Calcium in PDB 5t4n: Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
Protein crystallography data
The structure of Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant, PDB code: 5t4n
was solved by
R.E.Powers,
R.Gaudet,
M.Sotomayor,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.38 /
2.70
|
|
Space group
|
P 65
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.655,
105.655,
193.767,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
20.2 /
23.9
|
Other elements in 5t4n:
The structure of Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
(pdb code 5t4n). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant, PDB code: 5t4n:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 1 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 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 Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca701
b:80.4
occ:1.00
|
O
|
A:GLU367
|
2.4
|
77.9
|
1.0
|
|
OD1
|
A:ASP411
|
2.4
|
74.7
|
1.0
|
|
O
|
A:HOH827
|
2.4
|
69.7
|
1.0
|
|
OD1
|
A:ASN369
|
2.4
|
87.4
|
1.0
|
|
O
|
A:HOH833
|
2.4
|
70.1
|
1.0
|
|
O
|
A:HOH898
|
2.4
|
61.2
|
1.0
|
|
O
|
A:HOH895
|
2.4
|
52.0
|
1.0
|
|
CG
|
A:ASN369
|
3.4
|
88.9
|
1.0
|
|
CG
|
A:ASP411
|
3.4
|
75.5
|
1.0
|
|
C
|
A:GLU367
|
3.6
|
78.0
|
1.0
|
|
ND2
|
A:ASN369
|
3.9
|
94.7
|
1.0
|
|
N
|
A:ASN369
|
4.0
|
75.2
|
1.0
|
|
N
|
A:GLU367
|
4.1
|
83.2
|
1.0
|
|
OD2
|
A:ASP411
|
4.2
|
88.8
|
1.0
|
|
OD1
|
A:ASP366
|
4.2
|
98.1
|
1.0
|
|
CB
|
A:ASP411
|
4.2
|
76.3
|
1.0
|
|
CG
|
A:GLN370
|
4.3
|
91.6
|
1.0
|
|
CA
|
A:ASP411
|
4.4
|
81.1
|
1.0
|
|
CA
|
A:GLU367
|
4.4
|
81.9
|
1.0
|
|
N
|
A:ASN368
|
4.5
|
77.0
|
1.0
|
|
CB
|
A:ASN369
|
4.6
|
83.6
|
1.0
|
|
CA
|
A:ASN368
|
4.7
|
77.6
|
1.0
|
|
CA
|
A:ASN369
|
4.7
|
77.4
|
1.0
|
|
N
|
A:GLN370
|
4.8
|
78.7
|
1.0
|
|
C
|
A:ASN368
|
4.8
|
81.1
|
1.0
|
|
OE1
|
A:GLU267
|
4.9
|
93.9
|
1.0
|
|
C
|
A:ASN369
|
5.0
|
78.4
|
1.0
|
|
Calcium binding site 2 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 2 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 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 Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca702
b:75.4
occ:1.00
|
O
|
A:GLN370
|
2.4
|
76.7
|
1.0
|
|
OD2
|
A:ASP409
|
2.4
|
93.3
|
1.0
|
|
OD2
|
A:ASP411
|
2.4
|
88.8
|
1.0
|
|
O
|
A:HOH854
|
2.4
|
61.0
|
1.0
|
|
OD2
|
A:ASP464
|
2.4
|
75.5
|
1.0
|
|
OD1
|
A:ASN368
|
2.4
|
78.1
|
1.0
|
|
OD1
|
A:ASP409
|
2.4
|
78.2
|
1.0
|
|
CG
|
A:ASP409
|
2.7
|
86.5
|
1.0
|
|
CG
|
A:ASP411
|
3.3
|
75.5
|
1.0
|
|
CG
|
A:ASP464
|
3.3
|
69.6
|
1.0
|
|
CG
|
A:ASN368
|
3.4
|
77.2
|
1.0
|
|
C
|
A:GLN370
|
3.5
|
80.4
|
1.0
|
|
CB
|
A:ASP411
|
3.6
|
76.3
|
1.0
|
|
CB
|
A:ASP464
|
3.7
|
65.3
|
1.0
|
|
ND2
|
A:ASN368
|
3.9
|
76.8
|
1.0
|
|
N
|
A:GLN370
|
4.1
|
78.7
|
1.0
|
|
CA
|
A:GLN370
|
4.2
|
84.8
|
1.0
|
|
OE1
|
A:GLN467
|
4.2
|
86.0
|
1.0
|
|
CB
|
A:ASP409
|
4.3
|
81.8
|
1.0
|
|
OD1
|
A:ASP464
|
4.4
|
67.4
|
1.0
|
|
OD1
|
A:ASP411
|
4.4
|
74.7
|
1.0
|
|
CB
|
A:GLN370
|
4.5
|
87.8
|
1.0
|
|
CB
|
A:ASN368
|
4.6
|
76.3
|
1.0
|
|
C
|
A:ASN368
|
4.6
|
81.1
|
1.0
|
|
N
|
A:SER371
|
4.6
|
82.7
|
1.0
|
|
CA
|
A:ASN368
|
4.6
|
77.6
|
1.0
|
|
CD
|
A:PRO372
|
4.6
|
60.1
|
1.0
|
|
N
|
A:PRO372
|
4.7
|
63.8
|
1.0
|
|
N
|
A:ASP411
|
4.7
|
84.3
|
1.0
|
|
C
|
A:SER371
|
4.8
|
70.5
|
1.0
|
|
CA
|
A:ASP411
|
4.8
|
81.1
|
1.0
|
|
N
|
A:ASN369
|
4.8
|
75.2
|
1.0
|
|
CA
|
A:SER371
|
4.8
|
75.3
|
1.0
|
|
O
|
A:HOH836
|
4.9
|
79.4
|
1.0
|
|
O
|
A:ASN368
|
4.9
|
91.2
|
1.0
|
|
Calcium binding site 3 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 3 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 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 Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca703
b:72.2
occ:1.00
|
OE1
|
A:GLU451
|
2.2
|
75.3
|
1.0
|
|
OD2
|
A:ASP483
|
2.3
|
82.2
|
1.0
|
|
OE2
|
A:GLU385
|
2.3
|
68.7
|
1.0
|
|
O
|
A:HOH823
|
2.4
|
44.7
|
1.0
|
|
O
|
A:HOH856
|
2.4
|
66.9
|
1.0
|
|
OD1
|
A:ASP449
|
2.5
|
77.6
|
1.0
|
|
OD1
|
A:ASP483
|
2.6
|
74.5
|
1.0
|
|
CG
|
A:ASP483
|
2.8
|
78.8
|
1.0
|
|
CD
|
A:GLU385
|
3.2
|
75.3
|
1.0
|
|
CA
|
A:CA704
|
3.4
|
75.5
|
1.0
|
|
CG
|
A:ASP449
|
3.4
|
83.0
|
1.0
|
|
CD
|
A:GLU451
|
3.5
|
68.8
|
1.0
|
|
OE1
|
A:GLU385
|
3.6
|
85.0
|
1.0
|
|
ND2
|
A:ASN484
|
3.7
|
65.5
|
1.0
|
|
OD2
|
A:ASP449
|
4.0
|
91.1
|
1.0
|
|
CB
|
A:ASP483
|
4.3
|
81.2
|
1.0
|
|
OE2
|
A:GLU451
|
4.3
|
72.1
|
1.0
|
|
CG
|
A:GLU385
|
4.4
|
75.0
|
1.0
|
|
CG
|
A:GLU451
|
4.4
|
68.3
|
1.0
|
|
CB
|
A:ASP449
|
4.5
|
77.5
|
1.0
|
|
CB
|
A:GLU451
|
4.5
|
69.4
|
1.0
|
|
N
|
A:ARG450
|
4.5
|
61.1
|
1.0
|
|
N
|
A:GLU451
|
4.5
|
62.5
|
1.0
|
|
CA
|
A:ASP449
|
4.6
|
72.5
|
1.0
|
|
C
|
A:ASP449
|
4.8
|
63.9
|
1.0
|
|
CG
|
A:ASN484
|
4.9
|
67.5
|
1.0
|
|
OD1
|
A:ASP516
|
5.0
|
86.4
|
1.0
|
|
Calcium binding site 4 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 4 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 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 Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca704
b:75.5
occ:1.00
|
OD1
|
A:ASP516
|
2.4
|
86.4
|
1.0
|
|
OD1
|
A:ASP480
|
2.4
|
70.8
|
1.0
|
|
OE1
|
A:GLU451
|
2.4
|
75.3
|
1.0
|
|
OE1
|
A:GLU385
|
2.4
|
85.0
|
1.0
|
|
OE2
|
A:GLU451
|
2.5
|
72.1
|
1.0
|
|
OD1
|
A:ASP483
|
2.5
|
74.5
|
1.0
|
|
O
|
A:ALA481
|
2.6
|
64.5
|
1.0
|
|
CD
|
A:GLU451
|
2.7
|
68.8
|
1.0
|
|
CD
|
A:GLU385
|
3.3
|
75.3
|
1.0
|
|
CA
|
A:CA703
|
3.4
|
72.2
|
1.0
|
|
CG
|
A:ASP516
|
3.5
|
86.5
|
1.0
|
|
CG
|
A:ASP480
|
3.5
|
79.9
|
1.0
|
|
OE2
|
A:GLU385
|
3.6
|
68.7
|
1.0
|
|
ND2
|
A:ASN484
|
3.6
|
65.5
|
1.0
|
|
CG
|
A:ASP483
|
3.6
|
78.8
|
1.0
|
|
C
|
A:ALA481
|
3.8
|
67.1
|
1.0
|
|
N
|
A:ALA481
|
4.0
|
73.4
|
1.0
|
|
OD2
|
A:ASP480
|
4.1
|
92.8
|
1.0
|
|
N
|
A:ASP483
|
4.1
|
69.5
|
1.0
|
|
CG
|
A:GLU451
|
4.2
|
68.3
|
1.0
|
|
OD2
|
A:ASP483
|
4.2
|
82.2
|
1.0
|
|
CB
|
A:ASP516
|
4.2
|
82.3
|
1.0
|
|
CA
|
A:ASP516
|
4.3
|
79.1
|
1.0
|
|
NE
|
A:ARG450
|
4.4
|
74.7
|
1.0
|
|
OD2
|
A:ASP516
|
4.5
|
87.4
|
1.0
|
|
CA
|
A:ALA481
|
4.5
|
68.0
|
1.0
|
|
CG
|
A:GLU385
|
4.7
|
75.0
|
1.0
|
|
CB
|
A:ASP480
|
4.7
|
71.8
|
1.0
|
|
CB
|
A:ASP483
|
4.7
|
81.2
|
1.0
|
|
CA
|
A:ASP480
|
4.7
|
69.3
|
1.0
|
|
NH2
|
A:ARG450
|
4.7
|
83.9
|
1.0
|
|
N
|
A:ASN482
|
4.8
|
68.6
|
1.0
|
|
CG
|
A:ASN484
|
4.8
|
67.5
|
1.0
|
|
C
|
A:ASP480
|
4.8
|
71.6
|
1.0
|
|
N
|
A:ASN484
|
4.8
|
60.1
|
1.0
|
|
CA
|
A:ASP483
|
4.8
|
73.3
|
1.0
|
|
CA
|
A:ASN482
|
4.9
|
68.2
|
1.0
|
|
O
|
A:HOH856
|
4.9
|
66.9
|
1.0
|
|
CB
|
A:ARG450
|
5.0
|
59.8
|
1.0
|
|
Calcium binding site 5 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 5 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 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 Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca705
b:66.6
occ:1.00
|
OD2
|
A:ASP514
|
2.3
|
74.4
|
1.0
|
|
OD2
|
A:ASP516
|
2.4
|
87.4
|
1.0
|
|
OD1
|
A:ASN482
|
2.4
|
70.8
|
1.0
|
|
O
|
A:ASN520
|
2.4
|
71.9
|
1.0
|
|
O
|
A:ASN484
|
2.4
|
63.1
|
1.0
|
|
OD2
|
A:ASP566
|
2.5
|
67.3
|
1.0
|
|
OD1
|
A:ASP514
|
2.5
|
72.0
|
1.0
|
|
CG
|
A:ASP514
|
2.7
|
72.4
|
1.0
|
|
CG
|
A:ASP566
|
3.4
|
72.5
|
1.0
|
|
CG
|
A:ASP516
|
3.4
|
86.5
|
1.0
|
|
CG
|
A:ASN482
|
3.5
|
69.9
|
1.0
|
|
C
|
A:ASN484
|
3.6
|
62.6
|
1.0
|
|
C
|
A:ASN520
|
3.6
|
78.4
|
1.0
|
|
CB
|
A:ASP566
|
3.6
|
75.6
|
1.0
|
|
CB
|
A:ASP516
|
3.7
|
82.3
|
1.0
|
|
ND2
|
A:ASN482
|
4.1
|
71.6
|
1.0
|
|
CB
|
A:ASP514
|
4.3
|
74.7
|
1.0
|
|
CA
|
A:ASN484
|
4.4
|
59.9
|
1.0
|
|
N
|
A:ASN484
|
4.4
|
60.1
|
1.0
|
|
CA
|
A:ASN520
|
4.5
|
83.7
|
1.0
|
|
OD1
|
A:ASP566
|
4.5
|
76.7
|
1.0
|
|
N
|
A:GLY521
|
4.5
|
77.7
|
1.0
|
|
CD
|
A:PRO486
|
4.5
|
73.4
|
1.0
|
|
OD1
|
A:ASP516
|
4.5
|
86.4
|
1.0
|
|
CB
|
A:ASN484
|
4.5
|
58.8
|
1.0
|
|
CA
|
A:GLY521
|
4.6
|
80.1
|
1.0
|
|
N
|
A:THR485
|
4.6
|
64.4
|
1.0
|
|
CB
|
A:ASN520
|
4.7
|
78.7
|
1.0
|
|
CB
|
A:ASN482
|
4.7
|
65.5
|
1.0
|
|
CA
|
A:THR485
|
4.8
|
64.8
|
1.0
|
|
CA
|
A:ASN482
|
4.9
|
68.2
|
1.0
|
|
N
|
A:ASP516
|
4.9
|
73.8
|
1.0
|
|
CA
|
A:ASP516
|
4.9
|
79.1
|
1.0
|
|
CD
|
A:ARG574
|
5.0
|
70.8
|
1.0
|
|
Calcium binding site 6 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 6 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 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 Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca701
b:66.9
occ:1.00
|
OD1
|
B:ASP480
|
2.3
|
64.2
|
1.0
|
|
OD1
|
B:ASP516
|
2.4
|
70.7
|
1.0
|
|
O
|
B:ALA481
|
2.4
|
81.4
|
1.0
|
|
OE2
|
B:GLU451
|
2.5
|
75.8
|
1.0
|
|
OE2
|
B:GLU385
|
2.5
|
66.3
|
1.0
|
|
OE1
|
B:GLU451
|
2.5
|
63.4
|
1.0
|
|
OD1
|
B:ASP483
|
2.5
|
72.7
|
1.0
|
|
CD
|
B:GLU451
|
2.8
|
66.3
|
1.0
|
|
CG
|
B:ASP480
|
3.3
|
65.9
|
1.0
|
|
CG
|
B:ASP516
|
3.4
|
79.3
|
1.0
|
|
C
|
B:ALA481
|
3.6
|
79.6
|
1.0
|
|
CG
|
B:ASP483
|
3.7
|
73.1
|
1.0
|
|
CD
|
B:GLU385
|
3.8
|
72.5
|
1.0
|
|
OD2
|
B:ASP480
|
3.8
|
75.4
|
1.0
|
|
ND2
|
B:ASN484
|
3.9
|
65.2
|
1.0
|
|
CA
|
B:CA703
|
3.9
|
76.1
|
1.0
|
|
N
|
B:ASP483
|
4.0
|
77.0
|
1.0
|
|
N
|
B:ALA481
|
4.0
|
74.2
|
1.0
|
|
CB
|
B:ASP516
|
4.0
|
74.7
|
1.0
|
|
CA
|
B:ASP516
|
4.1
|
67.9
|
1.0
|
|
CG
|
B:GLU451
|
4.2
|
63.9
|
1.0
|
|
OD2
|
B:ASP483
|
4.3
|
84.6
|
1.0
|
|
OD2
|
B:ASP516
|
4.4
|
87.6
|
1.0
|
|
NE
|
B:ARG450
|
4.4
|
70.0
|
1.0
|
|
CA
|
B:ALA481
|
4.4
|
76.4
|
1.0
|
|
OE1
|
B:GLU385
|
4.4
|
83.6
|
1.0
|
|
CB
|
B:ASP480
|
4.5
|
66.8
|
1.0
|
|
N
|
B:ASN482
|
4.6
|
79.0
|
1.0
|
|
CA
|
B:ASP480
|
4.6
|
68.8
|
1.0
|
|
CA
|
B:ASN482
|
4.6
|
73.3
|
1.0
|
|
NH2
|
B:ARG450
|
4.7
|
72.3
|
1.0
|
|
C
|
B:ASP480
|
4.7
|
71.8
|
1.0
|
|
CB
|
B:ASP483
|
4.8
|
71.6
|
1.0
|
|
CA
|
B:ASP483
|
4.8
|
74.5
|
1.0
|
|
C
|
B:ASN482
|
4.8
|
69.6
|
1.0
|
|
CG
|
B:GLU385
|
4.9
|
65.8
|
1.0
|
|
N
|
B:GLU517
|
4.9
|
78.4
|
1.0
|
|
N
|
B:ASP516
|
4.9
|
72.1
|
1.0
|
|
N
|
B:ASN484
|
5.0
|
67.8
|
1.0
|
|
O
|
B:ALA515
|
5.0
|
78.6
|
1.0
|
|
Calcium binding site 7 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 7 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 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 Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca702
b:65.9
occ:1.00
|
OD2
|
B:ASP514
|
2.4
|
75.6
|
1.0
|
|
OD2
|
B:ASP516
|
2.4
|
87.6
|
1.0
|
|
OD1
|
B:ASN482
|
2.4
|
89.5
|
1.0
|
|
O
|
B:ASN520
|
2.4
|
63.8
|
1.0
|
|
O
|
B:ASN484
|
2.4
|
65.5
|
1.0
|
|
OD1
|
B:ASP514
|
2.5
|
71.6
|
1.0
|
|
OD2
|
B:ASP566
|
2.5
|
78.0
|
1.0
|
|
CG
|
B:ASP514
|
2.8
|
72.4
|
1.0
|
|
CG
|
B:ASP566
|
3.4
|
73.0
|
1.0
|
|
CG
|
B:ASP516
|
3.4
|
79.3
|
1.0
|
|
CG
|
B:ASN482
|
3.5
|
82.0
|
1.0
|
|
C
|
B:ASN520
|
3.6
|
66.6
|
1.0
|
|
C
|
B:ASN484
|
3.6
|
66.1
|
1.0
|
|
CB
|
B:ASP566
|
3.6
|
72.5
|
1.0
|
|
CB
|
B:ASP516
|
3.7
|
74.7
|
1.0
|
|
ND2
|
B:ASN482
|
4.0
|
86.1
|
1.0
|
|
CB
|
B:ASP514
|
4.3
|
74.8
|
1.0
|
|
CA
|
B:ASN484
|
4.4
|
62.3
|
1.0
|
|
OD1
|
B:ASP566
|
4.4
|
69.6
|
1.0
|
|
N
|
B:ASN484
|
4.4
|
67.8
|
1.0
|
|
CD
|
B:PRO486
|
4.5
|
59.1
|
1.0
|
|
N
|
B:GLY521
|
4.5
|
65.8
|
1.0
|
|
CA
|
B:ASN520
|
4.5
|
71.9
|
1.0
|
|
OD1
|
B:ASP516
|
4.5
|
70.7
|
1.0
|
|
CA
|
B:GLY521
|
4.5
|
66.7
|
1.0
|
|
CB
|
B:ASN484
|
4.6
|
62.2
|
1.0
|
|
N
|
B:THR485
|
4.6
|
69.1
|
1.0
|
|
CB
|
B:ASN520
|
4.7
|
72.0
|
1.0
|
|
CB
|
B:ASN482
|
4.8
|
69.8
|
1.0
|
|
CA
|
B:THR485
|
4.9
|
70.4
|
1.0
|
|
N
|
B:PRO486
|
5.0
|
64.5
|
1.0
|
|
CG
|
B:PRO486
|
5.0
|
55.6
|
1.0
|
|
CA
|
B:ASN482
|
5.0
|
73.3
|
1.0
|
|
N
|
B:ASP516
|
5.0
|
72.1
|
1.0
|
|
CA
|
B:ASP516
|
5.0
|
67.9
|
1.0
|
|
Calcium binding site 8 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 8 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 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 Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca703
b:76.1
occ:1.00
|
OD2
|
B:ASP483
|
2.2
|
84.6
|
1.0
|
|
OE1
|
B:GLU385
|
2.2
|
83.6
|
1.0
|
|
OE1
|
B:GLU451
|
2.3
|
63.4
|
1.0
|
|
O
|
B:HOH881
|
2.4
|
61.1
|
1.0
|
|
O
|
B:HOH849
|
2.4
|
45.9
|
1.0
|
|
OD1
|
B:ASP449
|
2.5
|
74.5
|
1.0
|
|
CD
|
B:GLU385
|
2.7
|
72.5
|
1.0
|
|
OE2
|
B:GLU385
|
2.7
|
66.3
|
1.0
|
|
OD1
|
B:ASP483
|
2.7
|
72.7
|
1.0
|
|
CG
|
B:ASP483
|
2.8
|
73.1
|
1.0
|
|
CG
|
B:ASP449
|
3.3
|
74.0
|
1.0
|
|
CD
|
B:GLU451
|
3.6
|
66.3
|
1.0
|
|
OD2
|
B:ASP449
|
3.8
|
79.0
|
1.0
|
|
CA
|
B:CA701
|
3.9
|
66.9
|
1.0
|
|
CG
|
B:GLU385
|
4.0
|
65.8
|
1.0
|
|
ND2
|
B:ASN484
|
4.2
|
65.2
|
1.0
|
|
CB
|
B:ASP449
|
4.2
|
71.2
|
1.0
|
|
CB
|
B:ASP483
|
4.2
|
71.6
|
1.0
|
|
N
|
B:ARG450
|
4.4
|
57.9
|
1.0
|
|
CG
|
B:GLU451
|
4.4
|
63.9
|
1.0
|
|
CB
|
B:GLU451
|
4.4
|
64.1
|
1.0
|
|
CA
|
B:ASP449
|
4.4
|
66.2
|
1.0
|
|
N
|
B:GLU451
|
4.4
|
74.2
|
1.0
|
|
OE2
|
B:GLU451
|
4.4
|
75.8
|
1.0
|
|
C
|
B:ASP449
|
4.7
|
60.1
|
1.0
|
|
CB
|
B:GLU385
|
4.9
|
65.7
|
1.0
|
|
Calcium binding site 9 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 9 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca704
b:67.4
occ:1.00
|
OD2
|
B:ASP464
|
2.3
|
76.4
|
1.0
|
|
OD1
|
B:ASP409
|
2.3
|
63.9
|
1.0
|
|
OD2
|
B:ASP411
|
2.4
|
81.3
|
1.0
|
|
O
|
B:GLN370
|
2.4
|
77.1
|
1.0
|
|
OD1
|
B:ASN368
|
2.4
|
86.8
|
1.0
|
|
OD2
|
B:ASP409
|
2.4
|
70.9
|
1.0
|
|
O
|
B:HOH866
|
2.4
|
74.3
|
1.0
|
|
CG
|
B:ASP409
|
2.7
|
68.7
|
1.0
|
|
CG
|
B:ASP464
|
3.4
|
71.4
|
1.0
|
|
CG
|
B:ASP411
|
3.4
|
72.6
|
1.0
|
|
CG
|
B:ASN368
|
3.4
|
79.3
|
1.0
|
|
C
|
B:GLN370
|
3.6
|
75.3
|
1.0
|
|
CB
|
B:ASP411
|
3.7
|
75.0
|
1.0
|
|
CB
|
B:ASP464
|
3.7
|
63.8
|
1.0
|
|
ND2
|
B:ASN368
|
3.9
|
81.1
|
1.0
|
|
N
|
B:GLN370
|
4.1
|
71.3
|
1.0
|
|
CB
|
B:ASP409
|
4.2
|
69.7
|
1.0
|
|
OE1
|
B:GLN467
|
4.2
|
0.7
|
1.0
|
|
CA
|
B:GLN370
|
4.2
|
72.2
|
1.0
|
|
OD1
|
B:ASP464
|
4.5
|
73.6
|
1.0
|
|
OD1
|
B:ASP411
|
4.5
|
73.2
|
1.0
|
|
CB
|
B:GLN370
|
4.5
|
74.4
|
1.0
|
|
N
|
B:SER371
|
4.6
|
79.1
|
1.0
|
|
CB
|
B:ASN368
|
4.6
|
73.9
|
1.0
|
|
CD
|
B:PRO372
|
4.7
|
66.1
|
1.0
|
|
N
|
B:ASP411
|
4.7
|
80.9
|
1.0
|
|
N
|
B:PRO372
|
4.7
|
68.3
|
1.0
|
|
C
|
B:SER371
|
4.8
|
69.9
|
1.0
|
|
CA
|
B:ASN368
|
4.8
|
74.5
|
1.0
|
|
C
|
B:ASN368
|
4.8
|
74.2
|
1.0
|
|
N
|
B:ASN369
|
4.8
|
74.5
|
1.0
|
|
CA
|
B:SER371
|
4.9
|
75.5
|
1.0
|
|
CA
|
B:ASP411
|
4.9
|
75.2
|
1.0
|
|
O
|
B:HOH844
|
4.9
|
76.1
|
1.0
|
|
Calcium binding site 10 out
of 10 in 5t4n
Go back to
Calcium Binding Sites List in 5t4n
Calcium binding site 10 out
of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca705
b:79.0
occ:1.00
|
O
|
B:GLU367
|
2.3
|
81.0
|
1.0
|
|
OD1
|
B:ASP366
|
2.4
|
84.6
|
1.0
|
|
OD1
|
B:ASP411
|
2.4
|
73.2
|
1.0
|
|
O
|
B:HOH845
|
2.4
|
90.8
|
1.0
|
|
OD2
|
B:ASP366
|
2.5
|
97.4
|
1.0
|
|
OD1
|
B:ASN369
|
2.5
|
79.8
|
1.0
|
|
CG
|
B:ASP366
|
2.7
|
86.7
|
1.0
|
|
CL
|
B:CL706
|
2.9
|
74.6
|
1.0
|
|
CG
|
B:ASP411
|
3.4
|
72.6
|
1.0
|
|
CG
|
B:ASN369
|
3.4
|
79.6
|
1.0
|
|
C
|
B:GLU367
|
3.5
|
82.1
|
1.0
|
|
ND2
|
B:ASN369
|
3.8
|
90.5
|
1.0
|
|
N
|
B:ASN369
|
4.0
|
74.5
|
1.0
|
|
N
|
B:GLU367
|
4.0
|
79.7
|
1.0
|
|
CB
|
B:ASP411
|
4.1
|
75.0
|
1.0
|
|
CB
|
B:ASP366
|
4.2
|
74.0
|
1.0
|
|
CA
|
B:ASP411
|
4.3
|
75.2
|
1.0
|
|
OD2
|
B:ASP411
|
4.3
|
81.3
|
1.0
|
|
CA
|
B:GLU367
|
4.3
|
82.6
|
1.0
|
|
OE1
|
B:GLU267
|
4.3
|
0.3
|
1.0
|
|
N
|
B:ASN368
|
4.4
|
79.5
|
1.0
|
|
CA
|
B:ASN368
|
4.5
|
74.5
|
1.0
|
|
CG
|
B:GLN370
|
4.5
|
78.1
|
1.0
|
|
CB
|
B:ASN369
|
4.7
|
73.7
|
1.0
|
|
C
|
B:ASP366
|
4.7
|
75.1
|
1.0
|
|
C
|
B:ASN368
|
4.8
|
74.2
|
1.0
|
|
CA
|
B:ASN369
|
4.8
|
73.3
|
1.0
|
|
OE1
|
B:GLN370
|
4.8
|
94.5
|
1.0
|
|
O
|
B:HOH863
|
4.9
|
68.5
|
1.0
|
|
O
|
B:HOH802
|
4.9
|
88.8
|
1.0
|
|
N
|
B:GLN370
|
4.9
|
71.3
|
1.0
|
|
CA
|
B:ASP366
|
4.9
|
74.6
|
1.0
|
|
CB
|
B:GLU367
|
4.9
|
86.8
|
1.0
|
|
Reference:
R.E.Powers,
R.Gaudet,
M.Sotomayor.
A Partial Calcium-Free Linker Confers Flexibility to Inner-Ear Protocadherin-15. Structure V. 25 482 2017.
ISSN: ISSN 1878-4186
PubMed: 28238533
DOI: 10.1016/J.STR.2017.01.014
Page generated: Mon Jul 15 10:46:53 2024
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