Calcium in PDB 8umz: Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
Protein crystallography data
The structure of Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection, PDB code: 8umz
was solved by
P.De-La-Torre,
K.Martinez-Perez,
A.Indzhykulian,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.20 /
1.63
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.276,
50.613,
88.263,
90,
94.01,
90
|
|
R / Rfree (%)
|
22.3 /
27.4
|
Other elements in 8umz:
The structure of Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
(pdb code 8umz). 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection, PDB code: 8umz:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 1 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:18.4
occ:1.00
|
O
|
A:GLN370
|
2.3
|
21.5
|
1.0
|
|
OD2
|
A:ASP411
|
2.3
|
19.3
|
1.0
|
|
OD2
|
A:ASP409
|
2.3
|
20.2
|
1.0
|
|
OD2
|
A:ASP464
|
2.3
|
17.3
|
1.0
|
|
OD1
|
A:ASN368
|
2.4
|
24.5
|
1.0
|
|
O
|
A:HOH838
|
2.5
|
25.1
|
1.0
|
|
OD1
|
A:ASP409
|
2.6
|
21.0
|
1.0
|
|
CG
|
A:ASP409
|
2.8
|
21.6
|
1.0
|
|
CG
|
A:ASP464
|
3.2
|
18.2
|
1.0
|
|
CG
|
A:ASP411
|
3.4
|
27.1
|
1.0
|
|
C
|
A:GLN370
|
3.5
|
20.3
|
1.0
|
|
CG
|
A:ASN368
|
3.6
|
23.7
|
1.0
|
|
CB
|
A:ASP464
|
3.7
|
17.1
|
1.0
|
|
CB
|
A:ASP411
|
3.9
|
23.8
|
1.0
|
|
NE2
|
A:GLN467
|
4.0
|
20.5
|
1.0
|
|
N
|
A:GLN370
|
4.0
|
23.7
|
1.0
|
|
CA
|
A:GLN370
|
4.2
|
24.9
|
1.0
|
|
CB
|
A:ASP409
|
4.3
|
18.4
|
1.0
|
|
OD1
|
A:ASP464
|
4.3
|
16.6
|
1.0
|
|
ND2
|
A:ASN368
|
4.3
|
21.1
|
1.0
|
|
O
|
A:HOH807
|
4.4
|
28.3
|
1.0
|
|
O
|
A:HOH791
|
4.4
|
32.4
|
1.0
|
|
CB
|
A:GLN370
|
4.5
|
28.3
|
1.0
|
|
OD1
|
A:ASP411
|
4.5
|
27.8
|
1.0
|
|
CA
|
A:ASN368
|
4.5
|
22.1
|
1.0
|
|
N
|
A:SER371
|
4.6
|
18.5
|
1.0
|
|
C
|
A:ASN368
|
4.6
|
24.7
|
1.0
|
|
CB
|
A:ASN368
|
4.7
|
22.2
|
1.0
|
|
CD
|
A:PRO372
|
4.7
|
16.5
|
1.0
|
|
N
|
A:ASN369
|
4.7
|
24.9
|
1.0
|
|
N
|
A:PRO372
|
4.8
|
18.3
|
1.0
|
|
N
|
A:ASP411
|
4.8
|
24.1
|
1.0
|
|
CA
|
A:SER371
|
4.8
|
19.6
|
1.0
|
|
C
|
A:SER371
|
4.8
|
18.4
|
1.0
|
|
CA
|
A:ASP411
|
5.0
|
23.4
|
1.0
|
|
Calcium binding site 2 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 2 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:21.1
occ:1.00
|
OE2
|
A:GLU385
|
2.2
|
21.0
|
1.0
|
|
OD1
|
A:ASP483
|
2.3
|
23.7
|
1.0
|
|
OD1
|
A:ASP480
|
2.3
|
19.2
|
1.0
|
|
OD1
|
A:ASP516
|
2.3
|
17.8
|
1.0
|
|
O
|
A:ALA481
|
2.5
|
24.4
|
1.0
|
|
OE2
|
A:GLU451
|
2.6
|
22.4
|
1.0
|
|
OE1
|
A:GLU451
|
2.9
|
23.5
|
1.0
|
|
CD
|
A:GLU451
|
3.1
|
21.5
|
1.0
|
|
CG
|
A:ASP516
|
3.4
|
21.3
|
1.0
|
|
CG
|
A:ASP480
|
3.4
|
21.9
|
1.0
|
|
CG
|
A:ASP483
|
3.4
|
28.7
|
1.0
|
|
CD
|
A:GLU385
|
3.4
|
22.2
|
1.0
|
|
C
|
A:ALA481
|
3.7
|
19.8
|
1.0
|
|
CB
|
A:ASP516
|
3.9
|
19.0
|
1.0
|
|
OE1
|
A:GLU385
|
3.9
|
23.7
|
1.0
|
|
N
|
A:ALA481
|
3.9
|
19.0
|
1.0
|
|
OD2
|
A:ASP480
|
3.9
|
23.8
|
1.0
|
|
OD2
|
A:ASP483
|
4.0
|
34.3
|
1.0
|
|
NA
|
A:NA606
|
4.1
|
15.7
|
1.0
|
|
OD1
|
A:ASN484
|
4.1
|
28.9
|
1.0
|
|
N
|
A:ASP483
|
4.2
|
21.4
|
1.0
|
|
CA
|
A:ASP516
|
4.2
|
19.3
|
1.0
|
|
OD2
|
A:ASP516
|
4.3
|
17.9
|
1.0
|
|
NE
|
A:ARG450
|
4.3
|
24.3
|
1.0
|
|
CA
|
A:ALA481
|
4.4
|
23.9
|
1.0
|
|
CB
|
A:ASP483
|
4.5
|
25.7
|
1.0
|
|
CB
|
A:ASP480
|
4.5
|
23.0
|
1.0
|
|
CG
|
A:GLU451
|
4.5
|
24.3
|
1.0
|
|
CG
|
A:GLU385
|
4.6
|
24.1
|
1.0
|
|
CA
|
A:ASP480
|
4.6
|
20.8
|
1.0
|
|
C
|
A:ASP480
|
4.7
|
17.4
|
1.0
|
|
N
|
A:ASN482
|
4.7
|
22.0
|
1.0
|
|
CB
|
A:ALA481
|
4.8
|
27.7
|
1.0
|
|
CA
|
A:ASP483
|
4.8
|
24.2
|
1.0
|
|
NH2
|
A:ARG450
|
4.8
|
27.6
|
1.0
|
|
CA
|
A:ASN482
|
4.9
|
20.2
|
1.0
|
|
CB
|
A:ARG450
|
4.9
|
25.4
|
1.0
|
|
Calcium binding site 3 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 3 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca603
b:17.6
occ:1.00
|
OD2
|
A:ASP516
|
2.3
|
17.9
|
1.0
|
|
O
|
A:ASN520
|
2.3
|
14.9
|
1.0
|
|
OD1
|
A:ASN482
|
2.4
|
20.8
|
1.0
|
|
O
|
A:ASN484
|
2.4
|
19.5
|
1.0
|
|
OD2
|
A:ASP564
|
2.4
|
15.4
|
1.0
|
|
OD2
|
A:ASP514
|
2.4
|
17.3
|
1.0
|
|
OD1
|
A:ASP514
|
2.6
|
18.5
|
1.0
|
|
CG
|
A:ASP514
|
2.8
|
23.7
|
1.0
|
|
CG
|
A:ASP516
|
3.4
|
21.3
|
1.0
|
|
CG
|
A:ASP564
|
3.4
|
14.7
|
1.0
|
|
CG
|
A:ASN482
|
3.5
|
19.4
|
1.0
|
|
C
|
A:ASN484
|
3.5
|
19.0
|
1.0
|
|
C
|
A:ASN520
|
3.5
|
15.4
|
1.0
|
|
CB
|
A:ASP516
|
3.8
|
19.0
|
1.0
|
|
CB
|
A:ASP564
|
3.8
|
14.8
|
1.0
|
|
ND2
|
A:ASN482
|
4.0
|
17.2
|
1.0
|
|
CA
|
A:ASN484
|
4.2
|
19.4
|
1.0
|
|
N
|
A:ASN484
|
4.2
|
21.6
|
1.0
|
|
CA
|
A:ASN520
|
4.3
|
19.0
|
1.0
|
|
CB
|
A:ASP514
|
4.3
|
19.3
|
1.0
|
|
OD1
|
A:ASP564
|
4.4
|
17.4
|
1.0
|
|
CB
|
A:ASN484
|
4.4
|
20.2
|
1.0
|
|
CB
|
A:ASN520
|
4.4
|
17.9
|
1.0
|
|
OD1
|
A:ASP516
|
4.5
|
17.8
|
1.0
|
|
N
|
A:ALA485
|
4.5
|
19.7
|
1.0
|
|
N
|
A:GLY521
|
4.5
|
16.4
|
1.0
|
|
CA
|
A:ALA485
|
4.6
|
19.9
|
1.0
|
|
CA
|
A:GLY521
|
4.7
|
18.9
|
1.0
|
|
CB
|
A:ASN482
|
4.7
|
20.9
|
1.0
|
|
CA
|
A:ASN482
|
4.8
|
20.2
|
1.0
|
|
C
|
A:ALA485
|
4.8
|
18.3
|
1.0
|
|
C
|
A:ASN482
|
4.9
|
18.2
|
1.0
|
|
N
|
A:ASP516
|
4.9
|
20.0
|
1.0
|
|
CA
|
A:ASP516
|
4.9
|
19.3
|
1.0
|
|
Calcium binding site 4 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 4 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca604
b:17.2
occ:1.00
|
O
|
A:HOH843
|
2.4
|
18.2
|
1.0
|
|
OE2
|
A:GLU501
|
2.4
|
17.7
|
1.0
|
|
OE1
|
A:GLU500
|
2.4
|
14.2
|
1.0
|
|
OE1
|
A:GLU551
|
2.4
|
17.9
|
1.0
|
|
OD1
|
A:ASN549
|
2.5
|
14.6
|
1.0
|
|
OE2
|
A:GLU588
|
2.5
|
20.5
|
1.0
|
|
OE1
|
A:GLU588
|
2.6
|
22.9
|
1.0
|
|
CD
|
A:GLU588
|
2.9
|
21.4
|
1.0
|
|
CD
|
A:GLU501
|
3.3
|
18.6
|
1.0
|
|
CD
|
A:GLU500
|
3.4
|
15.4
|
1.0
|
|
CG
|
A:ASN549
|
3.4
|
15.5
|
1.0
|
|
CD
|
A:GLU551
|
3.6
|
15.1
|
1.0
|
|
CG
|
A:GLU501
|
3.7
|
16.4
|
1.0
|
|
OE2
|
A:GLU500
|
3.7
|
14.6
|
1.0
|
|
O
|
A:HOH839
|
3.8
|
25.4
|
1.0
|
|
O
|
A:HOH723
|
3.9
|
36.2
|
1.0
|
|
CA
|
A:CA605
|
4.0
|
16.2
|
1.0
|
|
ND2
|
A:ASN549
|
4.2
|
18.5
|
1.0
|
|
CA
|
A:ASN549
|
4.2
|
14.2
|
1.0
|
|
CB
|
A:ASN549
|
4.3
|
14.4
|
1.0
|
|
N
|
A:ARG550
|
4.3
|
12.5
|
1.0
|
|
CG
|
A:GLU588
|
4.4
|
20.0
|
1.0
|
|
O
|
A:HOH702
|
4.4
|
31.5
|
1.0
|
|
CG
|
A:GLU551
|
4.5
|
16.1
|
1.0
|
|
OE1
|
A:GLU501
|
4.5
|
18.7
|
1.0
|
|
OE2
|
A:GLU551
|
4.5
|
15.9
|
1.0
|
|
C
|
A:ASN549
|
4.6
|
13.3
|
1.0
|
|
CG
|
A:GLU500
|
4.6
|
16.3
|
1.0
|
|
CB
|
A:GLU551
|
4.6
|
15.8
|
1.0
|
|
N
|
A:GLU551
|
4.6
|
17.7
|
1.0
|
|
OD1
|
A:ASP585
|
4.8
|
16.9
|
1.0
|
|
Calcium binding site 5 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 5 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca605
b:16.2
occ:1.00
|
OD1
|
A:ASP585
|
2.3
|
16.9
|
1.0
|
|
OD1
|
A:ASP582
|
2.3
|
15.7
|
1.0
|
|
O
|
A:ILE583
|
2.3
|
14.9
|
1.0
|
|
OE2
|
A:GLU500
|
2.4
|
14.6
|
1.0
|
|
OE2
|
A:GLU551
|
2.5
|
15.9
|
1.0
|
|
OE2
|
A:GLU588
|
2.5
|
20.5
|
1.0
|
|
OE1
|
A:GLU551
|
2.7
|
17.9
|
1.0
|
|
CD
|
A:GLU551
|
2.8
|
15.1
|
1.0
|
|
CG
|
A:ASP582
|
3.4
|
18.6
|
1.0
|
|
CD
|
A:GLU500
|
3.4
|
15.4
|
1.0
|
|
C
|
A:ILE583
|
3.5
|
16.2
|
1.0
|
|
CG
|
A:ASP585
|
3.5
|
16.6
|
1.0
|
|
CD
|
A:GLU588
|
3.7
|
21.4
|
1.0
|
|
OE1
|
A:GLU500
|
3.8
|
14.2
|
1.0
|
|
N
|
A:ILE583
|
3.9
|
17.5
|
1.0
|
|
CA
|
A:CA604
|
4.0
|
17.2
|
1.0
|
|
O
|
A:HOH776
|
4.0
|
20.8
|
1.0
|
|
OD2
|
A:ASP582
|
4.0
|
18.8
|
1.0
|
|
N
|
A:ASP585
|
4.1
|
15.6
|
1.0
|
|
CA
|
A:ILE583
|
4.2
|
16.1
|
1.0
|
|
CG
|
A:GLU551
|
4.2
|
16.1
|
1.0
|
|
OD2
|
A:ASP585
|
4.3
|
14.7
|
1.0
|
|
O
|
A:HOH839
|
4.3
|
25.4
|
1.0
|
|
CG
|
A:GLU588
|
4.4
|
20.0
|
1.0
|
|
CA
|
A:ASP585
|
4.4
|
16.9
|
1.0
|
|
C
|
A:ASP584
|
4.4
|
16.0
|
1.0
|
|
NE
|
A:ARG550
|
4.5
|
20.2
|
1.0
|
|
N
|
A:ASP584
|
4.5
|
17.6
|
1.0
|
|
CB
|
A:ASP585
|
4.5
|
16.2
|
1.0
|
|
CB
|
A:ASP582
|
4.5
|
15.1
|
1.0
|
|
CB
|
A:ILE583
|
4.6
|
18.8
|
1.0
|
|
CA
|
A:ASP582
|
4.6
|
15.9
|
1.0
|
|
OE1
|
A:GLU588
|
4.7
|
22.9
|
1.0
|
|
CA
|
A:ASP584
|
4.7
|
17.2
|
1.0
|
|
C
|
A:ASP582
|
4.7
|
17.9
|
1.0
|
|
CG
|
A:GLU500
|
4.7
|
16.3
|
1.0
|
|
NH1
|
A:ARG550
|
4.9
|
25.3
|
1.0
|
|
O
|
A:ASP584
|
4.9
|
18.1
|
1.0
|
|
CB
|
A:ARG550
|
5.0
|
16.4
|
1.0
|
|
Calcium binding site 6 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 6 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca601
b:25.2
occ:1.00
|
O
|
B:HOH765
|
2.3
|
32.5
|
1.0
|
|
OD2
|
B:ASP464
|
2.3
|
19.7
|
1.0
|
|
OD1
|
B:ASN368
|
2.4
|
36.4
|
1.0
|
|
OD2
|
B:ASP411
|
2.5
|
26.8
|
1.0
|
|
O
|
B:GLN370
|
2.5
|
23.2
|
1.0
|
|
OD2
|
B:ASP409
|
2.6
|
23.6
|
1.0
|
|
OD1
|
B:ASP409
|
2.6
|
23.7
|
1.0
|
|
CG
|
B:ASP409
|
2.9
|
24.4
|
1.0
|
|
CG
|
B:ASP464
|
3.2
|
21.5
|
1.0
|
|
CG
|
B:ASP411
|
3.5
|
37.9
|
1.0
|
|
CG
|
B:ASN368
|
3.6
|
30.1
|
1.0
|
|
C
|
B:GLN370
|
3.7
|
25.9
|
1.0
|
|
CB
|
B:ASP464
|
3.7
|
22.9
|
1.0
|
|
CB
|
B:ASP411
|
3.9
|
34.6
|
1.0
|
|
NE2
|
B:GLN467
|
4.0
|
30.0
|
1.0
|
|
N
|
B:GLN370
|
4.1
|
27.2
|
1.0
|
|
OD1
|
B:ASP464
|
4.3
|
24.2
|
1.0
|
|
ND2
|
B:ASN368
|
4.3
|
28.4
|
1.0
|
|
CA
|
B:ASN368
|
4.4
|
31.1
|
1.0
|
|
CA
|
B:GLN370
|
4.4
|
28.1
|
1.0
|
|
CB
|
B:ASP409
|
4.4
|
23.7
|
1.0
|
|
C
|
B:ASN368
|
4.6
|
32.5
|
1.0
|
|
O
|
B:HOH740
|
4.6
|
40.6
|
1.0
|
|
CB
|
B:ASN368
|
4.6
|
31.0
|
1.0
|
|
OD1
|
B:ASP411
|
4.7
|
36.8
|
1.0
|
|
N
|
B:SER371
|
4.7
|
23.6
|
1.0
|
|
N
|
B:ASN369
|
4.7
|
30.4
|
1.0
|
|
N
|
B:PRO372
|
4.7
|
22.7
|
1.0
|
|
CA
|
B:SER371
|
4.8
|
22.4
|
1.0
|
|
C
|
B:SER371
|
4.8
|
22.9
|
1.0
|
|
CD
|
B:PRO372
|
4.8
|
20.6
|
1.0
|
|
CB
|
B:GLN370
|
4.8
|
29.7
|
1.0
|
|
N
|
B:ASP411
|
5.0
|
30.9
|
1.0
|
|
O
|
B:ASN368
|
5.0
|
34.7
|
1.0
|
|
Calcium binding site 7 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 7 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca602
b:27.6
occ:1.00
|
OE2
|
B:GLU385
|
2.3
|
25.2
|
1.0
|
|
OD1
|
B:ASP480
|
2.3
|
23.0
|
1.0
|
|
OE2
|
B:GLU451
|
2.3
|
33.0
|
1.0
|
|
OD1
|
B:ASP516
|
2.3
|
21.4
|
1.0
|
|
OD1
|
B:ASP483
|
2.4
|
32.3
|
1.0
|
|
O
|
B:ALA481
|
2.5
|
33.1
|
1.0
|
|
OE1
|
B:GLU451
|
2.6
|
26.4
|
1.0
|
|
CD
|
B:GLU451
|
2.8
|
29.7
|
1.0
|
|
CG
|
B:ASP480
|
3.4
|
27.9
|
1.0
|
|
CD
|
B:GLU385
|
3.4
|
25.5
|
1.0
|
|
CG
|
B:ASP483
|
3.4
|
37.0
|
1.0
|
|
CG
|
B:ASP516
|
3.4
|
27.8
|
1.0
|
|
C
|
B:ALA481
|
3.8
|
28.1
|
1.0
|
|
OD2
|
B:ASP483
|
3.8
|
42.1
|
1.0
|
|
OE1
|
B:GLU385
|
3.9
|
25.0
|
1.0
|
|
NA
|
B:NA606
|
3.9
|
17.3
|
1.0
|
|
CB
|
B:ASP516
|
3.9
|
25.6
|
1.0
|
|
OD2
|
B:ASP480
|
3.9
|
25.3
|
1.0
|
|
N
|
B:ALA481
|
4.0
|
31.0
|
1.0
|
|
OD1
|
B:ASN484
|
4.0
|
31.7
|
1.0
|
|
CA
|
B:ASP516
|
4.1
|
21.8
|
1.0
|
|
N
|
B:ASP483
|
4.2
|
32.4
|
1.0
|
|
CG
|
B:GLU451
|
4.3
|
27.5
|
1.0
|
|
NE
|
B:ARG450
|
4.4
|
29.6
|
1.0
|
|
OD2
|
B:ASP516
|
4.5
|
25.1
|
1.0
|
|
CB
|
B:ASP480
|
4.5
|
29.0
|
1.0
|
|
CA
|
B:ALA481
|
4.5
|
30.4
|
1.0
|
|
CA
|
B:ASP480
|
4.5
|
27.4
|
1.0
|
|
CG
|
B:GLU385
|
4.6
|
20.3
|
1.0
|
|
CB
|
B:ASP483
|
4.6
|
36.5
|
1.0
|
|
C
|
B:ASP480
|
4.7
|
30.3
|
1.0
|
|
NH1
|
B:ARG450
|
4.8
|
33.0
|
1.0
|
|
N
|
B:ASN482
|
4.8
|
35.9
|
1.0
|
|
CA
|
B:ASN482
|
4.8
|
31.6
|
1.0
|
|
CA
|
B:ASP483
|
4.9
|
34.1
|
1.0
|
|
N
|
B:ASP516
|
5.0
|
24.3
|
1.0
|
|
CB
|
B:ARG450
|
5.0
|
32.4
|
1.0
|
|
O
|
B:HOH775
|
5.0
|
30.7
|
1.0
|
|
Calcium binding site 8 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 8 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca603
b:25.4
occ:1.00
|
OD1
|
B:ASN482
|
1.8
|
19.9
|
1.0
|
|
OD2
|
B:ASP516
|
2.3
|
25.1
|
1.0
|
|
O
|
B:ASN484
|
2.4
|
25.9
|
1.0
|
|
O
|
B:ASN520
|
2.4
|
22.3
|
1.0
|
|
OD2
|
B:ASP564
|
2.4
|
20.3
|
1.0
|
|
OD2
|
B:ASP514
|
2.5
|
32.1
|
1.0
|
|
OD1
|
B:ASP514
|
2.7
|
25.8
|
1.0
|
|
CG
|
B:ASP514
|
2.9
|
27.1
|
1.0
|
|
CG
|
B:ASN482
|
3.0
|
33.3
|
1.0
|
|
CG
|
B:ASP516
|
3.4
|
27.8
|
1.0
|
|
C
|
B:ASN484
|
3.4
|
29.1
|
1.0
|
|
CG
|
B:ASP564
|
3.5
|
23.5
|
1.0
|
|
C
|
B:ASN520
|
3.6
|
28.1
|
1.0
|
|
ND2
|
B:ASN482
|
3.8
|
41.1
|
1.0
|
|
CB
|
B:ASP516
|
3.8
|
25.6
|
1.0
|
|
CB
|
B:ASP564
|
3.9
|
22.3
|
1.0
|
|
CB
|
B:ASN482
|
4.2
|
37.6
|
1.0
|
|
CA
|
B:ASN484
|
4.3
|
31.7
|
1.0
|
|
N
|
B:ASN484
|
4.3
|
28.2
|
1.0
|
|
CB
|
B:ASP514
|
4.4
|
27.4
|
1.0
|
|
N
|
B:ALA485
|
4.4
|
28.0
|
1.0
|
|
CA
|
B:ASN520
|
4.4
|
29.0
|
1.0
|
|
CB
|
B:ASN520
|
4.4
|
30.3
|
1.0
|
|
OD1
|
B:ASP564
|
4.5
|
25.9
|
1.0
|
|
N
|
B:GLY521
|
4.5
|
24.9
|
1.0
|
|
CA
|
B:ALA485
|
4.5
|
26.9
|
1.0
|
|
OD1
|
B:ASP516
|
4.5
|
21.4
|
1.0
|
|
CB
|
B:ASN484
|
4.5
|
31.5
|
1.0
|
|
CA
|
B:ASN482
|
4.6
|
31.6
|
1.0
|
|
CA
|
B:GLY521
|
4.6
|
25.9
|
1.0
|
|
C
|
B:ASN482
|
4.9
|
32.0
|
1.0
|
|
N
|
B:ASP516
|
4.9
|
24.3
|
1.0
|
|
CA
|
B:ASP516
|
4.9
|
21.8
|
1.0
|
|
C
|
B:ALA485
|
4.9
|
29.9
|
1.0
|
|
Calcium binding site 9 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 9 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca604
b:26.1
occ:1.00
|
OD1
|
B:ASP585
|
2.3
|
28.8
|
1.0
|
|
O
|
B:ILE583
|
2.3
|
21.2
|
1.0
|
|
OE2
|
B:GLU500
|
2.4
|
21.1
|
1.0
|
|
OE2
|
B:GLU588
|
2.5
|
31.7
|
1.0
|
|
OE2
|
B:GLU551
|
2.5
|
25.4
|
1.0
|
|
OD1
|
B:ASP582
|
2.5
|
26.4
|
1.0
|
|
OE1
|
B:GLU551
|
2.7
|
25.6
|
1.0
|
|
CD
|
B:GLU551
|
2.9
|
24.8
|
1.0
|
|
CD
|
B:GLU500
|
3.4
|
28.5
|
1.0
|
|
C
|
B:ILE583
|
3.5
|
24.6
|
1.0
|
|
CG
|
B:ASP582
|
3.5
|
30.0
|
1.0
|
|
CG
|
B:ASP585
|
3.5
|
28.3
|
1.0
|
|
CD
|
B:GLU588
|
3.7
|
33.7
|
1.0
|
|
OE1
|
B:GLU500
|
3.8
|
25.0
|
1.0
|
|
CA
|
B:CA605
|
3.9
|
27.8
|
1.0
|
|
N
|
B:ILE583
|
3.9
|
28.3
|
1.0
|
|
OD2
|
B:ASP582
|
4.0
|
30.5
|
1.0
|
|
O
|
B:HOH758
|
4.0
|
30.6
|
1.0
|
|
N
|
B:ASP585
|
4.1
|
25.5
|
1.0
|
|
OD2
|
B:ASP585
|
4.2
|
23.3
|
1.0
|
|
CA
|
B:ILE583
|
4.2
|
27.2
|
1.0
|
|
CG
|
B:GLU551
|
4.3
|
27.0
|
1.0
|
|
CA
|
B:ASP585
|
4.4
|
25.8
|
1.0
|
|
C
|
B:ASP584
|
4.4
|
24.6
|
1.0
|
|
CG
|
B:GLU588
|
4.5
|
33.4
|
1.0
|
|
N
|
B:ASP584
|
4.5
|
25.1
|
1.0
|
|
NE
|
B:ARG550
|
4.5
|
35.0
|
1.0
|
|
CB
|
B:ASP585
|
4.5
|
26.2
|
1.0
|
|
OE1
|
B:GLU588
|
4.6
|
30.9
|
1.0
|
|
CB
|
B:ILE583
|
4.7
|
26.2
|
1.0
|
|
CB
|
B:ASP582
|
4.7
|
27.2
|
1.0
|
|
CA
|
B:ASP584
|
4.7
|
25.7
|
1.0
|
|
CA
|
B:ASP582
|
4.7
|
29.0
|
1.0
|
|
CG
|
B:GLU500
|
4.7
|
23.6
|
1.0
|
|
NH2
|
B:ARG550
|
4.8
|
30.0
|
1.0
|
|
C
|
B:ASP582
|
4.8
|
28.2
|
1.0
|
|
O
|
B:ASP584
|
4.8
|
24.7
|
1.0
|
|
CB
|
B:ARG550
|
4.9
|
25.0
|
1.0
|
|
Calcium binding site 10 out
of 10 in 8umz
Go back to
Calcium Binding Sites List in 8umz
Calcium binding site 10 out
of 10 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca605
b:27.8
occ:1.00
|
OE2
|
B:GLU501
|
2.2
|
33.7
|
1.0
|
|
O
|
B:HOH762
|
2.3
|
30.1
|
1.0
|
|
OE1
|
B:GLU551
|
2.3
|
25.6
|
1.0
|
|
OD1
|
B:ASN549
|
2.4
|
26.4
|
1.0
|
|
OE1
|
B:GLU500
|
2.5
|
25.0
|
1.0
|
|
OE1
|
B:GLU588
|
2.6
|
30.9
|
1.0
|
|
OE2
|
B:GLU588
|
2.6
|
31.7
|
1.0
|
|
CD
|
B:GLU588
|
3.0
|
33.7
|
1.0
|
|
CD
|
B:GLU501
|
3.2
|
30.2
|
1.0
|
|
CG
|
B:ASN549
|
3.3
|
25.6
|
1.0
|
|
CD
|
B:GLU500
|
3.4
|
28.5
|
1.0
|
|
CD
|
B:GLU551
|
3.6
|
24.8
|
1.0
|
|
CG
|
B:GLU501
|
3.6
|
28.6
|
1.0
|
|
OE2
|
B:GLU500
|
3.8
|
21.1
|
1.0
|
|
CA
|
B:CA604
|
3.9
|
26.1
|
1.0
|
|
ND2
|
B:ASN549
|
4.1
|
30.1
|
1.0
|
|
O
|
B:HOH743
|
4.2
|
27.2
|
1.0
|
|
CB
|
B:ASN549
|
4.2
|
24.1
|
1.0
|
|
N
|
B:ARG550
|
4.3
|
19.2
|
1.0
|
|
CA
|
B:ASN549
|
4.3
|
25.0
|
1.0
|
|
OE1
|
B:GLU501
|
4.4
|
33.5
|
1.0
|
|
CG
|
B:GLU551
|
4.4
|
27.0
|
1.0
|
|
OE2
|
B:GLU551
|
4.5
|
25.4
|
1.0
|
|
CB
|
B:GLU551
|
4.5
|
25.7
|
1.0
|
|
N
|
B:GLU551
|
4.5
|
22.3
|
1.0
|
|
CG
|
B:GLU588
|
4.5
|
33.4
|
1.0
|
|
C
|
B:ASN549
|
4.6
|
23.8
|
1.0
|
|
CG
|
B:GLU500
|
4.6
|
23.6
|
1.0
|
|
OD1
|
B:ASP585
|
4.7
|
28.8
|
1.0
|
|
O
|
B:HOH707
|
4.7
|
34.5
|
1.0
|
|
Reference:
P.De-La-Torre,
K.Martinez-Perez,
A.Indzhykulian.
Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection To Be Published.
Page generated: Wed Nov 27 16:37:32 2024
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