 in the Crystal Structure of Human Desmoglein-3 Ectodomain
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 Human Desmoglein-3 Ectodomain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca604
b:45.5
occ:1.00
|
OD1
|
A:ASP100
|
2.4
|
55.8
|
1.0
|
OD1
|
A:ASP136
|
2.5
|
51.9
|
1.0
|
OE1
|
A:GLU69
|
2.5
|
56.0
|
1.0
|
O
|
A:ILE101
|
2.5
|
52.8
|
1.0
|
OE2
|
A:GLU11
|
2.6
|
53.0
|
1.0
|
OD1
|
A:ASP103
|
2.6
|
48.8
|
1.0
|
OE2
|
A:GLU69
|
2.7
|
57.3
|
1.0
|
CD
|
A:GLU69
|
2.9
|
56.7
|
1.0
|
H
|
A:ILE101
|
3.0
|
67.1
|
1.0
|
CG
|
A:ASP100
|
3.3
|
54.5
|
1.0
|
CD
|
A:GLU11
|
3.4
|
60.1
|
1.0
|
HA
|
A:ASP136
|
3.4
|
66.5
|
1.0
|
H
|
A:ASP103
|
3.5
|
54.2
|
1.0
|
CG
|
A:ASP136
|
3.5
|
51.7
|
1.0
|
HG2
|
A:ARG68
|
3.5
|
70.8
|
1.0
|
OE1
|
A:GLU11
|
3.6
|
62.2
|
1.0
|
CG
|
A:ASP103
|
3.6
|
46.1
|
1.0
|
HG13
|
A:ILE101
|
3.6
|
69.5
|
1.0
|
HH11
|
A:ARG68
|
3.6
|
70.3
|
1.0
|
C
|
A:ILE101
|
3.7
|
52.6
|
1.0
|
N
|
A:ILE101
|
3.7
|
55.9
|
1.0
|
OD2
|
A:ASP100
|
3.8
|
53.6
|
1.0
|
HG3
|
A:ARG68
|
3.9
|
70.8
|
1.0
|
HG12
|
A:ILE101
|
3.9
|
69.5
|
1.0
|
HB3
|
A:ASP136
|
3.9
|
67.0
|
1.0
|
OD2
|
A:ASP103
|
4.0
|
44.9
|
1.0
|
HA
|
A:ASP100
|
4.0
|
59.9
|
1.0
|
HD3
|
A:ARG68
|
4.0
|
69.2
|
1.0
|
CB
|
A:ASP136
|
4.1
|
55.8
|
1.0
|
CG
|
A:ARG68
|
4.1
|
59.0
|
1.0
|
CA
|
A:CA606
|
4.2
|
50.9
|
1.0
|
CG1
|
A:ILE101
|
4.2
|
57.9
|
1.0
|
CA
|
A:ASP136
|
4.2
|
55.4
|
1.0
|
CA
|
A:ILE101
|
4.3
|
55.7
|
1.0
|
N
|
A:ASP103
|
4.3
|
45.2
|
1.0
|
CG
|
A:GLU69
|
4.4
|
55.5
|
1.0
|
CB
|
A:ASP100
|
4.4
|
51.8
|
1.0
|
OD2
|
A:ASP136
|
4.4
|
45.2
|
1.0
|
NH1
|
A:ARG68
|
4.4
|
58.5
|
1.0
|
HA
|
A:ASN102
|
4.5
|
62.1
|
1.0
|
CA
|
A:ASP100
|
4.5
|
49.9
|
1.0
|
C
|
A:ASP100
|
4.6
|
49.3
|
1.0
|
CD
|
A:ARG68
|
4.6
|
57.7
|
1.0
|
HB2
|
A:ASP100
|
4.6
|
62.1
|
1.0
|
HG2
|
A:GLU69
|
4.6
|
66.6
|
1.0
|
H
|
A:GLU137
|
4.6
|
69.7
|
1.0
|
OD1
|
A:ASN104
|
4.6
|
55.5
|
1.0
|
HH12
|
A:ARG68
|
4.7
|
70.3
|
1.0
|
HB2
|
A:ASN104
|
4.7
|
60.4
|
1.0
|
H
|
A:ASN104
|
4.7
|
62.7
|
1.0
|
HG3
|
A:GLU69
|
4.8
|
66.6
|
1.0
|
N
|
A:ASN102
|
4.8
|
51.6
|
1.0
|
H
|
A:GLU69
|
4.8
|
79.8
|
1.0
|
CB
|
A:ASP103
|
4.8
|
45.0
|
1.0
|
CG
|
A:GLU11
|
4.8
|
61.7
|
1.0
|
HB3
|
A:GLU11
|
4.9
|
77.0
|
1.0
|
CB
|
A:ILE101
|
4.9
|
54.5
|
1.0
|
|
Calcium binding site 2 out
of 8 in 5eqx
Go back to
Calcium Binding Sites List in 5eqx
Calcium binding site 2 out
of 8 in the Crystal Structure of Human Desmoglein-3 Ectodomain
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 Human Desmoglein-3 Ectodomain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca605
b:51.4
occ:1.00
|
OD1
|
A:ASN212
|
2.3
|
48.5
|
1.0
|
OD2
|
A:ASP245
|
2.4
|
53.7
|
1.0
|
OD2
|
A:ASP243
|
2.4
|
49.8
|
1.0
|
OD1
|
A:ASN302
|
2.4
|
61.8
|
1.0
|
O
|
A:ASN214
|
2.4
|
50.2
|
1.0
|
O
|
A:ASN251
|
2.5
|
55.3
|
1.0
|
OD1
|
A:ASP243
|
2.7
|
52.1
|
1.0
|
CG
|
A:ASP243
|
2.9
|
50.9
|
1.0
|
HD21
|
A:ASN302
|
3.0
|
74.8
|
1.0
|
CG
|
A:ASN302
|
3.1
|
60.8
|
1.0
|
HD3
|
A:PRO216
|
3.2
|
65.1
|
1.0
|
ND2
|
A:ASN302
|
3.3
|
62.3
|
1.0
|
CG
|
A:ASP245
|
3.5
|
55.2
|
1.0
|
CG
|
A:ASN212
|
3.5
|
53.3
|
1.0
|
HB2
|
A:ASP245
|
3.6
|
69.3
|
1.0
|
C
|
A:ASN251
|
3.6
|
55.3
|
1.0
|
C
|
A:ASN214
|
3.6
|
51.2
|
1.0
|
HA
|
A:TRP252
|
3.6
|
70.2
|
1.0
|
H
|
A:ASN214
|
3.7
|
65.6
|
1.0
|
HD21
|
A:ASN212
|
3.9
|
73.3
|
1.0
|
HA
|
A:ASN212
|
4.0
|
59.4
|
1.0
|
CB
|
A:ASP245
|
4.1
|
57.7
|
1.0
|
HB2
|
A:ASN214
|
4.1
|
57.0
|
1.0
|
HD22
|
A:ASN302
|
4.1
|
74.8
|
1.0
|
ND2
|
A:ASN212
|
4.1
|
61.1
|
1.0
|
CD
|
A:PRO216
|
4.1
|
54.3
|
1.0
|
HA
|
A:PHE215
|
4.2
|
59.7
|
1.0
|
H
|
A:ASP245
|
4.3
|
53.9
|
1.0
|
HA
|
A:ASN251
|
4.3
|
66.9
|
1.0
|
N
|
A:TRP252
|
4.4
|
59.8
|
1.0
|
HB3
|
A:ASN251
|
4.4
|
64.2
|
1.0
|
CB
|
A:ASN302
|
4.4
|
58.2
|
1.0
|
CB
|
A:ASP243
|
4.4
|
52.7
|
1.0
|
N
|
A:ASN214
|
4.4
|
54.7
|
1.0
|
CA
|
A:TRP252
|
4.4
|
58.5
|
1.0
|
CA
|
A:ASN214
|
4.4
|
50.8
|
1.0
|
OD1
|
A:ASP245
|
4.5
|
53.5
|
1.0
|
HE1
|
A:PHE306
|
4.5
|
78.2
|
1.0
|
HB3
|
A:ASN302
|
4.5
|
69.8
|
1.0
|
CA
|
A:ASN251
|
4.5
|
55.7
|
1.0
|
HB2
|
A:ASN302
|
4.5
|
69.8
|
1.0
|
CB
|
A:ASN214
|
4.6
|
47.5
|
1.0
|
HB3
|
A:ASP245
|
4.6
|
69.3
|
1.0
|
N
|
A:PHE215
|
4.6
|
53.5
|
1.0
|
N
|
A:PRO216
|
4.6
|
45.2
|
1.0
|
HB3
|
A:ASN214
|
4.6
|
57.0
|
1.0
|
CB
|
A:ASN212
|
4.7
|
52.2
|
1.0
|
HB3
|
A:PRO216
|
4.7
|
65.6
|
1.0
|
HD2
|
A:PRO216
|
4.7
|
65.1
|
1.0
|
HB2
|
A:ASP243
|
4.7
|
63.2
|
1.0
|
HG3
|
A:PRO216
|
4.7
|
65.3
|
1.0
|
CA
|
A:ASN212
|
4.7
|
49.5
|
1.0
|
CA
|
A:PHE215
|
4.8
|
49.7
|
1.0
|
HB3
|
A:ASP243
|
4.8
|
63.2
|
1.0
|
HD1
|
A:PHE306
|
4.8
|
81.3
|
1.0
|
C
|
A:PHE215
|
4.9
|
46.2
|
1.0
|
CG
|
A:PRO216
|
4.9
|
54.4
|
1.0
|
CB
|
A:ASN251
|
5.0
|
53.5
|
1.0
|
HD22
|
A:ASN212
|
5.0
|
73.3
|
1.0
|
HB2
|
A:ASN212
|
5.0
|
62.6
|
1.0
|
|
Calcium binding site 3 out
of 8 in 5eqx
Go back to
Calcium Binding Sites List in 5eqx
Calcium binding site 3 out
of 8 in the Crystal Structure of Human Desmoglein-3 Ectodomain
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 Human Desmoglein-3 Ectodomain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca606
b:50.9
occ:1.00
|
OE1
|
A:GLU11
|
2.4
|
62.2
|
1.0
|
OE1
|
A:GLU69
|
2.4
|
56.0
|
1.0
|
OD2
|
A:ASP103
|
2.4
|
44.9
|
1.0
|
OD1
|
A:ASP67
|
2.4
|
61.1
|
1.0
|
O
|
A:HOH746
|
2.8
|
44.2
|
1.0
|
CG
|
A:ASP67
|
3.1
|
69.9
|
1.0
|
CG
|
A:ASP103
|
3.1
|
46.1
|
1.0
|
OD2
|
A:ASP67
|
3.2
|
62.0
|
1.0
|
HB2
|
A:GLU69
|
3.2
|
61.0
|
1.0
|
O
|
A:HOH705
|
3.2
|
45.2
|
1.0
|
OD1
|
A:ASP103
|
3.3
|
48.8
|
1.0
|
CD
|
A:GLU11
|
3.4
|
60.1
|
1.0
|
CD
|
A:GLU69
|
3.5
|
56.7
|
1.0
|
OD1
|
A:ASN104
|
3.6
|
55.5
|
1.0
|
H
|
A:GLU69
|
3.8
|
79.8
|
1.0
|
HG2
|
A:GLU69
|
3.9
|
66.6
|
1.0
|
OE2
|
A:GLU11
|
4.0
|
53.0
|
1.0
|
CG
|
A:GLU69
|
4.0
|
55.5
|
1.0
|
CB
|
A:GLU69
|
4.0
|
50.9
|
1.0
|
CA
|
A:CA604
|
4.2
|
45.5
|
1.0
|
HA
|
A:ASP67
|
4.3
|
64.1
|
1.0
|
HG2
|
A:GLU11
|
4.3
|
74.1
|
1.0
|
CG
|
A:GLU11
|
4.4
|
61.7
|
1.0
|
HB2
|
A:ASP103
|
4.5
|
54.0
|
1.0
|
CB
|
A:ASP103
|
4.5
|
45.0
|
1.0
|
CB
|
A:ASP67
|
4.5
|
59.7
|
1.0
|
OE2
|
A:GLU69
|
4.5
|
57.3
|
1.0
|
HG3
|
A:GLU11
|
4.5
|
74.1
|
1.0
|
H
|
A:ARG68
|
4.5
|
65.7
|
1.0
|
HB3
|
A:GLU69
|
4.6
|
61.0
|
1.0
|
N
|
A:GLU69
|
4.6
|
66.5
|
1.0
|
CG
|
A:ASN104
|
4.6
|
55.0
|
1.0
|
HD21
|
A:ASN104
|
4.7
|
71.2
|
1.0
|
HD11
|
A:ILE101
|
4.7
|
82.0
|
1.0
|
CA
|
A:ASP67
|
4.8
|
53.4
|
1.0
|
HB2
|
A:ASP67
|
4.9
|
71.6
|
1.0
|
HG13
|
A:ILE101
|
4.9
|
69.5
|
1.0
|
N
|
A:ARG68
|
5.0
|
54.7
|
1.0
|
HG3
|
A:GLU69
|
5.0
|
66.6
|
1.0
|
CA
|
A:GLU69
|
5.0
|
53.3
|
1.0
|
HB3
|
A:ASP103
|
5.0
|
54.0
|
1.0
|
|
Calcium binding site 4 out
of 8 in 5eqx
Go back to
Calcium Binding Sites List in 5eqx
Calcium binding site 4 out
of 8 in the Crystal Structure of Human Desmoglein-3 Ectodomain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Human Desmoglein-3 Ectodomain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca607
b:54.7
occ:1.00
|
OD2
|
A:ASP136
|
2.3
|
45.2
|
1.0
|
OD1
|
A:ASN102
|
2.4
|
55.2
|
1.0
|
O
|
A:ASN104
|
2.4
|
51.4
|
1.0
|
O
|
A:ASN142
|
2.5
|
55.6
|
1.0
|
OD2
|
A:ASP134
|
2.5
|
47.1
|
1.0
|
OD2
|
A:ASP192
|
2.5
|
51.8
|
1.0
|
OD1
|
A:ASP134
|
2.7
|
52.7
|
1.0
|
CG
|
A:ASP134
|
2.9
|
48.7
|
1.0
|
CG
|
A:ASP136
|
3.5
|
51.7
|
1.0
|
CG
|
A:ASP192
|
3.5
|
53.5
|
1.0
|
HB2
|
A:ASP136
|
3.5
|
67.0
|
1.0
|
HB2
|
A:ASP192
|
3.5
|
62.4
|
1.0
|
CG
|
A:ASN102
|
3.6
|
58.1
|
1.0
|
HB3
|
A:ASP192
|
3.6
|
62.4
|
1.0
|
C
|
A:ASN104
|
3.6
|
54.0
|
1.0
|
C
|
A:ASN142
|
3.7
|
58.2
|
1.0
|
CB
|
A:ASP192
|
3.8
|
52.0
|
1.0
|
HB3
|
A:ASN142
|
3.8
|
71.2
|
1.0
|
H
|
A:ASN104
|
3.8
|
62.7
|
1.0
|
HD3
|
A:PRO106
|
3.9
|
65.5
|
1.0
|
HA
|
A:PRO105
|
4.0
|
67.5
|
1.0
|
HA
|
A:ASN102
|
4.0
|
62.1
|
1.0
|
CB
|
A:ASP136
|
4.0
|
55.8
|
1.0
|
HA
|
A:SER143
|
4.0
|
66.4
|
1.0
|
HD21
|
A:ASN102
|
4.0
|
78.3
|
1.0
|
ND2
|
A:ASN102
|
4.2
|
65.3
|
1.0
|
HA
|
A:ASN142
|
4.3
|
70.3
|
1.0
|
HB2
|
A:ASN104
|
4.3
|
60.4
|
1.0
|
H
|
A:ASP136
|
4.3
|
71.0
|
1.0
|
CB
|
A:ASP134
|
4.4
|
54.8
|
1.0
|
CA
|
A:ASN142
|
4.4
|
58.6
|
1.0
|
N
|
A:ASN104
|
4.5
|
52.2
|
1.0
|
OD1
|
A:ASP136
|
4.5
|
51.9
|
1.0
|
CA
|
A:ASN104
|
4.5
|
50.4
|
1.0
|
HD22
|
A:LEU198
|
4.5
|
68.2
|
1.0
|
HB3
|
A:ASP136
|
4.5
|
67.0
|
1.0
|
CB
|
A:ASN142
|
4.5
|
59.3
|
1.0
|
CA
|
A:PRO105
|
4.6
|
56.3
|
1.0
|
N
|
A:PRO105
|
4.6
|
61.7
|
1.0
|
OD1
|
A:ASP192
|
4.6
|
58.2
|
1.0
|
CA
|
A:ASN102
|
4.7
|
51.8
|
1.0
|
N
|
A:SER143
|
4.7
|
65.5
|
1.0
|
HB3
|
A:ASP134
|
4.7
|
65.8
|
1.0
|
HB2
|
A:LEU198
|
4.7
|
74.9
|
1.0
|
CB
|
A:ASN102
|
4.7
|
55.0
|
1.0
|
CD
|
A:PRO106
|
4.7
|
54.6
|
1.0
|
HB2
|
A:ASP134
|
4.7
|
65.8
|
1.0
|
C
|
A:PRO105
|
4.8
|
55.7
|
1.0
|
CA
|
A:SER143
|
4.8
|
55.3
|
1.0
|
CB
|
A:ASN104
|
4.8
|
50.3
|
1.0
|
C
|
A:ASN102
|
4.8
|
46.3
|
1.0
|
N
|
A:PRO106
|
4.9
|
56.9
|
1.0
|
HB3
|
A:ASN104
|
5.0
|
60.4
|
1.0
|
|
Calcium binding site 5 out
of 8 in 5eqx
Go back to
Calcium Binding Sites List in 5eqx
Calcium binding site 5 out
of 8 in the Crystal Structure of Human Desmoglein-3 Ectodomain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Human Desmoglein-3 Ectodomain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca608
b:48.1
occ:1.00
|
OD2
|
A:ASP213
|
2.3
|
50.5
|
1.0
|
OE2
|
A:GLU119
|
2.3
|
56.9
|
1.0
|
OD1
|
A:ASP177
|
2.4
|
61.9
|
1.0
|
OE2
|
A:GLU179
|
2.8
|
56.8
|
1.0
|
CG
|
A:ASP177
|
2.9
|
65.4
|
1.0
|
HD21
|
A:ASN120
|
3.1
|
84.6
|
1.0
|
CG
|
A:ASP213
|
3.1
|
53.6
|
1.0
|
HA
|
A:ASP177
|
3.2
|
82.3
|
1.0
|
CD
|
A:GLU119
|
3.3
|
58.5
|
1.0
|
OD2
|
A:ASP177
|
3.4
|
63.7
|
1.0
|
OD1
|
A:ASP213
|
3.4
|
60.3
|
1.0
|
HG2
|
A:GLU179
|
3.6
|
68.7
|
1.0
|
O
|
A:HOH708
|
3.6
|
41.4
|
1.0
|
CD
|
A:GLU179
|
3.7
|
55.3
|
1.0
|
OD1
|
A:ASN120
|
3.8
|
64.6
|
1.0
|
O
|
A:HOH739
|
3.8
|
35.6
|
1.0
|
ND2
|
A:ASN120
|
3.8
|
70.5
|
1.0
|
HG2
|
A:GLU119
|
3.8
|
84.4
|
1.0
|
CB
|
A:ASP177
|
3.9
|
69.4
|
1.0
|
CA
|
A:ASP177
|
4.0
|
68.5
|
1.0
|
HB2
|
A:ASP177
|
4.0
|
83.3
|
1.0
|
OE1
|
A:GLU119
|
4.1
|
56.7
|
1.0
|
CG
|
A:GLU179
|
4.1
|
57.2
|
1.0
|
CG
|
A:GLU119
|
4.1
|
70.3
|
1.0
|
H
|
A:ARG178
|
4.2
|
79.9
|
1.0
|
CG
|
A:ASN120
|
4.2
|
68.0
|
1.0
|
H
|
A:GLU179
|
4.3
|
77.9
|
1.0
|
OD1
|
A:ASN214
|
4.3
|
49.2
|
1.0
|
HG3
|
A:GLU179
|
4.4
|
68.7
|
1.0
|
HG3
|
A:GLU119
|
4.4
|
84.4
|
1.0
|
HB2
|
A:ASP213
|
4.4
|
69.3
|
1.0
|
CB
|
A:ASP213
|
4.4
|
57.8
|
1.0
|
HD22
|
A:ASN120
|
4.5
|
84.6
|
1.0
|
N
|
A:ARG178
|
4.6
|
66.6
|
1.0
|
C
|
A:ASP177
|
4.6
|
66.7
|
1.0
|
O
|
A:LEU176
|
4.6
|
68.2
|
1.0
|
CA
|
A:CA609
|
4.7
|
39.8
|
1.0
|
HB3
|
A:ASP177
|
4.7
|
83.3
|
1.0
|
OE1
|
A:GLU179
|
4.7
|
52.9
|
1.0
|
HB3
|
A:ASP213
|
4.8
|
69.3
|
1.0
|
O
|
A:ASP213
|
5.0
|
54.7
|
1.0
|
|
Calcium binding site 6 out
of 8 in 5eqx
Go back to
Calcium Binding Sites List in 5eqx
Calcium binding site 6 out
of 8 in the Crystal Structure of Human Desmoglein-3 Ectodomain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Human Desmoglein-3 Ectodomain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca609
b:39.8
occ:1.00
|
OD1
|
A:ASP245
|
2.4
|
53.5
|
1.0
|
OD1
|
A:ASP213
|
2.4
|
60.3
|
1.0
|
O
|
A:VAL211
|
2.5
|
54.1
|
1.0
|
OE2
|
A:GLU179
|
2.6
|
56.8
|
1.0
|
OD1
|
A:ASP210
|
2.7
|
71.3
|
1.0
|
OE1
|
A:GLU179
|
2.7
|
52.9
|
1.0
|
OE1
|
A:GLU119
|
2.8
|
56.7
|
1.0
|
CD
|
A:GLU179
|
3.0
|
55.3
|
1.0
|
H
|
A:VAL211
|
3.2
|
75.0
|
1.0
|
H
|
A:ASP213
|
3.3
|
62.4
|
1.0
|
HA
|
A:ASP245
|
3.3
|
66.1
|
1.0
|
CG
|
A:ASP245
|
3.3
|
55.2
|
1.0
|
CG
|
A:ASP213
|
3.5
|
53.6
|
1.0
|
CD
|
A:GLU119
|
3.6
|
58.5
|
1.0
|
CG
|
A:ASP210
|
3.7
|
77.6
|
1.0
|
HB3
|
A:ASP245
|
3.7
|
69.3
|
1.0
|
OE2
|
A:GLU119
|
3.7
|
56.9
|
1.0
|
C
|
A:VAL211
|
3.7
|
58.2
|
1.0
|
CB
|
A:ASP245
|
3.9
|
57.7
|
1.0
|
HB3
|
A:ARG178
|
3.9
|
77.0
|
1.0
|
N
|
A:VAL211
|
3.9
|
62.5
|
1.0
|
CA
|
A:ASP245
|
4.0
|
55.1
|
1.0
|
HE
|
A:ARG178
|
4.0
|
87.9
|
1.0
|
OD2
|
A:ASP213
|
4.1
|
50.5
|
1.0
|
N
|
A:ASP213
|
4.1
|
52.0
|
1.0
|
OD2
|
A:ASP210
|
4.2
|
60.8
|
1.0
|
HA
|
A:ASP210
|
4.2
|
78.8
|
1.0
|
HD3
|
A:ARG178
|
4.2
|
87.7
|
1.0
|
H
|
A:GLU246
|
4.3
|
79.8
|
1.0
|
HG23
|
A:VAL211
|
4.3
|
77.2
|
1.0
|
OD2
|
A:ASP245
|
4.3
|
53.7
|
1.0
|
OD1
|
A:ASN214
|
4.4
|
49.2
|
1.0
|
HA
|
A:ASN212
|
4.4
|
59.4
|
1.0
|
CA
|
A:VAL211
|
4.5
|
62.6
|
1.0
|
CG
|
A:GLU179
|
4.5
|
57.2
|
1.0
|
HG22
|
A:VAL211
|
4.6
|
77.2
|
1.0
|
CB
|
A:ASP213
|
4.6
|
57.8
|
1.0
|
HB3
|
A:ASP213
|
4.7
|
69.3
|
1.0
|
HB2
|
A:ASN214
|
4.7
|
57.0
|
1.0
|
CA
|
A:CA608
|
4.7
|
48.1
|
1.0
|
H
|
A:GLU179
|
4.7
|
77.9
|
1.0
|
N
|
A:ASN212
|
4.7
|
57.2
|
1.0
|
CB
|
A:ASP210
|
4.7
|
84.1
|
1.0
|
NE
|
A:ARG178
|
4.8
|
73.2
|
1.0
|
CA
|
A:ASP210
|
4.8
|
65.6
|
1.0
|
CA
|
A:ASP213
|
4.8
|
58.7
|
1.0
|
HB2
|
A:ASP245
|
4.8
|
69.3
|
1.0
|
HG3
|
A:GLU179
|
4.8
|
68.7
|
1.0
|
CB
|
A:ARG178
|
4.8
|
64.2
|
1.0
|
C
|
A:ASP210
|
4.8
|
64.4
|
1.0
|
CG2
|
A:VAL211
|
4.9
|
64.3
|
1.0
|
H
|
A:ASN214
|
4.9
|
65.6
|
1.0
|
N
|
A:ASP245
|
4.9
|
45.0
|
1.0
|
CA
|
A:ASN212
|
4.9
|
49.5
|
1.0
|
HB2
|
A:ARG178
|
4.9
|
77.0
|
1.0
|
N
|
A:GLU246
|
4.9
|
66.5
|
1.0
|
HG2
|
A:GLU179
|
5.0
|
68.7
|
1.0
|
CD
|
A:ARG178
|
5.0
|
73.1
|
1.0
|
|
Calcium binding site 7 out
of 8 in 5eqx
Go back to
Calcium Binding Sites List in 5eqx
Calcium binding site 7 out
of 8 in the Crystal Structure of Human Desmoglein-3 Ectodomain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Human Desmoglein-3 Ectodomain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca610
b:64.1
occ:1.00
|
OE2
|
A:GLU289
|
2.3
|
60.6
|
1.0
|
OE1
|
A:GLU330
|
2.4
|
57.2
|
1.0
|
OD1
|
A:ASN327
|
2.4
|
76.7
|
1.0
|
O
|
A:VAL328
|
2.4
|
73.5
|
1.0
|
OE1
|
A:GLU229
|
2.5
|
63.8
|
1.0
|
H
|
A:VAL328
|
3.0
|
88.3
|
1.0
|
HD21
|
A:ASN327
|
3.1
|
88.7
|
1.0
|
HG3
|
A:GLU330
|
3.1
|
75.3
|
1.0
|
CG
|
A:ASN327
|
3.2
|
73.7
|
1.0
|
H
|
A:GLU330
|
3.3
|
83.0
|
1.0
|
OD1
|
A:ASP366
|
3.3
|
72.4
|
1.0
|
CD
|
A:GLU330
|
3.4
|
60.0
|
1.0
|
HA
|
A:ASP366
|
3.4
|
73.5
|
1.0
|
CD
|
A:GLU289
|
3.4
|
66.6
|
1.0
|
ND2
|
A:ASN327
|
3.4
|
73.9
|
1.0
|
CD
|
A:GLU229
|
3.5
|
61.3
|
1.0
|
C
|
A:VAL328
|
3.5
|
78.8
|
1.0
|
HB2
|
A:GLU330
|
3.6
|
72.2
|
1.0
|
CG
|
A:GLU330
|
3.6
|
62.8
|
1.0
|
N
|
A:VAL328
|
3.7
|
73.6
|
1.0
|
OE2
|
A:GLU229
|
3.8
|
61.7
|
1.0
|
OE1
|
A:GLU289
|
3.9
|
63.0
|
1.0
|
HG23
|
A:VAL328
|
4.0
|
82.6
|
1.0
|
HG22
|
A:VAL328
|
4.0
|
82.6
|
1.0
|
N
|
A:GLU330
|
4.0
|
69.2
|
1.0
|
CB
|
A:GLU330
|
4.1
|
60.1
|
1.0
|
HB3
|
A:TYR288
|
4.1
|
72.5
|
1.0
|
CG
|
A:ASP366
|
4.1
|
76.6
|
1.0
|
O
|
A:GLU365
|
4.2
|
61.2
|
1.0
|
CA
|
A:VAL328
|
4.2
|
76.0
|
1.0
|
HD22
|
A:ASN327
|
4.2
|
88.7
|
1.0
|
HA
|
A:ASN327
|
4.2
|
85.8
|
1.0
|
CA
|
A:CA611
|
4.3
|
46.2
|
1.0
|
CA
|
A:ASP366
|
4.3
|
61.2
|
1.0
|
HA
|
A:ARG329
|
4.4
|
99.0
|
1.0
|
CG2
|
A:VAL328
|
4.4
|
68.9
|
1.0
|
CB
|
A:ASN327
|
4.4
|
79.2
|
1.0
|
OE2
|
A:GLU330
|
4.5
|
53.9
|
1.0
|
HG2
|
A:GLU330
|
4.5
|
75.3
|
1.0
|
C
|
A:ASN327
|
4.6
|
69.8
|
1.0
|
N
|
A:ARG329
|
4.6
|
93.5
|
1.0
|
CG
|
A:GLU289
|
4.6
|
77.9
|
1.0
|
CA
|
A:ASN327
|
4.6
|
71.5
|
1.0
|
HD2
|
A:TYR288
|
4.7
|
95.7
|
1.0
|
CA
|
A:GLU330
|
4.7
|
64.1
|
1.0
|
CG
|
A:GLU229
|
4.7
|
61.1
|
1.0
|
HG3
|
A:GLU289
|
4.8
|
93.5
|
1.0
|
CB
|
A:ASP366
|
4.8
|
75.6
|
1.0
|
HG2
|
A:GLU289
|
4.8
|
93.5
|
1.0
|
C
|
A:GLU365
|
4.8
|
59.7
|
1.0
|
N
|
A:ASP366
|
4.9
|
62.8
|
1.0
|
CA
|
A:ARG329
|
4.9
|
82.5
|
1.0
|
HB2
|
A:ASN327
|
4.9
|
95.0
|
1.0
|
OD2
|
A:ASP366
|
4.9
|
84.0
|
1.0
|
HG2
|
A:GLU229
|
4.9
|
73.3
|
1.0
|
C
|
A:ARG329
|
4.9
|
77.4
|
1.0
|
HB3
|
A:GLU330
|
4.9
|
72.2
|
1.0
|
HG3
|
A:GLU229
|
4.9
|
73.3
|
1.0
|
HA
|
A:VAL328
|
5.0
|
91.2
|
1.0
|
HB3
|
A:ASP366
|
5.0
|
90.7
|
1.0
|
|
Calcium binding site 8 out
of 8 in 5eqx
Go back to
Calcium Binding Sites List in 5eqx
Calcium binding site 8 out
of 8 in the Crystal Structure of Human Desmoglein-3 Ectodomain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Human Desmoglein-3 Ectodomain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca611
b:46.2
occ:1.00
|
OE1
|
A:GLU330
|
2.3
|
57.2
|
1.0
|
OD1
|
A:ASP287
|
2.4
|
57.6
|
1.0
|
OE2
|
A:GLU330
|
2.5
|
53.9
|
1.0
|
OD2
|
A:ASP287
|
2.5
|
62.3
|
1.0
|
OE2
|
A:GLU229
|
2.5
|
61.7
|
1.0
|
OE1
|
A:GLU289
|
2.6
|
63.0
|
1.0
|
CG
|
A:ASP287
|
2.6
|
64.5
|
1.0
|
CD
|
A:GLU330
|
2.7
|
60.0
|
1.0
|
HD21
|
A:ASN230
|
3.3
|
55.7
|
1.0
|
CD
|
A:GLU289
|
3.4
|
66.6
|
1.0
|
CD
|
A:GLU229
|
3.5
|
61.3
|
1.0
|
OE2
|
A:GLU289
|
3.7
|
60.6
|
1.0
|
O
|
A:GLU365
|
3.7
|
61.2
|
1.0
|
HA
|
A:ASP287
|
3.7
|
73.6
|
1.0
|
H
|
A:TYR288
|
3.8
|
66.5
|
1.0
|
HB3
|
A:GLU365
|
3.8
|
67.3
|
1.0
|
H
|
A:GLU289
|
3.9
|
0.8
|
1.0
|
CB
|
A:ASP287
|
4.0
|
63.4
|
1.0
|
OE1
|
A:GLU229
|
4.1
|
63.8
|
1.0
|
ND2
|
A:ASN230
|
4.1
|
46.4
|
1.0
|
CG
|
A:GLU330
|
4.2
|
62.8
|
1.0
|
HB2
|
A:GLU229
|
4.3
|
63.9
|
1.0
|
CA
|
A:ASP287
|
4.3
|
61.3
|
1.0
|
CA
|
A:CA610
|
4.3
|
64.1
|
1.0
|
HB2
|
A:GLU289
|
4.3
|
81.2
|
1.0
|
N
|
A:TYR288
|
4.4
|
55.5
|
1.0
|
HG3
|
A:GLU229
|
4.4
|
73.3
|
1.0
|
OD1
|
A:ASN230
|
4.4
|
53.7
|
1.0
|
HB3
|
A:ASP287
|
4.5
|
76.1
|
1.0
|
CG
|
A:GLU229
|
4.5
|
61.1
|
1.0
|
HB2
|
A:ASP287
|
4.6
|
76.1
|
1.0
|
HB3
|
A:TYR288
|
4.6
|
72.5
|
1.0
|
HG3
|
A:GLU330
|
4.6
|
75.3
|
1.0
|
HB2
|
A:GLU330
|
4.7
|
72.2
|
1.0
|
HG2
|
A:GLU330
|
4.7
|
75.3
|
1.0
|
HD22
|
A:ASN230
|
4.7
|
55.7
|
1.0
|
CG
|
A:ASN230
|
4.7
|
50.2
|
1.0
|
CG
|
A:GLU289
|
4.7
|
77.9
|
1.0
|
C
|
A:ASP287
|
4.7
|
55.7
|
1.0
|
C
|
A:GLU365
|
4.7
|
59.7
|
1.0
|
CB
|
A:GLU365
|
4.8
|
56.1
|
1.0
|
N
|
A:GLU289
|
4.8
|
85.7
|
1.0
|
HG2
|
A:GLU365
|
4.8
|
65.5
|
1.0
|
CB
|
A:GLU229
|
4.9
|
53.3
|
1.0
|
CB
|
A:GLU330
|
5.0
|
60.1
|
1.0
|
CB
|
A:GLU289
|
5.0
|
67.7
|
1.0
|
|
Reference:
O.J.Harrison,
J.Brasch,
G.Lasso,
P.S.Katsamba,
G.Ahlsen,
B.Honig,
L.Shapiro.
Structural Basis of Adhesive Binding By Desmocollins and Desmogleins. Proc.Natl.Acad.Sci.Usa V. 113 7160 2016.
ISSN: ESSN 1091-6490
PubMed: 27298358
DOI: 10.1073/PNAS.1606272113
Page generated: Sun Jul 14 18:41:55 2024
|