Calcium in PDB 5dzx: Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
Protein crystallography data
The structure of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4, PDB code: 5dzx
was solved by
K.M.Goodman,
S.Mannepalli,
F.Bahna,
B.Honig,
L.Shapiro,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.97 /
2.88
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.040,
90.530,
258.130,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
24.2 /
28.9
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Calcium atom in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
(pdb code 5dzx). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the
Protocadherin Beta 6 Extracellular Cadherin Domains 1-4, PDB code: 5dzx:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 18 in 5dzx
Go back to
Calcium Binding Sites List in 5dzx
Calcium binding site 1 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca512
b:63.4
occ:1.00
|
OE2
|
A:GLU9
|
2.2
|
50.4
|
1.0
|
|
OD2
|
A:ASP100
|
2.3
|
46.2
|
1.0
|
|
OD1
|
A:ASP63
|
2.5
|
60.3
|
1.0
|
|
OE2
|
A:GLU10
|
2.6
|
67.9
|
1.0
|
|
OE1
|
A:GLU65
|
2.7
|
52.9
|
1.0
|
|
CG
|
A:ASP100
|
3.3
|
54.0
|
1.0
|
|
CD
|
A:GLU9
|
3.4
|
50.4
|
1.0
|
|
CE1
|
A:HIS101
|
3.5
|
55.1
|
1.0
|
|
CD
|
A:GLU10
|
3.5
|
74.7
|
1.0
|
|
CG
|
A:ASP63
|
3.6
|
63.6
|
1.0
|
|
CG
|
A:GLU10
|
3.7
|
64.9
|
1.0
|
|
OD1
|
A:ASP100
|
3.7
|
59.1
|
1.0
|
|
CD
|
A:GLU65
|
3.8
|
51.5
|
1.0
|
|
OE1
|
A:GLU9
|
4.1
|
50.3
|
1.0
|
|
OD2
|
A:ASP63
|
4.2
|
65.8
|
1.0
|
|
ND1
|
A:HIS101
|
4.3
|
48.8
|
1.0
|
|
OE2
|
A:GLU65
|
4.4
|
48.5
|
1.0
|
|
CA
|
A:CA513
|
4.4
|
39.8
|
1.0
|
|
CG
|
A:GLU9
|
4.4
|
56.6
|
1.0
|
|
NE2
|
A:HIS101
|
4.5
|
51.0
|
1.0
|
|
CB
|
A:ASP100
|
4.6
|
65.9
|
1.0
|
|
CB
|
A:ASP63
|
4.7
|
66.2
|
1.0
|
|
OE1
|
A:GLU10
|
4.7
|
82.8
|
1.0
|
|
CA
|
A:ASP63
|
4.8
|
59.1
|
1.0
|
|
CG
|
A:GLU65
|
4.9
|
57.8
|
1.0
|
|
N
|
A:ARG64
|
5.0
|
48.6
|
1.0
|
|
Calcium binding site 2 out
of 18 in 5dzx
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Calcium Binding Sites List in 5dzx
Calcium binding site 2 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca513
b:39.8
occ:1.00
|
OE2
|
A:GLU65
|
2.2
|
48.5
|
1.0
|
|
OE1
|
A:GLU9
|
2.4
|
50.3
|
1.0
|
|
OD1
|
A:ASP97
|
2.4
|
39.4
|
1.0
|
|
OD1
|
A:ASP100
|
2.4
|
59.1
|
1.0
|
|
OD1
|
A:ASP133
|
2.5
|
50.6
|
1.0
|
|
O
|
A:ILE98
|
2.5
|
60.4
|
1.0
|
|
CD
|
A:GLU65
|
3.2
|
51.5
|
1.0
|
|
CD
|
A:GLU9
|
3.4
|
50.4
|
1.0
|
|
CG
|
A:ASP100
|
3.4
|
54.0
|
1.0
|
|
OE1
|
A:GLU65
|
3.5
|
52.9
|
1.0
|
|
CG
|
A:ASP133
|
3.5
|
55.0
|
1.0
|
|
OE2
|
A:GLU9
|
3.6
|
50.4
|
1.0
|
|
CG
|
A:ASP97
|
3.6
|
44.7
|
1.0
|
|
C
|
A:ILE98
|
3.6
|
62.0
|
1.0
|
|
N
|
A:ILE98
|
3.9
|
56.4
|
1.0
|
|
OD2
|
A:ASP100
|
3.9
|
46.2
|
1.0
|
|
OD2
|
A:ASP97
|
4.2
|
60.0
|
1.0
|
|
N
|
A:ASP100
|
4.2
|
51.1
|
1.0
|
|
OD2
|
A:ASP133
|
4.3
|
62.0
|
1.0
|
|
CA
|
A:ILE98
|
4.4
|
58.2
|
1.0
|
|
ND1
|
A:HIS101
|
4.4
|
48.8
|
1.0
|
|
CA
|
A:CA512
|
4.4
|
63.4
|
1.0
|
|
CB
|
A:ASP133
|
4.4
|
47.3
|
1.0
|
|
CG
|
A:GLU65
|
4.5
|
57.8
|
1.0
|
|
CG1
|
A:ILE98
|
4.5
|
57.9
|
1.0
|
|
CD1
|
A:ILE98
|
4.6
|
55.2
|
1.0
|
|
CB
|
A:ASP100
|
4.6
|
65.9
|
1.0
|
|
N
|
A:ASN99
|
4.7
|
69.0
|
1.0
|
|
CA
|
A:ASP133
|
4.7
|
40.4
|
1.0
|
|
C
|
A:ASP97
|
4.7
|
55.4
|
1.0
|
|
CG
|
A:GLU9
|
4.7
|
56.6
|
1.0
|
|
CB
|
A:ASP97
|
4.8
|
55.8
|
1.0
|
|
CA
|
A:ASP97
|
4.8
|
51.5
|
1.0
|
|
CE1
|
A:HIS101
|
4.8
|
55.1
|
1.0
|
|
NH1
|
A:ARG64
|
4.8
|
53.8
|
1.0
|
|
CA
|
A:ASN99
|
4.8
|
49.6
|
1.0
|
|
CA
|
A:ASP100
|
4.9
|
49.8
|
1.0
|
|
CB
|
A:ARG64
|
5.0
|
50.3
|
1.0
|
|
Calcium binding site 3 out
of 18 in 5dzx
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Calcium Binding Sites List in 5dzx
Calcium binding site 3 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca514
b:36.9
occ:1.00
|
O
|
A:HIS101
|
2.3
|
38.4
|
1.0
|
|
OD1
|
A:ASN99
|
2.4
|
63.4
|
1.0
|
|
O
|
A:ASN137
|
2.5
|
47.4
|
1.0
|
|
OD2
|
A:ASP133
|
2.6
|
62.0
|
1.0
|
|
OD2
|
A:ASP188
|
2.6
|
50.7
|
1.0
|
|
OD2
|
A:ASP131
|
2.7
|
60.7
|
1.0
|
|
OD1
|
A:ASP131
|
3.0
|
56.2
|
1.0
|
|
CG
|
A:ASP131
|
3.2
|
54.2
|
1.0
|
|
C
|
A:HIS101
|
3.4
|
42.6
|
1.0
|
|
CG
|
A:ASP133
|
3.5
|
55.0
|
1.0
|
|
CG
|
A:ASN99
|
3.6
|
65.4
|
1.0
|
|
CG
|
A:ASP188
|
3.6
|
54.9
|
1.0
|
|
CB
|
A:ASP133
|
3.7
|
47.3
|
1.0
|
|
C
|
A:ASN137
|
3.7
|
45.6
|
1.0
|
|
OD1
|
A:ASP188
|
4.0
|
64.8
|
1.0
|
|
CA
|
A:HIS101
|
4.1
|
51.7
|
1.0
|
|
N
|
A:HIS101
|
4.1
|
58.8
|
1.0
|
|
ND2
|
A:ASN99
|
4.2
|
64.3
|
1.0
|
|
CB
|
A:HIS101
|
4.2
|
50.0
|
1.0
|
|
N
|
A:SER102
|
4.5
|
46.8
|
1.0
|
|
CA
|
A:ALA138
|
4.6
|
49.1
|
1.0
|
|
CD
|
A:PRO103
|
4.6
|
59.4
|
1.0
|
|
N
|
A:ALA138
|
4.6
|
47.8
|
1.0
|
|
OD1
|
A:ASP133
|
4.6
|
50.6
|
1.0
|
|
CA
|
A:ASN137
|
4.7
|
49.8
|
1.0
|
|
CA
|
A:SER102
|
4.7
|
53.9
|
1.0
|
|
CB
|
A:ASP131
|
4.7
|
54.6
|
1.0
|
|
CB
|
A:ASN99
|
4.7
|
52.6
|
1.0
|
|
CB
|
A:ASN137
|
4.7
|
55.9
|
1.0
|
|
CB
|
A:ASP188
|
4.8
|
61.0
|
1.0
|
|
CA
|
A:ASN99
|
4.8
|
49.6
|
1.0
|
|
CA
|
A:ASP133
|
4.9
|
40.4
|
1.0
|
|
N
|
A:ASP133
|
4.9
|
42.6
|
1.0
|
|
N
|
A:PRO103
|
4.9
|
51.5
|
1.0
|
|
C
|
A:SER102
|
4.9
|
53.1
|
1.0
|
|
C
|
A:ALA138
|
5.0
|
57.0
|
1.0
|
|
Calcium binding site 4 out
of 18 in 5dzx
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Calcium Binding Sites List in 5dzx
Calcium binding site 4 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca515
b:47.8
occ:1.00
|
OE2
|
A:GLU116
|
2.2
|
59.4
|
1.0
|
|
OD2
|
A:ASP209
|
2.3
|
56.2
|
1.0
|
|
OE1
|
A:GLU175
|
2.4
|
57.2
|
1.0
|
|
OD1
|
A:ASP173
|
2.5
|
71.9
|
1.0
|
|
CD
|
A:GLU175
|
3.2
|
50.7
|
1.0
|
|
CG
|
A:ASP209
|
3.3
|
59.1
|
1.0
|
|
CG
|
A:ASP173
|
3.3
|
69.7
|
1.0
|
|
CD
|
A:GLU116
|
3.4
|
63.6
|
1.0
|
|
OD2
|
A:ASP173
|
3.5
|
77.5
|
1.0
|
|
ND2
|
A:ASN210
|
3.7
|
71.2
|
1.0
|
|
OD1
|
A:ASP209
|
3.7
|
57.7
|
1.0
|
|
OE2
|
A:GLU175
|
3.8
|
46.4
|
1.0
|
|
CG
|
A:GLU175
|
4.0
|
59.5
|
1.0
|
|
OE1
|
A:GLU116
|
4.0
|
61.7
|
1.0
|
|
OD1
|
A:ASN210
|
4.1
|
67.5
|
1.0
|
|
CG
|
A:ASN210
|
4.2
|
64.3
|
1.0
|
|
CA
|
A:CA516
|
4.4
|
39.8
|
1.0
|
|
CB
|
A:GLU175
|
4.4
|
70.3
|
1.0
|
|
CG
|
A:GLU116
|
4.5
|
61.5
|
1.0
|
|
CB
|
A:ASP209
|
4.5
|
63.5
|
1.0
|
|
CB
|
A:ASP173
|
4.7
|
68.0
|
1.0
|
|
N
|
A:GLU175
|
4.9
|
59.1
|
1.0
|
|
N
|
A:ARG174
|
5.0
|
50.4
|
1.0
|
|
CA
|
A:ASP173
|
5.0
|
60.4
|
1.0
|
|
Calcium binding site 5 out
of 18 in 5dzx
Go back to
Calcium Binding Sites List in 5dzx
Calcium binding site 5 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca516
b:39.8
occ:1.00
|
OE2
|
A:GLU175
|
2.4
|
46.4
|
1.0
|
|
OD1
|
A:ASP206
|
2.4
|
54.5
|
1.0
|
|
OE1
|
A:GLU116
|
2.5
|
61.7
|
1.0
|
|
OD1
|
A:ASP242
|
2.6
|
56.5
|
1.0
|
|
O
|
A:ILE207
|
2.8
|
50.6
|
1.0
|
|
OD1
|
A:ASP209
|
2.8
|
57.7
|
1.0
|
|
CD
|
A:GLU175
|
3.3
|
50.7
|
1.0
|
|
CD
|
A:GLU116
|
3.5
|
63.6
|
1.0
|
|
CG
|
A:ASP242
|
3.5
|
53.2
|
1.0
|
|
OE1
|
A:GLU175
|
3.6
|
57.2
|
1.0
|
|
CG
|
A:ASP206
|
3.7
|
58.7
|
1.0
|
|
OE2
|
A:GLU116
|
3.7
|
59.4
|
1.0
|
|
N
|
A:ILE207
|
3.8
|
54.4
|
1.0
|
|
CG
|
A:ASP209
|
3.8
|
59.1
|
1.0
|
|
C
|
A:ILE207
|
3.9
|
57.1
|
1.0
|
|
OD2
|
A:ASP209
|
4.1
|
56.2
|
1.0
|
|
NH1
|
A:ARG174
|
4.1
|
64.4
|
1.0
|
|
CB
|
A:ASP242
|
4.2
|
53.7
|
1.0
|
|
CA
|
A:CA515
|
4.4
|
47.8
|
1.0
|
|
CA
|
A:ASP242
|
4.4
|
54.7
|
1.0
|
|
OD2
|
A:ASP242
|
4.4
|
56.0
|
1.0
|
|
OD2
|
A:ASP206
|
4.4
|
55.2
|
1.0
|
|
CA
|
A:ILE207
|
4.5
|
59.3
|
1.0
|
|
CA
|
A:ASP206
|
4.5
|
62.3
|
1.0
|
|
C
|
A:ASP206
|
4.6
|
58.5
|
1.0
|
|
CB
|
A:ASP206
|
4.6
|
73.2
|
1.0
|
|
CG1
|
A:ILE207
|
4.6
|
52.9
|
1.0
|
|
ND2
|
A:ASN210
|
4.6
|
71.2
|
1.0
|
|
CG
|
A:GLU175
|
4.7
|
59.5
|
1.0
|
|
CB
|
A:ARG174
|
4.7
|
44.0
|
1.0
|
|
N
|
A:ASP209
|
4.7
|
63.9
|
1.0
|
|
CD
|
A:ARG174
|
4.8
|
56.9
|
1.0
|
|
CG
|
A:GLU116
|
4.9
|
61.5
|
1.0
|
|
N
|
A:ASN208
|
5.0
|
63.7
|
1.0
|
|
Calcium binding site 6 out
of 18 in 5dzx
Go back to
Calcium Binding Sites List in 5dzx
Calcium binding site 6 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca517
b:52.1
occ:1.00
|
OD2
|
A:ASP240
|
2.3
|
58.2
|
1.0
|
|
O
|
A:ASN210
|
2.4
|
52.7
|
1.0
|
|
OD2
|
A:ASP294
|
2.5
|
74.6
|
1.0
|
|
O
|
A:HIS246
|
2.7
|
46.9
|
1.0
|
|
OD1
|
A:ASP240
|
2.8
|
51.1
|
1.0
|
|
CG
|
A:ASP240
|
2.9
|
54.4
|
1.0
|
|
OD2
|
A:ASP242
|
2.9
|
56.0
|
1.0
|
|
OD1
|
A:ASN208
|
2.9
|
55.5
|
1.0
|
|
CG
|
A:ASP294
|
3.2
|
55.7
|
1.0
|
|
C
|
A:ASN210
|
3.6
|
56.4
|
1.0
|
|
CG
|
A:ASP242
|
3.8
|
53.2
|
1.0
|
|
OD1
|
A:ASP294
|
3.9
|
67.0
|
1.0
|
|
C
|
A:HIS246
|
3.9
|
54.1
|
1.0
|
|
CB
|
A:ASP294
|
4.0
|
46.5
|
1.0
|
|
CG
|
A:ASN208
|
4.1
|
49.4
|
1.0
|
|
CB
|
A:ASP242
|
4.1
|
53.7
|
1.0
|
|
CD
|
A:PRO212
|
4.2
|
43.8
|
1.0
|
|
CD1
|
A:LEU298
|
4.3
|
35.0
|
1.0
|
|
CB
|
A:ASP240
|
4.4
|
57.1
|
1.0
|
|
CA
|
A:ALA211
|
4.5
|
50.4
|
1.0
|
|
N
|
A:PRO212
|
4.5
|
44.1
|
1.0
|
|
N
|
A:ALA211
|
4.5
|
57.7
|
1.0
|
|
CA
|
A:ASN210
|
4.6
|
67.7
|
1.0
|
|
ND2
|
A:ASN208
|
4.6
|
65.5
|
1.0
|
|
C
|
A:ALA211
|
4.6
|
46.7
|
1.0
|
|
N
|
A:ASN210
|
4.6
|
61.6
|
1.0
|
|
CA
|
A:HIS246
|
4.7
|
59.4
|
1.0
|
|
CB
|
A:LEU298
|
4.8
|
60.9
|
1.0
|
|
CB
|
A:HIS246
|
4.9
|
65.0
|
1.0
|
|
CB
|
A:ASN210
|
4.9
|
63.6
|
1.0
|
|
OD1
|
A:ASP242
|
4.9
|
56.5
|
1.0
|
|
N
|
A:GLY247
|
4.9
|
57.7
|
1.0
|
|
CG
|
A:LEU298
|
5.0
|
34.6
|
1.0
|
|
N
|
A:ASP242
|
5.0
|
59.2
|
1.0
|
|
Calcium binding site 7 out
of 18 in 5dzx
Go back to
Calcium Binding Sites List in 5dzx
Calcium binding site 7 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca518
b:62.1
occ:1.00
|
OD2
|
A:ASP313
|
2.4
|
47.7
|
1.0
|
|
OE1
|
A:GLU281
|
2.5
|
53.5
|
1.0
|
|
OD1
|
A:ASP279
|
2.5
|
66.1
|
1.0
|
|
OE1
|
A:GLU225
|
3.0
|
70.4
|
1.0
|
|
OE2
|
A:GLU225
|
3.0
|
40.0
|
1.0
|
|
CD
|
A:GLU225
|
3.2
|
50.5
|
1.0
|
|
CG
|
A:ASP313
|
3.3
|
46.0
|
1.0
|
|
CG
|
A:ASP279
|
3.4
|
64.7
|
1.0
|
|
OD1
|
A:ASP313
|
3.4
|
51.1
|
1.0
|
|
CD
|
A:GLU281
|
3.4
|
45.7
|
1.0
|
|
OD1
|
A:ASN314
|
3.7
|
64.2
|
1.0
|
|
CA
|
A:CA519
|
3.8
|
27.6
|
1.0
|
|
OD2
|
A:ASP279
|
3.8
|
64.7
|
1.0
|
|
OE2
|
A:GLU281
|
3.9
|
42.5
|
1.0
|
|
CB
|
A:ASP279
|
4.4
|
57.2
|
1.0
|
|
CG
|
A:GLU225
|
4.5
|
62.5
|
1.0
|
|
CA
|
A:ASP279
|
4.6
|
68.6
|
1.0
|
|
CG
|
A:ASN314
|
4.6
|
54.1
|
1.0
|
|
CG
|
A:GLU281
|
4.6
|
49.3
|
1.0
|
|
N
|
A:PHE280
|
4.6
|
59.1
|
1.0
|
|
CB
|
A:ASP313
|
4.7
|
49.2
|
1.0
|
|
ND2
|
A:ASN314
|
4.7
|
47.3
|
1.0
|
|
N
|
A:GLU281
|
4.9
|
46.7
|
1.0
|
|
CB
|
A:GLU281
|
5.0
|
65.8
|
1.0
|
|
Calcium binding site 8 out
of 18 in 5dzx
Go back to
Calcium Binding Sites List in 5dzx
Calcium binding site 8 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca519
b:27.6
occ:1.00
|
O
|
A:VAL311
|
2.4
|
49.3
|
1.0
|
|
OE2
|
A:GLU281
|
2.5
|
42.5
|
1.0
|
|
OE1
|
A:GLU225
|
2.5
|
70.4
|
1.0
|
|
OD1
|
A:ASP313
|
2.6
|
51.1
|
1.0
|
|
OD1
|
A:ASP345
|
2.8
|
46.6
|
1.0
|
|
OD1
|
A:ASP310
|
2.8
|
47.1
|
1.0
|
|
CD
|
A:GLU281
|
3.4
|
45.7
|
1.0
|
|
C
|
A:VAL311
|
3.4
|
56.1
|
1.0
|
|
CD
|
A:GLU225
|
3.5
|
50.5
|
1.0
|
|
CG
|
A:ASP313
|
3.5
|
46.0
|
1.0
|
|
OE1
|
A:GLU281
|
3.5
|
53.5
|
1.0
|
|
CG
|
A:ASP310
|
3.6
|
48.5
|
1.0
|
|
N
|
A:VAL311
|
3.7
|
40.2
|
1.0
|
|
CG
|
A:ASP345
|
3.8
|
53.5
|
1.0
|
|
CA
|
A:CA518
|
3.8
|
62.1
|
1.0
|
|
OE2
|
A:GLU225
|
3.8
|
40.0
|
1.0
|
|
OD2
|
A:ASP310
|
4.0
|
46.4
|
1.0
|
|
OD2
|
A:ASP313
|
4.0
|
47.7
|
1.0
|
|
N
|
A:ASP313
|
4.1
|
57.5
|
1.0
|
|
CA
|
A:VAL311
|
4.2
|
51.1
|
1.0
|
|
OD1
|
A:ASN314
|
4.3
|
64.2
|
1.0
|
|
C
|
A:ASP310
|
4.4
|
44.7
|
1.0
|
|
CB
|
A:ASP345
|
4.4
|
54.9
|
1.0
|
|
N
|
A:ASN312
|
4.4
|
57.6
|
1.0
|
|
CA
|
A:ASP310
|
4.5
|
46.9
|
1.0
|
|
CB
|
A:ASP313
|
4.6
|
49.2
|
1.0
|
|
CB
|
A:ASP310
|
4.6
|
54.2
|
1.0
|
|
CB
|
A:PHE280
|
4.6
|
44.1
|
1.0
|
|
CA
|
A:ASN312
|
4.6
|
59.5
|
1.0
|
|
OD2
|
A:ASP345
|
4.6
|
59.3
|
1.0
|
|
CA
|
A:ASP345
|
4.6
|
53.8
|
1.0
|
|
CG
|
A:GLU225
|
4.7
|
62.5
|
1.0
|
|
CG
|
A:GLU281
|
4.8
|
49.3
|
1.0
|
|
CA
|
A:ASP313
|
4.9
|
54.1
|
1.0
|
|
C
|
A:ASN312
|
4.9
|
60.6
|
1.0
|
|
CB
|
A:VAL311
|
4.9
|
48.7
|
1.0
|
|
Calcium binding site 9 out
of 18 in 5dzx
Go back to
Calcium Binding Sites List in 5dzx
Calcium binding site 9 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca520
b:41.8
occ:1.00
|
OD2
|
A:ASP345
|
2.3
|
59.3
|
1.0
|
|
OD1
|
A:ASN312
|
2.3
|
55.7
|
1.0
|
|
O
|
A:ASN349
|
2.4
|
48.5
|
1.0
|
|
O
|
A:ASN314
|
2.5
|
39.0
|
1.0
|
|
OD2
|
A:ASP343
|
2.6
|
36.4
|
1.0
|
|
OD1
|
A:ASP343
|
2.7
|
54.8
|
1.0
|
|
OD2
|
A:ASP396
|
2.8
|
58.7
|
1.0
|
|
CG
|
A:ASP343
|
3.0
|
48.0
|
1.0
|
|
CG
|
A:ASP345
|
3.3
|
53.5
|
1.0
|
|
CG
|
A:ASN312
|
3.5
|
60.6
|
1.0
|
|
C
|
A:ASN349
|
3.5
|
51.5
|
1.0
|
|
CB
|
A:ASP345
|
3.6
|
54.9
|
1.0
|
|
C
|
A:ASN314
|
3.7
|
46.6
|
1.0
|
|
CG
|
A:ASP396
|
3.8
|
62.0
|
1.0
|
|
ND2
|
A:ASN312
|
4.0
|
62.6
|
1.0
|
|
CB
|
A:ASP396
|
4.1
|
57.4
|
1.0
|
|
CD
|
A:PRO316
|
4.3
|
57.6
|
1.0
|
|
CA
|
A:ASN349
|
4.3
|
50.8
|
1.0
|
|
CB
|
A:ASN349
|
4.4
|
52.1
|
1.0
|
|
OD1
|
A:ASP345
|
4.5
|
46.6
|
1.0
|
|
N
|
A:GLY350
|
4.5
|
54.3
|
1.0
|
|
CD1
|
A:LEU402
|
4.5
|
50.6
|
1.0
|
|
CB
|
A:ASP343
|
4.5
|
46.3
|
1.0
|
|
CA
|
A:ASN314
|
4.6
|
59.2
|
1.0
|
|
N
|
A:ALA315
|
4.6
|
56.8
|
1.0
|
|
N
|
A:ASN314
|
4.6
|
55.4
|
1.0
|
|
CA
|
A:GLY350
|
4.6
|
50.6
|
1.0
|
|
CA
|
A:ALA315
|
4.7
|
58.0
|
1.0
|
|
CB
|
A:ASN312
|
4.7
|
56.4
|
1.0
|
|
CB
|
A:ASN314
|
4.8
|
53.0
|
1.0
|
|
N
|
A:PRO316
|
4.8
|
54.5
|
1.0
|
|
CA
|
A:ASP345
|
4.8
|
53.8
|
1.0
|
|
C
|
A:ALA315
|
4.9
|
53.1
|
1.0
|
|
N
|
A:ASP345
|
4.9
|
58.6
|
1.0
|
|
CA
|
A:ASN312
|
4.9
|
59.5
|
1.0
|
|
OD1
|
A:ASP396
|
4.9
|
58.6
|
1.0
|
|
Calcium binding site 10 out
of 18 in 5dzx
Go back to
Calcium Binding Sites List in 5dzx
Calcium binding site 10 out
of 18 in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca505
b:53.1
occ:1.00
|
OD1
|
B:ASP63
|
2.3
|
52.2
|
1.0
|
|
OE2
|
B:GLU9
|
2.3
|
36.9
|
1.0
|
|
OD2
|
B:ASP100
|
2.4
|
52.4
|
1.0
|
|
OE1
|
B:GLU65
|
2.4
|
49.2
|
1.0
|
|
OE2
|
B:GLU10
|
2.8
|
49.6
|
1.0
|
|
CE1
|
B:HIS101
|
3.3
|
58.5
|
1.0
|
|
CG
|
B:ASP100
|
3.3
|
55.3
|
1.0
|
|
CG
|
B:ASP63
|
3.4
|
56.3
|
1.0
|
|
CD
|
B:GLU9
|
3.6
|
43.2
|
1.0
|
|
CD
|
B:GLU65
|
3.6
|
47.3
|
1.0
|
|
OD1
|
B:ASP100
|
3.6
|
53.2
|
1.0
|
|
OD2
|
B:ASP63
|
3.8
|
79.3
|
1.0
|
|
CD
|
B:GLU10
|
3.9
|
57.8
|
1.0
|
|
ND1
|
B:HIS101
|
4.0
|
55.4
|
1.0
|
|
CG
|
B:GLU10
|
4.1
|
51.0
|
1.0
|
|
OE1
|
B:GLU9
|
4.2
|
39.7
|
1.0
|
|
OE2
|
B:GLU65
|
4.3
|
45.1
|
1.0
|
|
NE2
|
B:HIS101
|
4.3
|
43.9
|
1.0
|
|
CA
|
B:CA506
|
4.5
|
37.3
|
1.0
|
|
CG
|
B:GLU65
|
4.6
|
54.8
|
1.0
|
|
CB
|
B:ASP63
|
4.6
|
61.6
|
1.0
|
|
CB
|
B:GLU65
|
4.6
|
58.3
|
1.0
|
|
CB
|
B:ASP100
|
4.7
|
66.7
|
1.0
|
|
CG
|
B:GLU9
|
4.7
|
56.0
|
1.0
|
|
N
|
B:GLU65
|
4.9
|
59.0
|
1.0
|
|
CA
|
B:ASP63
|
4.9
|
59.7
|
1.0
|
|
N
|
B:ARG64
|
5.0
|
45.1
|
1.0
|
|
Reference:
K.M.Goodman,
R.Rubinstein,
C.A.Thu,
F.Bahna,
S.Mannepalli,
G.Ahlsen,
C.Rittenhouse,
T.Maniatis,
B.Honig,
L.Shapiro.
Structural Basis of Diverse Homophilic Recognition By Clustered Alpha- and Beta-Protocadherins. Neuron V. 90 709 2016.
ISSN: ISSN 0896-6273
PubMed: 27161523
DOI: 10.1016/J.NEURON.2016.04.004
Page generated: Sat Dec 12 05:22:24 2020
|
