Calcium in PDB 5k8r: Structure of Human Clustered Protocadherin Gamma B3 EC1-4
Protein crystallography data
The structure of Structure of Human Clustered Protocadherin Gamma B3 EC1-4, PDB code: 5k8r
was solved by
J.M.Nicoludis,
B.E.Vogt,
R.Gaudet,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.35 /
2.50
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.881,
161.229,
53.659,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
20.5 /
25.9
|
Other elements in 5k8r:
The structure of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
(pdb code 5k8r). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the
Structure of Human Clustered Protocadherin Gamma B3 EC1-4, PDB code: 5k8r:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Calcium binding site 1 out
of 9 in 5k8r
Go back to
Calcium Binding Sites List in 5k8r
Calcium binding site 1 out
of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:32.5
occ:1.00
|
O
|
A:ASN99
|
2.4
|
28.6
|
1.0
|
|
OD2
|
A:ASP129
|
2.4
|
36.6
|
1.0
|
|
O
|
A:ASN135
|
2.4
|
26.6
|
1.0
|
|
OD1
|
A:ASN97
|
2.4
|
34.9
|
1.0
|
|
OD2
|
A:ASP131
|
2.5
|
33.0
|
1.0
|
|
OD1
|
A:ASP129
|
2.7
|
44.6
|
1.0
|
|
OD2
|
A:ASP186
|
2.7
|
47.2
|
1.0
|
|
CG
|
A:ASP129
|
2.9
|
33.2
|
1.0
|
|
CG
|
A:ASP131
|
3.5
|
34.0
|
1.0
|
|
C
|
A:ASN135
|
3.6
|
24.3
|
1.0
|
|
C
|
A:ASN99
|
3.6
|
45.1
|
1.0
|
|
CG
|
A:ASN97
|
3.6
|
30.0
|
1.0
|
|
CG
|
A:ASP186
|
3.6
|
43.7
|
1.0
|
|
CB
|
A:ASP131
|
3.9
|
30.5
|
1.0
|
|
CB
|
A:ASP186
|
3.9
|
42.6
|
1.0
|
|
ND2
|
A:ASN97
|
4.3
|
16.6
|
1.0
|
|
CB
|
A:ASP129
|
4.4
|
31.4
|
1.0
|
|
CA
|
A:ASN135
|
4.4
|
32.3
|
1.0
|
|
CB
|
A:ASN135
|
4.5
|
33.9
|
1.0
|
|
N
|
A:SER136
|
4.5
|
29.0
|
1.0
|
|
CA
|
A:ASN99
|
4.5
|
40.9
|
1.0
|
|
N
|
A:ASN99
|
4.5
|
44.8
|
1.0
|
|
CA
|
A:PRO100
|
4.5
|
33.2
|
1.0
|
|
N
|
A:PRO100
|
4.5
|
41.9
|
1.0
|
|
CA
|
A:SER136
|
4.5
|
32.4
|
1.0
|
|
C
|
A:PRO100
|
4.6
|
30.4
|
1.0
|
|
OD1
|
A:ASP131
|
4.6
|
29.7
|
1.0
|
|
CB
|
A:ASN99
|
4.6
|
38.7
|
1.0
|
|
OD1
|
A:ASP186
|
4.7
|
41.4
|
1.0
|
|
CD
|
A:PRO101
|
4.7
|
27.0
|
1.0
|
|
N
|
A:PRO101
|
4.7
|
27.0
|
1.0
|
|
CB
|
A:ASN97
|
4.8
|
32.6
|
1.0
|
|
CA
|
A:ASN97
|
4.8
|
32.8
|
1.0
|
|
NE2
|
A:GLN138
|
4.9
|
29.0
|
1.0
|
|
Calcium binding site 2 out
of 9 in 5k8r
Go back to
Calcium Binding Sites List in 5k8r
Calcium binding site 2 out
of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:42.4
occ:1.00
|
OD1
|
A:ASP61
|
2.4
|
34.1
|
1.0
|
|
OE1
|
A:GLU63
|
2.4
|
41.8
|
1.0
|
|
OD2
|
A:ASP98
|
2.4
|
40.6
|
1.0
|
|
OE2
|
A:GLU10
|
2.6
|
58.3
|
1.0
|
|
OE1
|
A:GLU9
|
2.7
|
26.3
|
1.0
|
|
CG
|
A:ASP98
|
3.3
|
29.6
|
1.0
|
|
OD1
|
A:ASP98
|
3.5
|
35.2
|
1.0
|
|
CD
|
A:GLU9
|
3.5
|
30.6
|
1.0
|
|
CD
|
A:GLU10
|
3.5
|
44.4
|
1.0
|
|
CG
|
A:ASP61
|
3.5
|
44.1
|
1.0
|
|
CG
|
A:GLU10
|
3.7
|
37.2
|
1.0
|
|
CD
|
A:GLU63
|
3.7
|
38.9
|
1.0
|
|
OE2
|
A:GLU9
|
3.8
|
42.2
|
1.0
|
|
CA
|
A:CA503
|
4.0
|
34.5
|
1.0
|
|
OD1
|
A:ASN99
|
4.2
|
45.8
|
1.0
|
|
N
|
A:ARG62
|
4.3
|
30.8
|
1.0
|
|
CA
|
A:ASP61
|
4.3
|
27.5
|
1.0
|
|
CB
|
A:ASP61
|
4.3
|
30.4
|
1.0
|
|
NH2
|
A:ARG59
|
4.4
|
43.9
|
1.0
|
|
OD2
|
A:ASP61
|
4.4
|
41.5
|
1.0
|
|
OE2
|
A:GLU63
|
4.5
|
38.1
|
1.0
|
|
N
|
A:GLU63
|
4.5
|
29.6
|
1.0
|
|
CG
|
A:GLU63
|
4.6
|
32.1
|
1.0
|
|
CG
|
A:GLU9
|
4.6
|
33.9
|
1.0
|
|
O
|
A:HOH674
|
4.6
|
36.0
|
1.0
|
|
CB
|
A:GLU63
|
4.6
|
31.6
|
1.0
|
|
C
|
A:ASP61
|
4.7
|
38.6
|
1.0
|
|
OE1
|
A:GLU10
|
4.7
|
40.8
|
1.0
|
|
CB
|
A:ASP98
|
4.7
|
28.9
|
1.0
|
|
Calcium binding site 3 out
of 9 in 5k8r
Go back to
Calcium Binding Sites List in 5k8r
Calcium binding site 3 out
of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:34.5
occ:1.00
|
O
|
A:ILE96
|
2.4
|
33.0
|
1.0
|
|
OE2
|
A:GLU63
|
2.4
|
38.1
|
1.0
|
|
OD1
|
A:ASP95
|
2.4
|
34.5
|
1.0
|
|
OD1
|
A:ASP98
|
2.5
|
35.2
|
1.0
|
|
OD1
|
A:ASP131
|
2.5
|
29.7
|
1.0
|
|
OE2
|
A:GLU9
|
2.5
|
42.2
|
1.0
|
|
OE1
|
A:GLU63
|
2.8
|
41.8
|
1.0
|
|
CD
|
A:GLU63
|
2.9
|
38.9
|
1.0
|
|
CG
|
A:ASP131
|
3.4
|
34.0
|
1.0
|
|
CD
|
A:GLU9
|
3.5
|
30.6
|
1.0
|
|
CG
|
A:ASP95
|
3.5
|
37.7
|
1.0
|
|
C
|
A:ILE96
|
3.6
|
32.7
|
1.0
|
|
CG
|
A:ASP98
|
3.6
|
29.6
|
1.0
|
|
N
|
A:ILE96
|
3.9
|
23.3
|
1.0
|
|
OE1
|
A:GLU9
|
4.0
|
26.3
|
1.0
|
|
OD1
|
A:ASN99
|
4.0
|
45.8
|
1.0
|
|
CA
|
A:CA502
|
4.0
|
42.4
|
1.0
|
|
OD2
|
A:ASP95
|
4.1
|
37.3
|
1.0
|
|
OD2
|
A:ASP98
|
4.1
|
40.6
|
1.0
|
|
OD2
|
A:ASP131
|
4.1
|
33.0
|
1.0
|
|
N
|
A:ASP98
|
4.2
|
27.7
|
1.0
|
|
CB
|
A:ASP131
|
4.2
|
30.5
|
1.0
|
|
CG
|
A:GLU63
|
4.3
|
32.1
|
1.0
|
|
CA
|
A:ILE96
|
4.3
|
31.5
|
1.0
|
|
CG1
|
A:ILE96
|
4.3
|
29.6
|
1.0
|
|
CA
|
A:ASP131
|
4.5
|
27.2
|
1.0
|
|
NE
|
A:ARG62
|
4.5
|
31.9
|
1.0
|
|
N
|
A:ASN97
|
4.6
|
32.6
|
1.0
|
|
CB
|
A:ASP95
|
4.7
|
35.8
|
1.0
|
|
C
|
A:ASP95
|
4.7
|
26.5
|
1.0
|
|
NH2
|
A:ARG62
|
4.7
|
45.0
|
1.0
|
|
CB
|
A:ASP98
|
4.8
|
28.9
|
1.0
|
|
CA
|
A:ASP95
|
4.8
|
29.5
|
1.0
|
|
CG
|
A:GLU9
|
4.8
|
33.9
|
1.0
|
|
CA
|
A:ASN97
|
4.8
|
32.8
|
1.0
|
|
CA
|
A:ASP98
|
4.9
|
35.0
|
1.0
|
|
CG
|
A:ASN99
|
5.0
|
39.6
|
1.0
|
|
Calcium binding site 4 out
of 9 in 5k8r
Go back to
Calcium Binding Sites List in 5k8r
Calcium binding site 4 out
of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca504
b:38.7
occ:1.00
|
O
|
A:ASN313
|
2.4
|
38.2
|
1.0
|
|
OD1
|
A:ASN311
|
2.5
|
51.4
|
1.0
|
|
OD1
|
A:ASP343
|
2.5
|
45.2
|
1.0
|
|
O
|
A:ASN349
|
2.5
|
49.1
|
1.0
|
|
OD2
|
A:ASP345
|
2.5
|
48.0
|
1.0
|
|
OD2
|
A:ASP343
|
2.6
|
54.3
|
1.0
|
|
OD2
|
A:ASP396
|
2.7
|
50.0
|
1.0
|
|
CG
|
A:ASP343
|
2.9
|
43.2
|
1.0
|
|
CG
|
A:ASP345
|
3.4
|
44.9
|
1.0
|
|
C
|
A:ASN349
|
3.6
|
41.8
|
1.0
|
|
C
|
A:ASN313
|
3.6
|
48.0
|
1.0
|
|
CG
|
A:ASP396
|
3.6
|
50.6
|
1.0
|
|
CG
|
A:ASN311
|
3.7
|
50.9
|
1.0
|
|
CB
|
A:ASP345
|
3.7
|
33.7
|
1.0
|
|
CB
|
A:ASP396
|
3.9
|
40.3
|
1.0
|
|
ND2
|
A:ASN311
|
4.3
|
36.9
|
1.0
|
|
CB
|
A:ASP343
|
4.3
|
35.2
|
1.0
|
|
CA
|
A:ASN349
|
4.4
|
46.9
|
1.0
|
|
N
|
A:ASN313
|
4.4
|
49.7
|
1.0
|
|
CA
|
A:ASN313
|
4.4
|
53.4
|
1.0
|
|
CB
|
A:ASN349
|
4.4
|
49.9
|
1.0
|
|
OD1
|
A:ASP345
|
4.5
|
46.8
|
1.0
|
|
CB
|
A:ASN313
|
4.5
|
59.0
|
1.0
|
|
N
|
A:GLY350
|
4.6
|
38.0
|
1.0
|
|
N
|
A:ALA314
|
4.6
|
41.4
|
1.0
|
|
N
|
A:ASP345
|
4.7
|
35.0
|
1.0
|
|
OD1
|
A:ASP396
|
4.7
|
54.9
|
1.0
|
|
CA
|
A:GLY350
|
4.7
|
30.5
|
1.0
|
|
CA
|
A:ALA314
|
4.8
|
34.4
|
1.0
|
|
CB
|
A:ASN311
|
4.8
|
52.0
|
1.0
|
|
CD
|
A:PRO315
|
4.8
|
55.7
|
1.0
|
|
CA
|
A:ASN311
|
4.8
|
42.5
|
1.0
|
|
CA
|
A:ASP345
|
4.8
|
32.9
|
1.0
|
|
C
|
A:ALA314
|
4.9
|
42.1
|
1.0
|
|
N
|
A:PRO315
|
4.9
|
50.3
|
1.0
|
|
Calcium binding site 5 out
of 9 in 5k8r
Go back to
Calcium Binding Sites List in 5k8r
Calcium binding site 5 out
of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca505
b:37.4
occ:1.00
|
O
|
A:GLU310
|
2.4
|
41.0
|
1.0
|
|
OE2
|
A:GLU223
|
2.5
|
58.5
|
1.0
|
|
OD1
|
A:ASP309
|
2.5
|
31.5
|
1.0
|
|
OE2
|
A:GLU280
|
2.5
|
51.4
|
1.0
|
|
OD1
|
A:ASP345
|
2.5
|
46.8
|
1.0
|
|
OD1
|
A:ASP312
|
2.7
|
31.1
|
1.0
|
|
OE1
|
A:GLU280
|
2.7
|
45.9
|
1.0
|
|
CD
|
A:GLU280
|
2.9
|
39.3
|
1.0
|
|
CG
|
A:ASP345
|
3.4
|
44.9
|
1.0
|
|
CD
|
A:GLU223
|
3.4
|
47.2
|
1.0
|
|
C
|
A:GLU310
|
3.6
|
42.3
|
1.0
|
|
OE1
|
A:GLU223
|
3.6
|
46.8
|
1.0
|
|
CA
|
A:CA506
|
3.7
|
47.1
|
1.0
|
|
CG
|
A:ASP309
|
3.7
|
41.3
|
1.0
|
|
N
|
A:GLU310
|
3.8
|
40.5
|
1.0
|
|
ND2
|
A:ASN313
|
3.9
|
65.0
|
1.0
|
|
CG
|
A:ASP312
|
3.9
|
44.8
|
1.0
|
|
CB
|
A:ASP345
|
4.1
|
33.7
|
1.0
|
|
OD2
|
A:ASP345
|
4.2
|
48.0
|
1.0
|
|
CA
|
A:GLU310
|
4.3
|
42.1
|
1.0
|
|
CA
|
A:ASP345
|
4.3
|
32.9
|
1.0
|
|
OD2
|
A:ASP309
|
4.3
|
37.4
|
1.0
|
|
N
|
A:ASP312
|
4.3
|
37.3
|
1.0
|
|
CG
|
A:GLU280
|
4.4
|
30.1
|
1.0
|
|
OD2
|
A:ASP312
|
4.5
|
44.3
|
1.0
|
|
CB
|
A:PHE279
|
4.6
|
45.6
|
1.0
|
|
CD2
|
A:PHE279
|
4.7
|
40.3
|
1.0
|
|
N
|
A:ASN311
|
4.7
|
47.3
|
1.0
|
|
C
|
A:ASP309
|
4.7
|
31.8
|
1.0
|
|
CA
|
A:ASP309
|
4.8
|
34.9
|
1.0
|
|
CB
|
A:ASP309
|
4.8
|
44.6
|
1.0
|
|
CG
|
A:GLU223
|
4.8
|
51.9
|
1.0
|
|
CB
|
A:GLU310
|
4.9
|
56.6
|
1.0
|
|
CA
|
A:ASN311
|
4.9
|
42.5
|
1.0
|
|
CB
|
A:ASP312
|
5.0
|
37.9
|
1.0
|
|
Calcium binding site 6 out
of 9 in 5k8r
Go back to
Calcium Binding Sites List in 5k8r
Calcium binding site 6 out
of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca506
b:47.1
occ:1.00
|
OE1
|
A:GLU280
|
2.4
|
45.9
|
1.0
|
|
OD2
|
A:ASP312
|
2.4
|
44.3
|
1.0
|
|
OE1
|
A:GLU223
|
2.5
|
46.8
|
1.0
|
|
OD1
|
A:ASP278
|
2.5
|
37.9
|
1.0
|
|
O
|
A:HOH609
|
2.5
|
38.9
|
1.0
|
|
OD1
|
A:ASP312
|
2.9
|
31.1
|
1.0
|
|
CG
|
A:ASP312
|
3.0
|
44.8
|
1.0
|
|
CD
|
A:GLU223
|
3.3
|
47.2
|
1.0
|
|
O
|
A:HOH685
|
3.5
|
40.6
|
1.0
|
|
OE2
|
A:GLU223
|
3.6
|
58.5
|
1.0
|
|
CD
|
A:GLU280
|
3.6
|
39.3
|
1.0
|
|
ND2
|
A:ASN313
|
3.7
|
65.0
|
1.0
|
|
CA
|
A:CA505
|
3.7
|
37.4
|
1.0
|
|
CG
|
A:ASP278
|
3.7
|
43.2
|
1.0
|
|
N
|
A:PHE279
|
4.3
|
41.3
|
1.0
|
|
O
|
A:HOH688
|
4.4
|
38.1
|
1.0
|
|
OE2
|
A:GLU280
|
4.4
|
51.4
|
1.0
|
|
N
|
A:GLU280
|
4.5
|
40.3
|
1.0
|
|
CG
|
A:GLU223
|
4.5
|
51.9
|
1.0
|
|
OD2
|
A:ASP278
|
4.5
|
35.2
|
1.0
|
|
CA
|
A:ASP278
|
4.5
|
47.1
|
1.0
|
|
CG
|
A:GLU280
|
4.5
|
30.1
|
1.0
|
|
CB
|
A:ASP312
|
4.5
|
37.9
|
1.0
|
|
CB
|
A:GLU280
|
4.6
|
33.3
|
1.0
|
|
CB
|
A:ASP278
|
4.7
|
45.7
|
1.0
|
|
C
|
A:ASP278
|
4.8
|
44.5
|
1.0
|
|
CG
|
A:ASN313
|
4.9
|
63.8
|
1.0
|
|
CB
|
A:GLU223
|
5.0
|
44.9
|
1.0
|
|
Calcium binding site 7 out
of 9 in 5k8r
Go back to
Calcium Binding Sites List in 5k8r
Calcium binding site 7 out
of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca507
b:42.8
occ:1.00
|
O
|
A:ASN208
|
2.4
|
32.7
|
1.0
|
|
O
|
A:ASN244
|
2.4
|
49.1
|
1.0
|
|
OD1
|
A:ASN206
|
2.4
|
41.2
|
1.0
|
|
OD2
|
A:ASP238
|
2.4
|
53.8
|
1.0
|
|
OD1
|
A:ASP238
|
2.5
|
44.4
|
1.0
|
|
OD2
|
A:ASP293
|
2.7
|
36.5
|
1.0
|
|
CG
|
A:ASP238
|
2.8
|
45.4
|
1.0
|
|
OD2
|
A:ASP240
|
2.8
|
54.9
|
1.0
|
|
CG
|
A:ASP240
|
3.5
|
44.0
|
1.0
|
|
CG
|
A:ASN206
|
3.5
|
48.7
|
1.0
|
|
C
|
A:ASN208
|
3.6
|
42.5
|
1.0
|
|
C
|
A:ASN244
|
3.6
|
54.8
|
1.0
|
|
CG
|
A:ASP293
|
3.7
|
53.9
|
1.0
|
|
CB
|
A:ASP240
|
3.8
|
30.2
|
1.0
|
|
CB
|
A:ASP293
|
4.1
|
43.2
|
1.0
|
|
ND2
|
A:ASN206
|
4.1
|
63.3
|
1.0
|
|
CB
|
A:ASP238
|
4.3
|
40.5
|
1.0
|
|
CA
|
A:ASN244
|
4.3
|
44.4
|
1.0
|
|
CB
|
A:ASN244
|
4.3
|
49.2
|
1.0
|
|
OD1
|
A:ASP240
|
4.3
|
49.5
|
1.0
|
|
CA
|
A:ASN208
|
4.4
|
42.0
|
1.0
|
|
N
|
A:ASN208
|
4.4
|
44.6
|
1.0
|
|
CB
|
A:ASN208
|
4.5
|
46.3
|
1.0
|
|
N
|
A:PRO209
|
4.5
|
46.9
|
1.0
|
|
CA
|
A:PRO209
|
4.6
|
41.2
|
1.0
|
|
N
|
A:ALA245
|
4.6
|
53.9
|
1.0
|
|
CA
|
A:ASN206
|
4.6
|
40.6
|
1.0
|
|
CB
|
A:ASN206
|
4.6
|
36.2
|
1.0
|
|
CA
|
A:ALA245
|
4.8
|
49.5
|
1.0
|
|
C
|
A:PRO209
|
4.8
|
45.0
|
1.0
|
|
OD1
|
A:ASP293
|
4.8
|
58.9
|
1.0
|
|
N
|
A:ASP240
|
4.8
|
42.4
|
1.0
|
|
CD2
|
A:HIS297
|
4.8
|
46.3
|
1.0
|
|
C
|
A:ASN206
|
4.9
|
44.1
|
1.0
|
|
CA
|
A:ASP240
|
5.0
|
38.7
|
1.0
|
|
Calcium binding site 8 out
of 9 in 5k8r
Go back to
Calcium Binding Sites List in 5k8r
Calcium binding site 8 out
of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca508
b:51.6
occ:1.00
|
OE1
|
A:GLU173
|
1.8
|
41.0
|
1.0
|
|
OD1
|
A:ASP171
|
2.4
|
38.5
|
1.0
|
|
O
|
A:HOH663
|
2.5
|
38.4
|
1.0
|
|
OD2
|
A:ASP207
|
2.5
|
56.4
|
1.0
|
|
OE1
|
A:GLU114
|
2.5
|
43.7
|
1.0
|
|
CD
|
A:GLU173
|
2.8
|
43.7
|
1.0
|
|
CG
|
A:ASP207
|
3.0
|
50.2
|
1.0
|
|
OD1
|
A:ASP207
|
3.1
|
50.0
|
1.0
|
|
OE2
|
A:GLU173
|
3.2
|
43.6
|
1.0
|
|
CG
|
A:ASP171
|
3.5
|
48.5
|
1.0
|
|
CD
|
A:GLU114
|
3.5
|
39.6
|
1.0
|
|
CA
|
A:CA509
|
3.8
|
44.6
|
1.0
|
|
ND2
|
A:ASN208
|
4.0
|
51.3
|
1.0
|
|
OE2
|
A:GLU114
|
4.0
|
55.5
|
1.0
|
|
CG
|
A:GLU173
|
4.1
|
39.2
|
1.0
|
|
CA
|
A:ASP171
|
4.2
|
34.0
|
1.0
|
|
OD2
|
A:ASP171
|
4.2
|
44.1
|
1.0
|
|
CB
|
A:ASP171
|
4.3
|
43.1
|
1.0
|
|
CB
|
A:ASP207
|
4.3
|
39.8
|
1.0
|
|
CB
|
A:GLU173
|
4.5
|
36.2
|
1.0
|
|
N
|
A:ARG172
|
4.5
|
38.4
|
1.0
|
|
CG
|
A:GLU114
|
4.5
|
43.2
|
1.0
|
|
N
|
A:GLU173
|
4.6
|
41.7
|
1.0
|
|
C
|
A:ASP171
|
4.7
|
37.8
|
1.0
|
|
CB
|
A:GLU114
|
4.8
|
40.3
|
1.0
|
|
Calcium binding site 9 out
of 9 in 5k8r
Go back to
Calcium Binding Sites List in 5k8r
Calcium binding site 9 out
of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca509
b:44.6
occ:1.00
|
OE2
|
A:GLU173
|
1.8
|
43.6
|
1.0
|
|
OE2
|
A:GLU114
|
2.4
|
55.5
|
1.0
|
|
O
|
A:ALA205
|
2.4
|
44.1
|
1.0
|
|
OD1
|
A:ASP207
|
2.5
|
50.0
|
1.0
|
|
OD1
|
A:ASP204
|
2.6
|
42.3
|
1.0
|
|
OD1
|
A:ASP240
|
2.8
|
49.5
|
1.0
|
|
CD
|
A:GLU173
|
2.9
|
43.7
|
1.0
|
|
CD
|
A:GLU114
|
3.3
|
39.6
|
1.0
|
|
CG
|
A:ASP207
|
3.3
|
50.2
|
1.0
|
|
CG
|
A:ASP240
|
3.3
|
44.0
|
1.0
|
|
OE1
|
A:GLU114
|
3.5
|
43.7
|
1.0
|
|
ND2
|
A:ASN208
|
3.5
|
51.3
|
1.0
|
|
OD2
|
A:ASP207
|
3.5
|
56.4
|
1.0
|
|
OE1
|
A:GLU173
|
3.6
|
41.0
|
1.0
|
|
C
|
A:ALA205
|
3.6
|
49.2
|
1.0
|
|
CG
|
A:ASP204
|
3.7
|
53.6
|
1.0
|
|
CA
|
A:CA508
|
3.8
|
51.6
|
1.0
|
|
N
|
A:ALA205
|
3.8
|
43.3
|
1.0
|
|
OD2
|
A:ASP240
|
3.8
|
54.9
|
1.0
|
|
CB
|
A:ASP240
|
4.0
|
30.2
|
1.0
|
|
CG
|
A:GLU173
|
4.1
|
39.2
|
1.0
|
|
N
|
A:ASP207
|
4.1
|
41.5
|
1.0
|
|
OD2
|
A:ASP204
|
4.3
|
54.9
|
1.0
|
|
CA
|
A:ALA205
|
4.3
|
49.3
|
1.0
|
|
CA
|
A:ASP240
|
4.3
|
38.7
|
1.0
|
|
CB
|
A:ASP207
|
4.6
|
39.8
|
1.0
|
|
CG
|
A:GLU114
|
4.6
|
43.2
|
1.0
|
|
N
|
A:ASN206
|
4.7
|
43.7
|
1.0
|
|
CG
|
A:ASN208
|
4.7
|
48.4
|
1.0
|
|
C
|
A:ASP204
|
4.8
|
37.0
|
1.0
|
|
NE
|
A:ARG172
|
4.8
|
60.1
|
1.0
|
|
CA
|
A:ASP204
|
4.8
|
36.5
|
1.0
|
|
CA
|
A:ASP207
|
4.8
|
39.4
|
1.0
|
|
CB
|
A:ASP204
|
4.8
|
37.0
|
1.0
|
|
CB
|
A:ALA205
|
4.9
|
46.5
|
1.0
|
|
CA
|
A:ASN206
|
4.9
|
40.6
|
1.0
|
|
N
|
A:ASN208
|
5.0
|
44.6
|
1.0
|
|
Reference:
J.M.Nicoludis,
B.E.Vogt,
A.G.Green,
C.P.Scharfe,
D.S.Marks,
R.Gaudet.
Antiparallel Protocadherin Homodimers Use Distinct Affinity- and Specificity-Mediating Regions in Cadherin Repeats 1-4. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27472898
DOI: 10.7554/ELIFE.18449
Page generated: Wed Jul 9 07:19:52 2025
|
