Calcium in PDB 6vg4: Human Protocadherin 10 Ectodomain
Protein crystallography data
The structure of Human Protocadherin 10 Ectodomain, PDB code: 6vg4
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)
|
20.00 /
3.30
|
|
Space group
|
P 41 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.087,
84.087,
543.917,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
23 /
28.4
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Calcium atom in the Human Protocadherin 10 Ectodomain
(pdb code 6vg4). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the
Human Protocadherin 10 Ectodomain, PDB code: 6vg4:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 1 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca703
b:78.2
occ:1.00
|
OD1
|
A:ASP63
|
2.3
|
85.1
|
1.0
|
|
OD2
|
A:ASP100
|
2.3
|
0.5
|
1.0
|
|
OE1
|
A:GLU10
|
2.4
|
92.4
|
1.0
|
|
OE2
|
A:GLU65
|
2.4
|
66.8
|
1.0
|
|
OE1
|
A:GLU9
|
2.4
|
0.3
|
1.0
|
|
HD21
|
A:ASN101
|
3.3
|
0.1
|
1.0
|
|
CD
|
A:GLU10
|
3.3
|
93.4
|
1.0
|
|
HG3
|
A:GLU10
|
3.3
|
1.0
|
1.0
|
|
HG2
|
A:GLU10
|
3.3
|
1.0
|
1.0
|
|
CG
|
A:ASP100
|
3.3
|
0.5
|
1.0
|
|
CD
|
A:GLU9
|
3.3
|
100.0
|
1.0
|
|
CG
|
A:ASP63
|
3.5
|
98.1
|
1.0
|
|
CG
|
A:GLU10
|
3.5
|
0.1
|
1.0
|
|
CD
|
A:GLU65
|
3.6
|
79.6
|
1.0
|
|
HA
|
A:ASP63
|
3.6
|
0.0
|
1.0
|
|
OD1
|
A:ASP100
|
3.7
|
0.7
|
1.0
|
|
H
|
A:GLU65
|
3.7
|
0.9
|
1.0
|
|
HD22
|
A:ASN101
|
3.7
|
0.1
|
1.0
|
|
OE2
|
A:GLU9
|
3.8
|
0.0
|
1.0
|
|
ND2
|
A:ASN101
|
3.8
|
0.6
|
1.0
|
|
HB2
|
A:GLU65
|
3.8
|
0.2
|
1.0
|
|
H
|
A:ARG64
|
3.9
|
99.3
|
1.0
|
|
OD2
|
A:ASP63
|
4.3
|
0.1
|
1.0
|
|
CA
|
A:ASP63
|
4.3
|
0.2
|
1.0
|
|
OE1
|
A:GLU65
|
4.4
|
67.2
|
1.0
|
|
CA
|
A:CA704
|
4.4
|
76.0
|
1.0
|
|
N
|
A:ARG64
|
4.4
|
82.8
|
1.0
|
|
CB
|
A:ASP63
|
4.4
|
0.6
|
1.0
|
|
OE2
|
A:GLU10
|
4.5
|
0.1
|
1.0
|
|
HG3
|
A:GLU9
|
4.5
|
0.7
|
1.0
|
|
CG
|
A:GLU9
|
4.5
|
96.4
|
1.0
|
|
N
|
A:GLU65
|
4.6
|
0.6
|
1.0
|
|
HB2
|
A:ASP63
|
4.6
|
0.3
|
1.0
|
|
CG
|
A:GLU65
|
4.6
|
82.5
|
1.0
|
|
CB
|
A:GLU65
|
4.6
|
86.8
|
1.0
|
|
HB2
|
A:ASP100
|
4.7
|
0.9
|
1.0
|
|
CB
|
A:ASP100
|
4.7
|
0.3
|
1.0
|
|
C
|
A:ASP63
|
4.7
|
99.0
|
1.0
|
|
HB2
|
A:GLU9
|
4.7
|
74.5
|
1.0
|
|
HG2
|
A:GLU65
|
4.8
|
99.0
|
1.0
|
|
HB3
|
A:ARG64
|
5.0
|
73.3
|
1.0
|
|
Calcium binding site 2 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 2 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca704
b:76.0
occ:1.00
|
O
|
A:ILE98
|
2.3
|
0.8
|
1.0
|
|
OE2
|
A:GLU9
|
2.3
|
0.0
|
1.0
|
|
OE1
|
A:GLU65
|
2.4
|
67.2
|
1.0
|
|
OD1
|
A:ASP100
|
2.4
|
0.7
|
1.0
|
|
OD1
|
A:ASP97
|
2.4
|
63.1
|
1.0
|
|
OD1
|
A:ASP133
|
2.4
|
88.8
|
1.0
|
|
CD
|
A:GLU65
|
2.9
|
79.6
|
1.0
|
|
OE2
|
A:GLU65
|
3.0
|
66.8
|
1.0
|
|
H
|
A:ILE98
|
3.1
|
0.5
|
1.0
|
|
H
|
A:ASP100
|
3.3
|
0.2
|
1.0
|
|
HD22
|
A:ASN101
|
3.4
|
0.1
|
1.0
|
|
CG
|
A:ASP133
|
3.4
|
0.2
|
1.0
|
|
CD
|
A:GLU9
|
3.4
|
100.0
|
1.0
|
|
C
|
A:ILE98
|
3.5
|
0.4
|
1.0
|
|
CG
|
A:ASP100
|
3.5
|
0.5
|
1.0
|
|
CG
|
A:ASP97
|
3.6
|
93.6
|
1.0
|
|
N
|
A:ILE98
|
3.7
|
0.4
|
1.0
|
|
HG13
|
A:ILE98
|
3.8
|
90.0
|
1.0
|
|
HG12
|
A:ILE98
|
3.8
|
90.0
|
1.0
|
|
HE
|
A:ARG64
|
4.0
|
0.4
|
1.0
|
|
OE1
|
A:GLU9
|
4.0
|
0.3
|
1.0
|
|
HA
|
A:ASP133
|
4.0
|
74.7
|
1.0
|
|
OD2
|
A:ASP100
|
4.1
|
0.5
|
1.0
|
|
HB3
|
A:ASP133
|
4.1
|
0.5
|
1.0
|
|
N
|
A:ASP100
|
4.1
|
0.8
|
1.0
|
|
OD2
|
A:ASP133
|
4.1
|
0.7
|
1.0
|
|
HA
|
A:ASP97
|
4.1
|
0.4
|
1.0
|
|
HA
|
A:ASN99
|
4.2
|
0.8
|
1.0
|
|
ND2
|
A:ASN101
|
4.2
|
0.6
|
1.0
|
|
CA
|
A:ILE98
|
4.2
|
0.2
|
1.0
|
|
HB2
|
A:ASN101
|
4.2
|
94.5
|
1.0
|
|
CB
|
A:ASP133
|
4.2
|
0.2
|
1.0
|
|
OD2
|
A:ASP97
|
4.3
|
71.3
|
1.0
|
|
CG
|
A:GLU65
|
4.3
|
82.5
|
1.0
|
|
CG1
|
A:ILE98
|
4.3
|
75.0
|
1.0
|
|
HB3
|
A:ARG64
|
4.3
|
73.3
|
1.0
|
|
CA
|
A:CA703
|
4.4
|
78.2
|
1.0
|
|
HG2
|
A:GLU9
|
4.4
|
0.7
|
1.0
|
|
HG2
|
A:GLU65
|
4.4
|
99.0
|
1.0
|
|
CG
|
A:GLU9
|
4.5
|
96.4
|
1.0
|
|
HG3
|
A:GLU65
|
4.5
|
99.0
|
1.0
|
|
N
|
A:ASN99
|
4.5
|
0.2
|
1.0
|
|
HD21
|
A:ASN101
|
4.6
|
0.1
|
1.0
|
|
C
|
A:ASP97
|
4.6
|
84.7
|
1.0
|
|
CA
|
A:ASP133
|
4.6
|
62.2
|
1.0
|
|
CA
|
A:ASP97
|
4.7
|
97.8
|
1.0
|
|
CB
|
A:ASP97
|
4.7
|
0.0
|
1.0
|
|
CB
|
A:ASP100
|
4.7
|
0.3
|
1.0
|
|
CA
|
A:ASN99
|
4.7
|
0.8
|
1.0
|
|
HG3
|
A:GLU9
|
4.8
|
0.7
|
1.0
|
|
H
|
A:ASN101
|
4.8
|
87.6
|
1.0
|
|
NE
|
A:ARG64
|
4.8
|
0.8
|
1.0
|
|
CA
|
A:ASP100
|
4.9
|
0.7
|
1.0
|
|
HD22
|
A:ASN137
|
4.9
|
0.1
|
1.0
|
|
HD3
|
A:ARG64
|
4.9
|
73.3
|
1.0
|
|
HH21
|
A:ARG64
|
4.9
|
1.0
|
1.0
|
|
CB
|
A:ILE98
|
4.9
|
91.8
|
1.0
|
|
H
|
A:GLU65
|
4.9
|
0.9
|
1.0
|
|
N
|
A:ASN101
|
5.0
|
73.0
|
1.0
|
|
C
|
A:ASN99
|
5.0
|
0.3
|
1.0
|
|
Calcium binding site 3 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 3 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca705
b:82.1
occ:1.00
|
OD2
|
A:ASP131
|
2.3
|
80.2
|
1.0
|
|
O
|
A:ASN101
|
2.3
|
84.8
|
1.0
|
|
OD2
|
A:ASP133
|
2.4
|
0.7
|
1.0
|
|
O
|
A:ASN137
|
2.4
|
82.0
|
1.0
|
|
OD2
|
A:ASP188
|
2.4
|
0.2
|
1.0
|
|
OD1
|
A:ASN99
|
2.5
|
0.7
|
1.0
|
|
OD1
|
A:ASP131
|
2.5
|
0.2
|
1.0
|
|
CG
|
A:ASP131
|
2.8
|
98.4
|
1.0
|
|
HB2
|
A:ASP133
|
3.2
|
0.5
|
1.0
|
|
CG
|
A:ASN99
|
3.4
|
0.4
|
1.0
|
|
CG
|
A:ASP133
|
3.4
|
0.2
|
1.0
|
|
CG
|
A:ASP188
|
3.4
|
0.2
|
1.0
|
|
HB3
|
A:ASP188
|
3.5
|
1.0
|
1.0
|
|
HD21
|
A:ASN99
|
3.5
|
0.4
|
1.0
|
|
HB2
|
A:ASP188
|
3.5
|
1.0
|
1.0
|
|
HB3
|
A:ASN137
|
3.6
|
73.5
|
1.0
|
|
C
|
A:ASN101
|
3.6
|
96.8
|
1.0
|
|
C
|
A:ASN137
|
3.7
|
94.0
|
1.0
|
|
CB
|
A:ASP188
|
3.7
|
1.0
|
1.0
|
|
HA
|
A:PRO102
|
3.7
|
0.2
|
1.0
|
|
CB
|
A:ASP133
|
3.8
|
0.2
|
1.0
|
|
HD3
|
A:PRO103
|
3.8
|
0.5
|
1.0
|
|
ND2
|
A:ASN99
|
3.8
|
0.3
|
1.0
|
|
H
|
A:ASN101
|
3.9
|
87.6
|
1.0
|
|
HA
|
A:SER138
|
4.0
|
0.3
|
1.0
|
|
HA
|
A:ASN99
|
4.1
|
0.8
|
1.0
|
|
H
|
A:ASP133
|
4.1
|
72.9
|
1.0
|
|
HD3
|
A:ARG213
|
4.3
|
0.5
|
1.0
|
|
CB
|
A:ASP131
|
4.3
|
1.0
|
1.0
|
|
HB2
|
A:ARG213
|
4.3
|
0.4
|
1.0
|
|
HB3
|
A:ASP133
|
4.3
|
0.5
|
1.0
|
|
HB2
|
A:ASN101
|
4.3
|
94.5
|
1.0
|
|
CA
|
A:PRO102
|
4.4
|
90.2
|
1.0
|
|
HG3
|
A:ARG213
|
4.4
|
0.3
|
1.0
|
|
CB
|
A:ASN137
|
4.4
|
61.3
|
1.0
|
|
N
|
A:PRO102
|
4.4
|
86.1
|
1.0
|
|
CA
|
A:ASN137
|
4.5
|
79.7
|
1.0
|
|
HA
|
A:ASN137
|
4.5
|
95.7
|
1.0
|
|
CA
|
A:ASN101
|
4.5
|
97.4
|
1.0
|
|
OD1
|
A:ASP133
|
4.5
|
88.8
|
1.0
|
|
OD1
|
A:ASP188
|
4.6
|
89.0
|
1.0
|
|
C
|
A:PRO102
|
4.6
|
85.4
|
1.0
|
|
N
|
A:ASN101
|
4.6
|
73.0
|
1.0
|
|
CD
|
A:PRO103
|
4.6
|
88.8
|
1.0
|
|
HD22
|
A:ASN99
|
4.6
|
0.4
|
1.0
|
|
N
|
A:SER138
|
4.6
|
87.1
|
1.0
|
|
HB2
|
A:ASP131
|
4.6
|
0.8
|
1.0
|
|
HB3
|
A:ASP131
|
4.6
|
0.8
|
1.0
|
|
CB
|
A:ASN99
|
4.6
|
0.3
|
1.0
|
|
HB3
|
A:ASN101
|
4.7
|
94.5
|
1.0
|
|
CA
|
A:SER138
|
4.7
|
84.4
|
1.0
|
|
CB
|
A:ASN101
|
4.7
|
78.8
|
1.0
|
|
N
|
A:PRO103
|
4.7
|
92.1
|
1.0
|
|
CA
|
A:ASN99
|
4.8
|
0.8
|
1.0
|
|
HD2
|
A:PRO132
|
4.8
|
67.6
|
1.0
|
|
N
|
A:ASP133
|
4.8
|
60.8
|
1.0
|
|
HB2
|
A:ASN137
|
4.9
|
73.5
|
1.0
|
|
CD
|
A:ARG213
|
4.9
|
0.2
|
1.0
|
|
CA
|
A:ASP133
|
4.9
|
62.2
|
1.0
|
|
CG
|
A:ARG213
|
4.9
|
0.9
|
1.0
|
|
HD2
|
A:PRO103
|
5.0
|
0.5
|
1.0
|
|
HA
|
A:ASP131
|
5.0
|
0.8
|
1.0
|
|
HD2
|
A:ARG213
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 4 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 4 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca706
b:0.3
occ:1.00
|
OE1
|
A:GLU116
|
2.3
|
88.6
|
1.0
|
|
OD1
|
A:ASP173
|
2.3
|
65.0
|
1.0
|
|
OD2
|
A:ASP228
|
2.3
|
40.6
|
1.0
|
|
O
|
A:HOH802
|
2.4
|
35.1
|
1.0
|
|
OE2
|
A:GLU175
|
2.4
|
67.4
|
1.0
|
|
O
|
A:HOH810
|
2.4
|
21.1
|
1.0
|
|
CD
|
A:GLU116
|
3.2
|
62.8
|
1.0
|
|
HA
|
A:ASP173
|
3.3
|
65.6
|
1.0
|
|
CG
|
A:ASP228
|
3.4
|
75.4
|
1.0
|
|
CG
|
A:ASP173
|
3.5
|
59.5
|
1.0
|
|
CD
|
A:GLU175
|
3.6
|
40.2
|
1.0
|
|
OE2
|
A:GLU116
|
3.6
|
51.9
|
1.0
|
|
OD1
|
A:ASP228
|
3.7
|
74.3
|
1.0
|
|
H
|
A:GLU175
|
3.8
|
90.7
|
1.0
|
|
H
|
A:ARG174
|
3.8
|
62.8
|
1.0
|
|
HB2
|
A:GLU175
|
4.0
|
48.6
|
1.0
|
|
CA
|
A:ASP173
|
4.1
|
54.7
|
1.0
|
|
HB2
|
A:GLU116
|
4.2
|
50.9
|
1.0
|
|
CB
|
A:ASP173
|
4.2
|
82.5
|
1.0
|
|
OE1
|
A:GLU175
|
4.2
|
40.0
|
1.0
|
|
HB2
|
A:ASP173
|
4.3
|
99.0
|
1.0
|
|
CG
|
A:GLU116
|
4.3
|
49.3
|
1.0
|
|
HG3
|
A:GLU116
|
4.3
|
59.1
|
1.0
|
|
N
|
A:ARG174
|
4.4
|
52.3
|
1.0
|
|
CA
|
A:CA707
|
4.4
|
48.9
|
1.0
|
|
OD2
|
A:ASP173
|
4.5
|
54.1
|
1.0
|
|
C
|
A:ASP173
|
4.6
|
63.0
|
1.0
|
|
N
|
A:GLU175
|
4.7
|
75.6
|
1.0
|
|
CG
|
A:GLU175
|
4.7
|
40.0
|
1.0
|
|
CB
|
A:ASP228
|
4.7
|
89.6
|
1.0
|
|
CB
|
A:GLU175
|
4.7
|
40.5
|
1.0
|
|
CB
|
A:GLU116
|
4.8
|
42.4
|
1.0
|
|
O
|
A:LEU172
|
4.8
|
43.1
|
1.0
|
|
HB2
|
A:ASP228
|
4.9
|
0.5
|
1.0
|
|
HG2
|
A:GLU175
|
4.9
|
48.0
|
1.0
|
|
HB3
|
A:ASP228
|
5.0
|
0.5
|
1.0
|
|
HB3
|
A:ARG174
|
5.0
|
0.8
|
1.0
|
|
Calcium binding site 5 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 5 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca707
b:48.9
occ:1.00
|
OD1
|
A:ASP228
|
2.3
|
74.3
|
1.0
|
|
OD1
|
A:ASP261
|
2.3
|
39.1
|
1.0
|
|
OD1
|
A:ASP225
|
2.3
|
61.5
|
1.0
|
|
OE1
|
A:GLU175
|
2.4
|
40.0
|
1.0
|
|
OE2
|
A:GLU116
|
2.4
|
51.9
|
1.0
|
|
O
|
A:SER226
|
2.4
|
65.9
|
1.0
|
|
H
|
A:ASP228
|
3.0
|
47.2
|
1.0
|
|
H
|
A:SER226
|
3.0
|
71.6
|
1.0
|
|
CG
|
A:ASP261
|
3.2
|
73.2
|
1.0
|
|
CG
|
A:ASP228
|
3.2
|
75.4
|
1.0
|
|
CD
|
A:GLU175
|
3.3
|
40.2
|
1.0
|
|
HH21
|
A:ARG174
|
3.3
|
81.7
|
1.0
|
|
CG
|
A:ASP225
|
3.4
|
72.4
|
1.0
|
|
OE2
|
A:GLU175
|
3.5
|
67.4
|
1.0
|
|
CD
|
A:GLU116
|
3.5
|
62.8
|
1.0
|
|
C
|
A:SER226
|
3.6
|
76.0
|
1.0
|
|
N
|
A:SER226
|
3.8
|
59.7
|
1.0
|
|
N
|
A:ASP228
|
3.8
|
39.4
|
1.0
|
|
OD2
|
A:ASP261
|
3.8
|
73.4
|
1.0
|
|
OD2
|
A:ASP228
|
3.8
|
40.6
|
1.0
|
|
OD2
|
A:ASP225
|
3.9
|
57.2
|
1.0
|
|
HA
|
A:ASP261
|
3.9
|
80.2
|
1.0
|
|
HE
|
A:ARG174
|
3.9
|
55.3
|
1.0
|
|
OE1
|
A:GLU116
|
4.0
|
88.6
|
1.0
|
|
NH2
|
A:ARG174
|
4.1
|
68.1
|
1.0
|
|
HA
|
A:ASP225
|
4.2
|
71.2
|
1.0
|
|
HB3
|
A:ASP261
|
4.2
|
0.2
|
1.0
|
|
CB
|
A:ASP261
|
4.2
|
88.5
|
1.0
|
|
CB
|
A:ASP228
|
4.3
|
89.6
|
1.0
|
|
H
|
A:ASN229
|
4.3
|
46.5
|
1.0
|
|
HA
|
A:ASN227
|
4.3
|
83.8
|
1.0
|
|
HB3
|
A:ASP228
|
4.3
|
0.5
|
1.0
|
|
CA
|
A:SER226
|
4.3
|
84.9
|
1.0
|
|
CA
|
A:CA706
|
4.4
|
0.3
|
1.0
|
|
CA
|
A:ASP228
|
4.5
|
61.3
|
1.0
|
|
CA
|
A:ASP261
|
4.6
|
66.8
|
1.0
|
|
N
|
A:ASN227
|
4.6
|
63.7
|
1.0
|
|
HH22
|
A:ARG174
|
4.6
|
81.7
|
1.0
|
|
OD1
|
A:ASN229
|
4.6
|
39.1
|
1.0
|
|
NE
|
A:ARG174
|
4.6
|
46.0
|
1.0
|
|
CB
|
A:ASP225
|
4.6
|
78.1
|
1.0
|
|
CG
|
A:GLU175
|
4.6
|
40.0
|
1.0
|
|
N
|
A:ASN229
|
4.7
|
38.7
|
1.0
|
|
HB2
|
A:ASN229
|
4.7
|
85.1
|
1.0
|
|
HB3
|
A:ARG174
|
4.7
|
0.8
|
1.0
|
|
CA
|
A:ASP225
|
4.7
|
59.3
|
1.0
|
|
CG
|
A:GLU116
|
4.8
|
49.3
|
1.0
|
|
CA
|
A:ASN227
|
4.8
|
69.8
|
1.0
|
|
C
|
A:ASP225
|
4.8
|
45.3
|
1.0
|
|
H
|
A:GLU262
|
4.8
|
0.4
|
1.0
|
|
HG2
|
A:GLU116
|
4.8
|
59.1
|
1.0
|
|
C
|
A:ASP228
|
4.8
|
67.2
|
1.0
|
|
C
|
A:ASN227
|
4.8
|
58.0
|
1.0
|
|
OG
|
A:SER226
|
4.8
|
63.1
|
1.0
|
|
HG3
|
A:GLU175
|
4.8
|
48.0
|
1.0
|
|
HG2
|
A:GLU175
|
4.8
|
48.0
|
1.0
|
|
CZ
|
A:ARG174
|
4.9
|
64.8
|
1.0
|
|
Calcium binding site 6 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 6 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca708
b:44.0
occ:1.00
|
OD2
|
A:ASP259
|
2.3
|
74.1
|
1.0
|
|
OD1
|
A:ASN227
|
2.4
|
60.5
|
1.0
|
|
O
|
A:ASN265
|
2.4
|
0.2
|
1.0
|
|
OD2
|
A:ASP261
|
2.4
|
73.4
|
1.0
|
|
O
|
A:ASN229
|
2.4
|
60.9
|
1.0
|
|
OD2
|
A:ASP315
|
2.5
|
46.6
|
1.0
|
|
OD1
|
A:ASP259
|
2.5
|
37.5
|
1.0
|
|
CG
|
A:ASP259
|
2.8
|
37.0
|
1.0
|
|
HB2
|
A:ASP261
|
3.0
|
0.2
|
1.0
|
|
CG
|
A:ASP261
|
3.3
|
73.2
|
1.0
|
|
CG
|
A:ASP315
|
3.4
|
64.3
|
1.0
|
|
CG
|
A:ASN227
|
3.5
|
62.8
|
1.0
|
|
C
|
A:ASN265
|
3.5
|
97.4
|
1.0
|
|
HB2
|
A:ASP315
|
3.6
|
0.5
|
1.0
|
|
C
|
A:ASN229
|
3.6
|
50.5
|
1.0
|
|
HB3
|
A:ASP315
|
3.6
|
0.5
|
1.0
|
|
CB
|
A:ASP261
|
3.6
|
88.5
|
1.0
|
|
H
|
A:ASN229
|
3.7
|
46.5
|
1.0
|
|
HB3
|
A:ASN265
|
3.7
|
77.6
|
1.0
|
|
CB
|
A:ASP315
|
3.8
|
93.8
|
1.0
|
|
HA
|
A:ASN227
|
3.8
|
83.8
|
1.0
|
|
HA2
|
A:GLY266
|
3.8
|
68.2
|
1.0
|
|
HB2
|
A:ASN229
|
3.9
|
85.1
|
1.0
|
|
HD21
|
A:ASN227
|
4.0
|
0.2
|
1.0
|
|
HB3
|
A:ASP261
|
4.0
|
0.2
|
1.0
|
|
HA
|
A:VAL230
|
4.0
|
90.5
|
1.0
|
|
HD3
|
A:PRO231
|
4.1
|
43.1
|
1.0
|
|
ND2
|
A:ASN227
|
4.2
|
97.7
|
1.0
|
|
CB
|
A:ASP259
|
4.3
|
36.6
|
1.0
|
|
HA
|
A:ASN265
|
4.3
|
0.5
|
1.0
|
|
H
|
A:ASP261
|
4.3
|
46.0
|
1.0
|
|
N
|
A:ASN229
|
4.4
|
38.7
|
1.0
|
|
CA
|
A:ASN265
|
4.4
|
87.9
|
1.0
|
|
CA
|
A:ASN229
|
4.4
|
38.3
|
1.0
|
|
N
|
A:GLY266
|
4.4
|
78.0
|
1.0
|
|
OD1
|
A:ASP261
|
4.5
|
39.1
|
1.0
|
|
CB
|
A:ASN265
|
4.5
|
64.7
|
1.0
|
|
CB
|
A:ASN229
|
4.5
|
70.9
|
1.0
|
|
CA
|
A:ASN227
|
4.5
|
69.8
|
1.0
|
|
OD1
|
A:ASP315
|
4.5
|
0.6
|
1.0
|
|
N
|
A:VAL230
|
4.5
|
72.8
|
1.0
|
|
CA
|
A:GLY266
|
4.6
|
56.8
|
1.0
|
|
CB
|
A:ASN227
|
4.6
|
42.0
|
1.0
|
|
HB3
|
A:ASP259
|
4.6
|
43.9
|
1.0
|
|
HB2
|
A:ASP259
|
4.6
|
43.9
|
1.0
|
|
CA
|
A:VAL230
|
4.7
|
75.5
|
1.0
|
|
HB3
|
A:ASN229
|
4.7
|
85.1
|
1.0
|
|
C
|
A:ASN227
|
4.9
|
58.0
|
1.0
|
|
CA
|
A:ASP261
|
4.9
|
66.8
|
1.0
|
|
HD22
|
A:ASN227
|
5.0
|
0.2
|
1.0
|
|
N
|
A:ASP261
|
5.0
|
38.3
|
1.0
|
|
Calcium binding site 7 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 7 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca709
b:51.5
occ:1.00
|
OD2
|
A:ASP336
|
2.3
|
76.0
|
1.0
|
|
OD1
|
A:ASP300
|
2.3
|
93.5
|
1.0
|
|
OE1
|
A:GLU302
|
2.4
|
73.6
|
1.0
|
|
OE1
|
A:GLU244
|
2.4
|
95.0
|
1.0
|
|
O
|
A:HOH804
|
2.5
|
57.7
|
1.0
|
|
HA
|
A:ASP300
|
3.0
|
0.5
|
1.0
|
|
CD
|
A:GLU244
|
3.2
|
87.6
|
1.0
|
|
CG
|
A:ASP336
|
3.2
|
90.3
|
1.0
|
|
H
|
A:TYR301
|
3.4
|
79.5
|
1.0
|
|
OD1
|
A:ASP336
|
3.5
|
93.7
|
1.0
|
|
CG
|
A:ASP300
|
3.5
|
0.2
|
1.0
|
|
OE2
|
A:GLU244
|
3.5
|
68.5
|
1.0
|
|
H
|
A:GLU302
|
3.5
|
0.1
|
1.0
|
|
HD21
|
A:ASN245
|
3.6
|
0.3
|
1.0
|
|
CD
|
A:GLU302
|
3.6
|
34.1
|
1.0
|
|
CA
|
A:ASP300
|
3.8
|
93.8
|
1.0
|
|
OD1
|
A:ASN245
|
3.8
|
68.3
|
1.0
|
|
N
|
A:TYR301
|
3.9
|
66.2
|
1.0
|
|
HB2
|
A:GLU302
|
4.0
|
95.5
|
1.0
|
|
HB2
|
A:GLU244
|
4.0
|
84.5
|
1.0
|
|
CB
|
A:ASP300
|
4.1
|
0.9
|
1.0
|
|
CA
|
A:CA710
|
4.2
|
35.6
|
1.0
|
|
C
|
A:ASP300
|
4.2
|
90.8
|
1.0
|
|
ND2
|
A:ASN245
|
4.2
|
0.6
|
1.0
|
|
HB3
|
A:TYR301
|
4.3
|
82.4
|
1.0
|
|
OE2
|
A:GLU302
|
4.3
|
32.4
|
1.0
|
|
HB2
|
A:ASP300
|
4.4
|
0.3
|
1.0
|
|
N
|
A:GLU302
|
4.4
|
89.2
|
1.0
|
|
CG
|
A:GLU244
|
4.4
|
97.0
|
1.0
|
|
CG
|
A:ASN245
|
4.4
|
93.6
|
1.0
|
|
OD2
|
A:ASP300
|
4.4
|
0.4
|
1.0
|
|
HG3
|
A:GLU244
|
4.5
|
0.5
|
1.0
|
|
O
|
A:LEU299
|
4.6
|
47.9
|
1.0
|
|
CB
|
A:ASP336
|
4.6
|
95.4
|
1.0
|
|
CG
|
A:GLU302
|
4.7
|
84.3
|
1.0
|
|
CB
|
A:GLU244
|
4.7
|
70.5
|
1.0
|
|
CB
|
A:GLU302
|
4.8
|
79.6
|
1.0
|
|
HB2
|
A:ASP336
|
4.8
|
0.4
|
1.0
|
|
CA
|
A:TYR301
|
4.9
|
70.2
|
1.0
|
|
HG2
|
A:GLU302
|
4.9
|
0.2
|
1.0
|
|
HD21
|
A:ASN337
|
4.9
|
0.2
|
1.0
|
|
HB3
|
A:ASP336
|
4.9
|
0.4
|
1.0
|
|
CB
|
A:TYR301
|
4.9
|
68.7
|
1.0
|
|
HD22
|
A:ASN245
|
5.0
|
0.3
|
1.0
|
|
Calcium binding site 8 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 8 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca710
b:35.6
occ:1.00
|
OD1
|
A:ASP336
|
2.3
|
93.7
|
1.0
|
|
OE2
|
A:GLU302
|
2.3
|
32.4
|
1.0
|
|
OD1
|
A:ASP369
|
2.3
|
93.6
|
1.0
|
|
OE2
|
A:GLU244
|
2.4
|
68.5
|
1.0
|
|
OD1
|
A:ASP333
|
2.4
|
97.7
|
1.0
|
|
O
|
A:ALA334
|
2.5
|
64.8
|
1.0
|
|
CD
|
A:GLU302
|
3.1
|
34.1
|
1.0
|
|
OE1
|
A:GLU302
|
3.2
|
73.6
|
1.0
|
|
CD
|
A:GLU244
|
3.2
|
87.6
|
1.0
|
|
H
|
A:ALA334
|
3.2
|
0.2
|
1.0
|
|
H
|
A:ASP336
|
3.3
|
88.3
|
1.0
|
|
CG
|
A:ASP369
|
3.4
|
92.8
|
1.0
|
|
CG
|
A:ASP336
|
3.4
|
90.3
|
1.0
|
|
CG
|
A:ASP333
|
3.5
|
95.4
|
1.0
|
|
OE1
|
A:GLU244
|
3.5
|
95.0
|
1.0
|
|
HB3
|
A:TYR301
|
3.6
|
82.4
|
1.0
|
|
C
|
A:ALA334
|
3.7
|
71.6
|
1.0
|
|
HA
|
A:ASP369
|
3.7
|
99.9
|
1.0
|
|
N
|
A:ALA334
|
3.9
|
83.5
|
1.0
|
|
OD2
|
A:ASP333
|
4.0
|
78.0
|
1.0
|
|
N
|
A:ASP336
|
4.1
|
73.6
|
1.0
|
|
OD2
|
A:ASP336
|
4.1
|
76.0
|
1.0
|
|
OD2
|
A:ASP369
|
4.2
|
0.5
|
1.0
|
|
HA
|
A:ASP333
|
4.2
|
0.5
|
1.0
|
|
CA
|
A:CA709
|
4.2
|
51.5
|
1.0
|
|
HB3
|
A:ASP369
|
4.2
|
70.4
|
1.0
|
|
CB
|
A:ASP369
|
4.3
|
58.7
|
1.0
|
|
HA
|
A:ASN335
|
4.4
|
0.1
|
1.0
|
|
HD22
|
A:ASN373
|
4.4
|
0.9
|
1.0
|
|
CA
|
A:ALA334
|
4.4
|
80.1
|
1.0
|
|
CA
|
A:ASP369
|
4.5
|
83.2
|
1.0
|
|
CB
|
A:ASP336
|
4.5
|
95.4
|
1.0
|
|
CG
|
A:GLU302
|
4.5
|
84.3
|
1.0
|
|
HG2
|
A:GLU244
|
4.5
|
0.5
|
1.0
|
|
CG
|
A:GLU244
|
4.5
|
97.0
|
1.0
|
|
CB
|
A:TYR301
|
4.6
|
68.7
|
1.0
|
|
HB3
|
A:ASP336
|
4.6
|
0.4
|
1.0
|
|
HD1
|
A:TYR301
|
4.6
|
0.3
|
1.0
|
|
CB
|
A:ASP333
|
4.7
|
95.2
|
1.0
|
|
HD22
|
A:ASN337
|
4.7
|
0.2
|
1.0
|
|
C
|
A:ASP333
|
4.7
|
96.6
|
1.0
|
|
CA
|
A:ASP333
|
4.7
|
87.1
|
1.0
|
|
N
|
A:ASN335
|
4.7
|
99.1
|
1.0
|
|
CA
|
A:ASP336
|
4.7
|
79.1
|
1.0
|
|
HG3
|
A:GLU302
|
4.7
|
0.2
|
1.0
|
|
ND2
|
A:ASN337
|
4.8
|
0.5
|
1.0
|
|
HB2
|
A:ASN337
|
4.8
|
82.8
|
1.0
|
|
H
|
A:ASN337
|
4.8
|
80.6
|
1.0
|
|
HB2
|
A:TYR301
|
4.8
|
82.4
|
1.0
|
|
HG2
|
A:GLU302
|
4.8
|
0.2
|
1.0
|
|
H
|
A:SER370
|
4.8
|
0.5
|
1.0
|
|
HB3
|
A:ALA334
|
4.9
|
0.1
|
1.0
|
|
CA
|
A:ASN335
|
4.9
|
91.8
|
1.0
|
|
HD21
|
A:ASN337
|
4.9
|
0.2
|
1.0
|
|
H
|
A:GLU302
|
4.9
|
0.1
|
1.0
|
|
C
|
A:ASN335
|
5.0
|
80.1
|
1.0
|
|
HG3
|
A:GLU244
|
5.0
|
0.5
|
1.0
|
|
C
|
A:ASP336
|
5.0
|
63.0
|
1.0
|
|
Calcium binding site 9 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 9 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca711
b:86.7
occ:1.00
|
O
|
A:ASN337
|
2.4
|
0.3
|
1.0
|
|
O
|
A:ASN373
|
2.4
|
96.2
|
1.0
|
|
OD2
|
A:ASP367
|
2.4
|
84.6
|
1.0
|
|
OD2
|
A:ASP369
|
2.4
|
0.5
|
1.0
|
|
OD2
|
A:ASP420
|
2.4
|
0.9
|
1.0
|
|
OD1
|
A:ASN335
|
2.4
|
94.2
|
1.0
|
|
OD1
|
A:ASP367
|
2.5
|
40.9
|
1.0
|
|
CG
|
A:ASP367
|
2.8
|
52.3
|
1.0
|
|
HB2
|
A:ASP369
|
3.0
|
70.4
|
1.0
|
|
HD12
|
A:LEU426
|
3.2
|
0.3
|
1.0
|
|
CG
|
A:ASP369
|
3.4
|
92.8
|
1.0
|
|
CG
|
A:ASP420
|
3.5
|
0.6
|
1.0
|
|
H
|
A:ASN337
|
3.5
|
80.6
|
1.0
|
|
C
|
A:ASN373
|
3.5
|
89.6
|
1.0
|
|
C
|
A:ASN337
|
3.6
|
0.3
|
1.0
|
|
HB3
|
A:ASN373
|
3.6
|
0.7
|
1.0
|
|
CB
|
A:ASP369
|
3.6
|
58.7
|
1.0
|
|
CG
|
A:ASN335
|
3.6
|
0.6
|
1.0
|
|
HB2
|
A:ASP420
|
3.8
|
0.2
|
1.0
|
|
HB3
|
A:ASP420
|
3.8
|
0.2
|
1.0
|
|
HA2
|
A:GLY374
|
3.9
|
97.0
|
1.0
|
|
HB2
|
A:ASN337
|
3.9
|
82.8
|
1.0
|
|
CB
|
A:ASP420
|
3.9
|
94.4
|
1.0
|
|
HB3
|
A:ASP369
|
4.0
|
70.4
|
1.0
|
|
HD21
|
A:ASN335
|
4.0
|
0.7
|
1.0
|
|
HA
|
A:ASN335
|
4.1
|
0.1
|
1.0
|
|
HD3
|
A:PRO339
|
4.1
|
36.2
|
1.0
|
|
HA
|
A:ALA338
|
4.1
|
70.8
|
1.0
|
|
CD1
|
A:LEU426
|
4.1
|
0.6
|
1.0
|
|
HB2
|
A:LEU426
|
4.2
|
74.2
|
1.0
|
|
N
|
A:ASN337
|
4.2
|
67.2
|
1.0
|
|
H
|
A:ASP369
|
4.2
|
0.1
|
1.0
|
|
HA
|
A:ASN373
|
4.2
|
0.5
|
1.0
|
|
CB
|
A:ASP367
|
4.3
|
89.8
|
1.0
|
|
CA
|
A:ASN373
|
4.3
|
0.1
|
1.0
|
|
ND2
|
A:ASN335
|
4.3
|
0.9
|
1.0
|
|
CB
|
A:ASN373
|
4.3
|
0.1
|
1.0
|
|
CA
|
A:ASN337
|
4.3
|
79.8
|
1.0
|
|
HD11
|
A:LEU426
|
4.5
|
0.3
|
1.0
|
|
N
|
A:GLY374
|
4.5
|
80.7
|
1.0
|
|
CB
|
A:ASN337
|
4.5
|
69.0
|
1.0
|
|
HB3
|
A:ASP367
|
4.5
|
0.7
|
1.0
|
|
OD1
|
A:ASP369
|
4.5
|
93.6
|
1.0
|
|
OD1
|
A:ASP420
|
4.5
|
0.1
|
1.0
|
|
HB2
|
A:ASN373
|
4.5
|
0.7
|
1.0
|
|
N
|
A:ALA338
|
4.6
|
88.8
|
1.0
|
|
HG
|
A:LEU426
|
4.6
|
86.2
|
1.0
|
|
CA
|
A:GLY374
|
4.7
|
80.9
|
1.0
|
|
HB3
|
A:ASN337
|
4.7
|
82.8
|
1.0
|
|
HB2
|
A:ASP367
|
4.7
|
0.7
|
1.0
|
|
HD13
|
A:LEU426
|
4.7
|
0.3
|
1.0
|
|
CA
|
A:ALA338
|
4.8
|
59.0
|
1.0
|
|
CA
|
A:ASN335
|
4.8
|
91.8
|
1.0
|
|
CB
|
A:ASN335
|
4.8
|
78.2
|
1.0
|
|
H
|
A:ASP336
|
4.8
|
88.3
|
1.0
|
|
CG
|
A:LEU426
|
4.8
|
71.8
|
1.0
|
|
CA
|
A:ASP369
|
4.9
|
83.2
|
1.0
|
|
N
|
A:ASP369
|
4.9
|
0.6
|
1.0
|
|
CB
|
A:LEU426
|
5.0
|
61.9
|
1.0
|
|
CD
|
A:PRO339
|
5.0
|
30.2
|
1.0
|
|
Calcium binding site 10 out
of 15 in 6vg4
Go back to
Calcium Binding Sites List in 6vg4
Calcium binding site 10 out
of 15 in the Human Protocadherin 10 Ectodomain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Human Protocadherin 10 Ectodomain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca712
b:52.5
occ:1.00
|
OD2
|
A:ASP441
|
2.3
|
97.6
|
1.0
|
|
OD1
|
A:ASP405
|
2.3
|
93.2
|
1.0
|
|
OE1
|
A:GLU407
|
2.3
|
73.7
|
1.0
|
|
OE1
|
A:GLU352
|
2.4
|
35.5
|
1.0
|
|
CG
|
A:ASP441
|
2.9
|
0.6
|
1.0
|
|
OD1
|
A:ASP441
|
3.0
|
91.0
|
1.0
|
|
HD21
|
A:ASN442
|
3.3
|
0.2
|
1.0
|
|
CD
|
A:GLU407
|
3.4
|
72.7
|
1.0
|
|
CD
|
A:GLU352
|
3.5
|
97.8
|
1.0
|
|
CG
|
A:ASP405
|
3.5
|
68.2
|
1.0
|
|
HB2
|
A:GLU407
|
3.6
|
0.4
|
1.0
|
|
H
|
A:GLU407
|
3.6
|
0.9
|
1.0
|
|
HD22
|
A:ASN442
|
3.7
|
0.2
|
1.0
|
|
OE2
|
A:GLU352
|
3.8
|
84.4
|
1.0
|
|
ND2
|
A:ASN442
|
3.8
|
0.6
|
1.0
|
|
CA
|
A:CA713
|
3.8
|
65.3
|
1.0
|
|
HA
|
A:ASP405
|
3.8
|
0.4
|
1.0
|
|
HG2
|
A:GLU407
|
4.1
|
0.6
|
1.0
|
|
H
|
A:ARG406
|
4.1
|
78.4
|
1.0
|
|
CG
|
A:GLU407
|
4.1
|
95.5
|
1.0
|
|
OD2
|
A:ASP405
|
4.3
|
94.5
|
1.0
|
|
OE2
|
A:GLU407
|
4.3
|
54.0
|
1.0
|
|
CB
|
A:GLU407
|
4.3
|
1.0
|
1.0
|
|
CB
|
A:ASP441
|
4.4
|
0.6
|
1.0
|
|
N
|
A:GLU407
|
4.4
|
1.0
|
1.0
|
|
HB2
|
A:ASP441
|
4.5
|
0.9
|
1.0
|
|
CA
|
A:ASP405
|
4.5
|
86.2
|
1.0
|
|
CB
|
A:ASP405
|
4.5
|
55.2
|
1.0
|
|
N
|
A:ARG406
|
4.5
|
65.3
|
1.0
|
|
HB2
|
A:GLU352
|
4.5
|
73.9
|
1.0
|
|
HB2
|
A:ASP405
|
4.7
|
66.3
|
1.0
|
|
HB3
|
A:ARG406
|
4.8
|
99.6
|
1.0
|
|
C
|
A:ASP405
|
4.8
|
68.9
|
1.0
|
|
CG
|
A:GLU352
|
4.8
|
93.8
|
1.0
|
|
HB3
|
A:ASP441
|
4.9
|
0.9
|
1.0
|
|
O
|
A:ASP441
|
4.9
|
68.1
|
1.0
|
|
Reference:
O.J.Harrison,
J.Brasch,
P.S.Katsamba,
G.Ahlsen,
A.J.Noble,
H.Dan,
R.V.Sampogna,
C.S.Potter,
B.Carragher,
B.Honig,
L.Shapiro.
Family-Wide Structural and Biophysical Analysis of Binding Interactions Among Non-Clustered Delta-Protocadherins. Cell Rep V. 30 2655 2020.
ISSN: ESSN 2211-1247
PubMed: 32101743
DOI: 10.1016/J.CELREP.2020.02.003
Page generated: Sat Dec 12 07:50:15 2020
|
