Calcium in PDB 7aml: Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
Enzymatic activity of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
All present enzymatic activity of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure:
2.7.10.1;
Calcium Binding Sites:
The binding sites of Calcium atom in the Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
(pdb code 7aml). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure, PDB code: 7aml:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 7aml
Go back to
Calcium Binding Sites List in 7aml
Calcium binding site 1 out
of 8 in the Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca701
b:30.9
occ:1.00
|
OD2
|
A:ASP253
|
2.3
|
32.6
|
1.0
|
|
OE1
|
A:GLU164
|
2.3
|
35.3
|
1.0
|
|
OE1
|
A:GLU218
|
2.3
|
34.0
|
1.0
|
|
OD1
|
A:ASN165
|
2.3
|
38.3
|
1.0
|
|
OD1
|
A:ASP216
|
2.3
|
35.2
|
1.0
|
|
CD
|
A:GLU164
|
2.5
|
35.3
|
1.0
|
|
OE2
|
A:GLU164
|
2.6
|
35.3
|
1.0
|
|
CG
|
A:ASP253
|
2.8
|
32.6
|
1.0
|
|
OD1
|
A:ASP253
|
2.8
|
32.6
|
1.0
|
|
HD21
|
A:ASN165
|
3.1
|
38.3
|
1.0
|
|
CG
|
A:ASN165
|
3.3
|
38.3
|
1.0
|
|
CD
|
A:GLU218
|
3.5
|
34.0
|
1.0
|
|
CG
|
A:ASP216
|
3.5
|
35.2
|
1.0
|
|
ND2
|
A:ASN165
|
3.6
|
38.3
|
1.0
|
|
HG3
|
A:GLU164
|
3.6
|
35.3
|
1.0
|
|
CG
|
A:GLU164
|
3.7
|
35.3
|
1.0
|
|
H
|
A:ARG217
|
3.7
|
32.5
|
1.0
|
|
HA
|
A:ASP216
|
3.7
|
35.2
|
1.0
|
|
H
|
A:GLU218
|
3.8
|
34.0
|
1.0
|
|
HB2
|
A:GLU164
|
3.9
|
35.3
|
1.0
|
|
OE2
|
A:GLU218
|
3.9
|
34.0
|
1.0
|
|
CA
|
A:CA702
|
4.1
|
21.9
|
1.0
|
|
CB
|
A:ASP253
|
4.1
|
32.6
|
1.0
|
|
HB2
|
A:GLU218
|
4.2
|
34.0
|
1.0
|
|
N
|
A:ARG217
|
4.3
|
32.5
|
1.0
|
|
HB3
|
A:ASP253
|
4.3
|
32.6
|
1.0
|
|
OD2
|
A:ASP216
|
4.3
|
35.2
|
1.0
|
|
CB
|
A:GLU164
|
4.3
|
35.3
|
1.0
|
|
HB3
|
A:ARG217
|
4.4
|
32.5
|
1.0
|
|
HG2
|
A:GLU164
|
4.4
|
35.3
|
1.0
|
|
CA
|
A:ASP216
|
4.4
|
35.2
|
1.0
|
|
HD22
|
A:ASN165
|
4.4
|
38.3
|
1.0
|
|
OD1
|
A:ASN254
|
4.4
|
30.4
|
1.0
|
|
CB
|
A:ASP216
|
4.4
|
35.2
|
1.0
|
|
HB2
|
A:ASP253
|
4.4
|
32.6
|
1.0
|
|
HB2
|
A:ASP216
|
4.6
|
35.2
|
1.0
|
|
N
|
A:GLU218
|
4.6
|
34.0
|
1.0
|
|
CB
|
A:ASN165
|
4.7
|
38.3
|
1.0
|
|
CG
|
A:GLU218
|
4.7
|
34.0
|
1.0
|
|
HG2
|
A:GLU251
|
4.7
|
34.8
|
1.0
|
|
C
|
A:ASP216
|
4.7
|
35.2
|
1.0
|
|
HB2
|
A:ASN165
|
4.8
|
38.3
|
1.0
|
|
O
|
A:GLU251
|
4.8
|
34.8
|
1.0
|
|
HG3
|
A:GLU251
|
4.8
|
34.8
|
1.0
|
|
HB3
|
A:GLU164
|
4.9
|
35.3
|
1.0
|
|
H
|
A:ASP253
|
4.9
|
32.6
|
1.0
|
|
CB
|
A:GLU218
|
4.9
|
34.0
|
1.0
|
|
Calcium binding site 2 out
of 8 in 7aml
Go back to
Calcium Binding Sites List in 7aml
Calcium binding site 2 out
of 8 in the Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca702
b:21.9
occ:1.00
|
OD1
|
A:ASP250
|
2.4
|
29.2
|
1.0
|
|
O
|
A:GLU251
|
2.4
|
34.8
|
1.0
|
|
OE2
|
A:GLU218
|
2.4
|
34.0
|
1.0
|
|
OD1
|
A:ASP253
|
2.4
|
32.6
|
1.0
|
|
OD2
|
A:ASP250
|
2.4
|
29.2
|
1.0
|
|
OE2
|
A:GLU164
|
2.5
|
35.3
|
1.0
|
|
OD1
|
A:ASP287
|
2.5
|
29.0
|
1.0
|
|
CG
|
A:ASP250
|
2.7
|
29.2
|
1.0
|
|
H
|
A:ASP253
|
2.9
|
32.6
|
1.0
|
|
CD
|
A:GLU218
|
3.4
|
34.0
|
1.0
|
|
C
|
A:GLU251
|
3.5
|
34.8
|
1.0
|
|
CD
|
A:GLU164
|
3.6
|
35.3
|
1.0
|
|
CG
|
A:ASP287
|
3.7
|
29.0
|
1.0
|
|
CG
|
A:ASP253
|
3.7
|
32.6
|
1.0
|
|
HA
|
A:ASP287
|
3.7
|
29.0
|
1.0
|
|
OE1
|
A:GLU218
|
3.7
|
34.0
|
1.0
|
|
HA
|
A:ASP252
|
3.7
|
31.6
|
1.0
|
|
H
|
A:GLU251
|
3.8
|
34.8
|
1.0
|
|
N
|
A:ASP253
|
3.8
|
32.6
|
1.0
|
|
N
|
A:GLU251
|
4.1
|
34.8
|
1.0
|
|
CA
|
A:CA701
|
4.1
|
30.9
|
1.0
|
|
OD1
|
A:ASN254
|
4.1
|
30.4
|
1.0
|
|
CB
|
A:ASP250
|
4.1
|
29.2
|
1.0
|
|
OE1
|
A:GLU164
|
4.1
|
35.3
|
1.0
|
|
HA
|
A:ASP250
|
4.2
|
29.2
|
1.0
|
|
HB2
|
A:ASN254
|
4.3
|
30.4
|
1.0
|
|
N
|
A:ASP252
|
4.3
|
31.6
|
1.0
|
|
CA
|
A:ASP252
|
4.4
|
31.6
|
1.0
|
|
HD2
|
A:ARG217
|
4.4
|
32.5
|
1.0
|
|
OD2
|
A:ASP253
|
4.4
|
32.6
|
1.0
|
|
H
|
A:ASN254
|
4.4
|
30.4
|
1.0
|
|
CA
|
A:GLU251
|
4.5
|
34.8
|
1.0
|
|
CA
|
A:ASP287
|
4.5
|
29.0
|
1.0
|
|
CB
|
A:ASP287
|
4.5
|
29.0
|
1.0
|
|
OD2
|
A:ASP287
|
4.5
|
29.0
|
1.0
|
|
HB3
|
A:ASP287
|
4.5
|
29.0
|
1.0
|
|
HB2
|
A:ASP250
|
4.5
|
29.2
|
1.0
|
|
CA
|
A:ASP250
|
4.5
|
29.2
|
1.0
|
|
HG3
|
A:GLU251
|
4.5
|
34.8
|
1.0
|
|
C
|
A:ASP252
|
4.6
|
31.6
|
1.0
|
|
C
|
A:ASP250
|
4.6
|
29.2
|
1.0
|
|
HB3
|
A:ARG217
|
4.6
|
32.5
|
1.0
|
|
CA
|
A:ASP253
|
4.6
|
32.6
|
1.0
|
|
CB
|
A:ASP253
|
4.7
|
32.6
|
1.0
|
|
CG
|
A:ASN254
|
4.7
|
30.4
|
1.0
|
|
HB3
|
A:ASP250
|
4.7
|
29.2
|
1.0
|
|
HG2
|
A:GLU164
|
4.7
|
35.3
|
1.0
|
|
N
|
A:ASN254
|
4.7
|
30.4
|
1.0
|
|
CG
|
A:GLU218
|
4.8
|
34.0
|
1.0
|
|
CG
|
A:GLU164
|
4.8
|
35.3
|
1.0
|
|
HB3
|
A:ASP253
|
4.8
|
32.6
|
1.0
|
|
HG3
|
A:GLU218
|
4.9
|
34.0
|
1.0
|
|
HH11
|
A:ARG217
|
4.9
|
32.5
|
1.0
|
|
C
|
A:ASP253
|
4.9
|
32.6
|
1.0
|
|
HG2
|
A:GLU251
|
4.9
|
34.8
|
1.0
|
|
CB
|
A:ASN254
|
5.0
|
30.4
|
1.0
|
|
Calcium binding site 3 out
of 8 in 7aml
Go back to
Calcium Binding Sites List in 7aml
Calcium binding site 3 out
of 8 in the Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca703
b:16.1
occ:1.00
|
OD2
|
A:ASP285
|
2.3
|
25.5
|
1.0
|
|
OD1
|
A:ASP252
|
2.3
|
31.6
|
1.0
|
|
OD2
|
A:ASP287
|
2.5
|
29.0
|
1.0
|
|
OD1
|
A:ASP285
|
2.5
|
25.5
|
1.0
|
|
OD1
|
A:ASN299
|
2.6
|
25.8
|
1.0
|
|
O
|
A:ASN254
|
2.6
|
30.4
|
1.0
|
|
OD2
|
A:ASP363
|
2.7
|
33.3
|
1.0
|
|
CG
|
A:ASP285
|
2.7
|
25.5
|
1.0
|
|
CG
|
A:ASP252
|
3.0
|
31.6
|
1.0
|
|
OD2
|
A:ASP252
|
3.1
|
31.6
|
1.0
|
|
HB2
|
A:ASP287
|
3.3
|
29.0
|
1.0
|
|
CG
|
A:ASP363
|
3.4
|
33.3
|
1.0
|
|
CG
|
A:ASP287
|
3.5
|
29.0
|
1.0
|
|
OD1
|
A:ASP363
|
3.6
|
33.3
|
1.0
|
|
HD2
|
A:PHE366
|
3.7
|
33.5
|
1.0
|
|
CG
|
A:ASN299
|
3.8
|
25.8
|
1.0
|
|
C
|
A:ASN254
|
3.9
|
30.4
|
1.0
|
|
HA
|
A:SER255
|
3.9
|
26.1
|
1.0
|
|
CB
|
A:ASP287
|
3.9
|
29.0
|
1.0
|
|
H
|
A:ASN254
|
4.1
|
30.4
|
1.0
|
|
HB2
|
A:PHE366
|
4.2
|
33.5
|
1.0
|
|
CB
|
A:ASP285
|
4.2
|
25.5
|
1.0
|
|
HA
|
A:ASN299
|
4.3
|
25.8
|
1.0
|
|
H
|
A:ASP287
|
4.3
|
29.0
|
1.0
|
|
CB
|
A:ASP252
|
4.3
|
31.6
|
1.0
|
|
HA
|
A:ASP252
|
4.4
|
31.6
|
1.0
|
|
HB3
|
A:ASP287
|
4.4
|
29.0
|
1.0
|
|
HB2
|
A:ASN299
|
4.5
|
25.8
|
1.0
|
|
HG1
|
A:THR365
|
4.5
|
34.7
|
1.0
|
|
HB2
|
A:ASP252
|
4.5
|
31.6
|
1.0
|
|
HB3
|
A:ASP285
|
4.5
|
25.5
|
1.0
|
|
CB
|
A:ASP363
|
4.6
|
33.3
|
1.0
|
|
OD1
|
A:ASP287
|
4.6
|
29.0
|
1.0
|
|
CD2
|
A:PHE366
|
4.6
|
33.5
|
1.0
|
|
HB2
|
A:ASP285
|
4.6
|
25.5
|
1.0
|
|
HD3
|
A:PRO256
|
4.6
|
25.6
|
1.0
|
|
HB3
|
A:ASP363
|
4.6
|
33.3
|
1.0
|
|
CB
|
A:ASN299
|
4.6
|
25.8
|
1.0
|
|
HD21
|
A:ASN299
|
4.7
|
25.8
|
1.0
|
|
HB2
|
A:ASN254
|
4.7
|
30.4
|
1.0
|
|
CA
|
A:SER255
|
4.7
|
26.1
|
1.0
|
|
HB2
|
A:ASP363
|
4.7
|
33.3
|
1.0
|
|
N
|
A:SER255
|
4.7
|
26.1
|
1.0
|
|
ND2
|
A:ASN299
|
4.7
|
25.8
|
1.0
|
|
N
|
A:ASN254
|
4.8
|
30.4
|
1.0
|
|
CA
|
A:ASP252
|
4.8
|
31.6
|
1.0
|
|
CA
|
A:ASN254
|
4.8
|
30.4
|
1.0
|
|
CA
|
A:ASN299
|
5.0
|
25.8
|
1.0
|
|
HA
|
A:ASP285
|
5.0
|
25.5
|
1.0
|
|
N
|
A:ASP287
|
5.0
|
29.0
|
1.0
|
|
Calcium binding site 4 out
of 8 in 7aml
Go back to
Calcium Binding Sites List in 7aml
Calcium binding site 4 out
of 8 in the Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca704
b:22.3
occ:1.00
|
O
|
A:THR559
|
2.2
|
14.7
|
1.0
|
|
O
|
A:TYR564
|
2.5
|
23.6
|
1.0
|
|
HA
|
A:CYS565
|
2.5
|
18.1
|
1.0
|
|
OD2
|
A:ASP579
|
2.6
|
14.4
|
1.0
|
|
HG3
|
A:GLU569
|
3.3
|
14.0
|
1.0
|
|
CG
|
A:ASP579
|
3.3
|
14.4
|
1.0
|
|
HB
|
A:THR559
|
3.4
|
14.7
|
1.0
|
|
C
|
A:THR559
|
3.4
|
14.7
|
1.0
|
|
CA
|
A:CYS565
|
3.5
|
18.1
|
1.0
|
|
C
|
A:TYR564
|
3.5
|
23.6
|
1.0
|
|
H
|
A:ASP566
|
3.6
|
17.2
|
1.0
|
|
HB3
|
A:ASP562
|
3.6
|
17.8
|
1.0
|
|
OE1
|
A:GLU569
|
3.7
|
14.0
|
1.0
|
|
OD1
|
A:ASP579
|
3.9
|
14.4
|
1.0
|
|
HA
|
A:CYS560
|
3.9
|
12.5
|
1.0
|
|
N
|
A:ASP566
|
4.0
|
17.2
|
1.0
|
|
N
|
A:CYS565
|
4.0
|
18.1
|
1.0
|
|
CD
|
A:GLU569
|
4.0
|
14.0
|
1.0
|
|
OD1
|
A:ASP566
|
4.1
|
17.2
|
1.0
|
|
C
|
A:CYS565
|
4.1
|
18.1
|
1.0
|
|
CB
|
A:THR559
|
4.1
|
14.7
|
1.0
|
|
CG
|
A:GLU569
|
4.1
|
14.0
|
1.0
|
|
HB2
|
A:ASP579
|
4.1
|
14.4
|
1.0
|
|
CG
|
A:ASP566
|
4.2
|
17.2
|
1.0
|
|
CA
|
A:THR559
|
4.2
|
14.7
|
1.0
|
|
HB3
|
A:CYS565
|
4.2
|
18.1
|
1.0
|
|
HA
|
A:THR559
|
4.2
|
14.7
|
1.0
|
|
OD2
|
A:ASP566
|
4.2
|
17.2
|
1.0
|
|
H
|
A:ASP562
|
4.2
|
17.8
|
1.0
|
|
O
|
A:CYS560
|
4.2
|
12.5
|
1.0
|
|
CB
|
A:ASP579
|
4.3
|
14.4
|
1.0
|
|
HB3
|
A:ASP579
|
4.4
|
14.4
|
1.0
|
|
N
|
A:CYS560
|
4.4
|
12.5
|
1.0
|
|
CA
|
A:CYS560
|
4.4
|
12.5
|
1.0
|
|
H
|
A:GLY563
|
4.5
|
18.4
|
1.0
|
|
CB
|
A:CYS565
|
4.5
|
18.1
|
1.0
|
|
OG1
|
A:THR559
|
4.5
|
14.7
|
1.0
|
|
C
|
A:CYS560
|
4.5
|
12.5
|
1.0
|
|
CB
|
A:ASP562
|
4.5
|
17.8
|
1.0
|
|
HB2
|
A:ASP562
|
4.7
|
17.8
|
1.0
|
|
H
|
A:TYR564
|
4.7
|
23.6
|
1.0
|
|
HG2
|
A:GLU569
|
4.7
|
14.0
|
1.0
|
|
HG1
|
A:THR559
|
4.8
|
14.7
|
1.0
|
|
N
|
A:ASP562
|
4.8
|
17.8
|
1.0
|
|
HB2
|
A:ASP566
|
4.8
|
17.2
|
1.0
|
|
CA
|
A:TYR564
|
4.8
|
23.6
|
1.0
|
|
OE2
|
A:GLU569
|
4.8
|
14.0
|
1.0
|
|
H
|
A:CYS565
|
4.8
|
18.1
|
1.0
|
|
N
|
A:TYR564
|
4.9
|
23.6
|
1.0
|
|
HB2
|
A:GLU569
|
4.9
|
14.0
|
1.0
|
|
HB2
|
A:CYS565
|
4.9
|
18.1
|
1.0
|
|
CB
|
A:ASP566
|
4.9
|
17.2
|
1.0
|
|
Calcium binding site 5 out
of 8 in 7aml
Go back to
Calcium Binding Sites List in 7aml
Calcium binding site 5 out
of 8 in the Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca701
b:32.7
occ:1.00
|
OD2
|
D:ASP253
|
2.3
|
31.5
|
1.0
|
|
OE1
|
D:GLU164
|
2.3
|
35.4
|
1.0
|
|
OE1
|
D:GLU218
|
2.3
|
34.9
|
1.0
|
|
OD1
|
D:ASN165
|
2.3
|
38.2
|
1.0
|
|
OD1
|
D:ASP216
|
2.3
|
35.8
|
1.0
|
|
CD
|
D:GLU164
|
2.5
|
35.4
|
1.0
|
|
OE2
|
D:GLU164
|
2.6
|
35.4
|
1.0
|
|
CG
|
D:ASP253
|
2.8
|
31.5
|
1.0
|
|
OD1
|
D:ASP253
|
2.8
|
31.5
|
1.0
|
|
HD21
|
D:ASN165
|
3.1
|
38.2
|
1.0
|
|
CG
|
D:ASN165
|
3.3
|
38.2
|
1.0
|
|
CD
|
D:GLU218
|
3.5
|
34.9
|
1.0
|
|
CG
|
D:ASP216
|
3.5
|
35.8
|
1.0
|
|
ND2
|
D:ASN165
|
3.6
|
38.2
|
1.0
|
|
HG3
|
D:GLU164
|
3.6
|
35.4
|
1.0
|
|
CG
|
D:GLU164
|
3.7
|
35.4
|
1.0
|
|
H
|
D:ARG217
|
3.7
|
32.4
|
1.0
|
|
HA
|
D:ASP216
|
3.7
|
35.8
|
1.0
|
|
H
|
D:GLU218
|
3.8
|
34.9
|
1.0
|
|
HB2
|
D:GLU164
|
3.9
|
35.4
|
1.0
|
|
OE2
|
D:GLU218
|
3.9
|
34.9
|
1.0
|
|
CA
|
D:CA702
|
4.1
|
22.6
|
1.0
|
|
CB
|
D:ASP253
|
4.1
|
31.5
|
1.0
|
|
HB2
|
D:GLU218
|
4.2
|
34.9
|
1.0
|
|
N
|
D:ARG217
|
4.3
|
32.4
|
1.0
|
|
HB3
|
D:ASP253
|
4.3
|
31.5
|
1.0
|
|
OD2
|
D:ASP216
|
4.3
|
35.8
|
1.0
|
|
CB
|
D:GLU164
|
4.3
|
35.4
|
1.0
|
|
HB3
|
D:ARG217
|
4.4
|
32.4
|
1.0
|
|
HG2
|
D:GLU164
|
4.4
|
35.4
|
1.0
|
|
CA
|
D:ASP216
|
4.4
|
35.8
|
1.0
|
|
HD22
|
D:ASN165
|
4.4
|
38.2
|
1.0
|
|
OD1
|
D:ASN254
|
4.4
|
28.9
|
1.0
|
|
CB
|
D:ASP216
|
4.4
|
35.8
|
1.0
|
|
HB2
|
D:ASP253
|
4.4
|
31.5
|
1.0
|
|
HB2
|
D:ASP216
|
4.6
|
35.8
|
1.0
|
|
N
|
D:GLU218
|
4.6
|
34.9
|
1.0
|
|
CB
|
D:ASN165
|
4.7
|
38.2
|
1.0
|
|
CG
|
D:GLU218
|
4.7
|
34.9
|
1.0
|
|
HG2
|
D:GLU251
|
4.7
|
33.6
|
1.0
|
|
C
|
D:ASP216
|
4.7
|
35.8
|
1.0
|
|
HB2
|
D:ASN165
|
4.8
|
38.2
|
1.0
|
|
O
|
D:GLU251
|
4.8
|
33.6
|
1.0
|
|
HG3
|
D:GLU251
|
4.8
|
33.6
|
1.0
|
|
HB3
|
D:GLU164
|
4.9
|
35.4
|
1.0
|
|
H
|
D:ASP253
|
4.9
|
31.5
|
1.0
|
|
CB
|
D:GLU218
|
4.9
|
34.9
|
1.0
|
|
Calcium binding site 6 out
of 8 in 7aml
Go back to
Calcium Binding Sites List in 7aml
Calcium binding site 6 out
of 8 in the Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca702
b:22.6
occ:1.00
|
OD1
|
D:ASP250
|
2.4
|
29.6
|
1.0
|
|
O
|
D:GLU251
|
2.4
|
33.6
|
1.0
|
|
OE2
|
D:GLU218
|
2.4
|
34.9
|
1.0
|
|
OD1
|
D:ASP253
|
2.4
|
31.5
|
1.0
|
|
OD2
|
D:ASP250
|
2.4
|
29.6
|
1.0
|
|
OE2
|
D:GLU164
|
2.5
|
35.4
|
1.0
|
|
OD1
|
D:ASP287
|
2.5
|
28.3
|
1.0
|
|
CG
|
D:ASP250
|
2.7
|
29.6
|
1.0
|
|
H
|
D:ASP253
|
2.9
|
31.5
|
1.0
|
|
CD
|
D:GLU218
|
3.4
|
34.9
|
1.0
|
|
C
|
D:GLU251
|
3.5
|
33.6
|
1.0
|
|
CD
|
D:GLU164
|
3.6
|
35.4
|
1.0
|
|
CG
|
D:ASP287
|
3.7
|
28.3
|
1.0
|
|
CG
|
D:ASP253
|
3.7
|
31.5
|
1.0
|
|
HA
|
D:ASP287
|
3.7
|
28.3
|
1.0
|
|
OE1
|
D:GLU218
|
3.7
|
34.9
|
1.0
|
|
HA
|
D:ASP252
|
3.7
|
30.7
|
1.0
|
|
H
|
D:GLU251
|
3.8
|
33.6
|
1.0
|
|
N
|
D:ASP253
|
3.8
|
31.5
|
1.0
|
|
N
|
D:GLU251
|
4.1
|
33.6
|
1.0
|
|
CA
|
D:CA701
|
4.1
|
32.7
|
1.0
|
|
OD1
|
D:ASN254
|
4.1
|
28.9
|
1.0
|
|
CB
|
D:ASP250
|
4.1
|
29.6
|
1.0
|
|
OE1
|
D:GLU164
|
4.1
|
35.4
|
1.0
|
|
HA
|
D:ASP250
|
4.2
|
29.6
|
1.0
|
|
HB2
|
D:ASN254
|
4.3
|
28.9
|
1.0
|
|
N
|
D:ASP252
|
4.3
|
30.7
|
1.0
|
|
CA
|
D:ASP252
|
4.4
|
30.7
|
1.0
|
|
HD2
|
D:ARG217
|
4.4
|
32.4
|
1.0
|
|
H
|
D:ASN254
|
4.4
|
28.9
|
1.0
|
|
OD2
|
D:ASP253
|
4.4
|
31.5
|
1.0
|
|
CA
|
D:GLU251
|
4.5
|
33.6
|
1.0
|
|
CB
|
D:ASP287
|
4.5
|
28.3
|
1.0
|
|
CA
|
D:ASP287
|
4.5
|
28.3
|
1.0
|
|
OD2
|
D:ASP287
|
4.5
|
28.3
|
1.0
|
|
HB2
|
D:ASP250
|
4.5
|
29.6
|
1.0
|
|
HB3
|
D:ASP287
|
4.5
|
28.3
|
1.0
|
|
CA
|
D:ASP250
|
4.5
|
29.6
|
1.0
|
|
HG3
|
D:GLU251
|
4.5
|
33.6
|
1.0
|
|
C
|
D:ASP252
|
4.6
|
30.7
|
1.0
|
|
C
|
D:ASP250
|
4.6
|
29.6
|
1.0
|
|
HB3
|
D:ARG217
|
4.6
|
32.4
|
1.0
|
|
CA
|
D:ASP253
|
4.6
|
31.5
|
1.0
|
|
CB
|
D:ASP253
|
4.7
|
31.5
|
1.0
|
|
CG
|
D:ASN254
|
4.7
|
28.9
|
1.0
|
|
HB3
|
D:ASP250
|
4.7
|
29.6
|
1.0
|
|
HG2
|
D:GLU164
|
4.7
|
35.4
|
1.0
|
|
N
|
D:ASN254
|
4.7
|
28.9
|
1.0
|
|
CG
|
D:GLU218
|
4.8
|
34.9
|
1.0
|
|
CG
|
D:GLU164
|
4.8
|
35.4
|
1.0
|
|
HB3
|
D:ASP253
|
4.8
|
31.5
|
1.0
|
|
HG3
|
D:GLU218
|
4.9
|
34.9
|
1.0
|
|
HH11
|
D:ARG217
|
4.9
|
32.4
|
1.0
|
|
C
|
D:ASP253
|
4.9
|
31.5
|
1.0
|
|
HG2
|
D:GLU251
|
4.9
|
33.6
|
1.0
|
|
CB
|
D:ASN254
|
5.0
|
28.9
|
1.0
|
|
Calcium binding site 7 out
of 8 in 7aml
Go back to
Calcium Binding Sites List in 7aml
Calcium binding site 7 out
of 8 in the Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca703
b:13.4
occ:1.00
|
OD2
|
D:ASP285
|
2.3
|
24.6
|
1.0
|
|
OD1
|
D:ASP252
|
2.4
|
30.7
|
1.0
|
|
OD2
|
D:ASP287
|
2.5
|
28.3
|
1.0
|
|
OD1
|
D:ASP285
|
2.5
|
24.6
|
1.0
|
|
OD1
|
D:ASN299
|
2.6
|
25.5
|
1.0
|
|
O
|
D:ASN254
|
2.6
|
28.9
|
1.0
|
|
OD2
|
D:ASP363
|
2.7
|
32.8
|
1.0
|
|
CG
|
D:ASP285
|
2.7
|
24.6
|
1.0
|
|
CG
|
D:ASP252
|
3.0
|
30.7
|
1.0
|
|
OD2
|
D:ASP252
|
3.1
|
30.7
|
1.0
|
|
HB2
|
D:ASP287
|
3.3
|
28.3
|
1.0
|
|
CG
|
D:ASP363
|
3.4
|
32.8
|
1.0
|
|
CG
|
D:ASP287
|
3.5
|
28.3
|
1.0
|
|
OD1
|
D:ASP363
|
3.6
|
32.8
|
1.0
|
|
HD2
|
D:PHE366
|
3.7
|
33.1
|
1.0
|
|
CG
|
D:ASN299
|
3.8
|
25.5
|
1.0
|
|
C
|
D:ASN254
|
3.9
|
28.9
|
1.0
|
|
HA
|
D:SER255
|
3.9
|
25.1
|
1.0
|
|
CB
|
D:ASP287
|
3.9
|
28.3
|
1.0
|
|
H
|
D:ASN254
|
4.1
|
28.9
|
1.0
|
|
HB2
|
D:PHE366
|
4.2
|
33.1
|
1.0
|
|
CB
|
D:ASP285
|
4.2
|
24.6
|
1.0
|
|
HA
|
D:ASN299
|
4.3
|
25.5
|
1.0
|
|
H
|
D:ASP287
|
4.3
|
28.3
|
1.0
|
|
CB
|
D:ASP252
|
4.3
|
30.7
|
1.0
|
|
HA
|
D:ASP252
|
4.4
|
30.7
|
1.0
|
|
HB3
|
D:ASP287
|
4.4
|
28.3
|
1.0
|
|
HB2
|
D:ASN299
|
4.5
|
25.5
|
1.0
|
|
HB2
|
D:ASP252
|
4.5
|
30.7
|
1.0
|
|
HB3
|
D:ASP285
|
4.5
|
24.6
|
1.0
|
|
CB
|
D:ASP363
|
4.6
|
32.8
|
1.0
|
|
HG1
|
D:THR365
|
4.6
|
34.9
|
1.0
|
|
OD1
|
D:ASP287
|
4.6
|
28.3
|
1.0
|
|
CD2
|
D:PHE366
|
4.6
|
33.1
|
1.0
|
|
HB2
|
D:ASP285
|
4.6
|
24.6
|
1.0
|
|
HD3
|
D:PRO256
|
4.6
|
24.5
|
1.0
|
|
HB3
|
D:ASP363
|
4.6
|
32.8
|
1.0
|
|
CB
|
D:ASN299
|
4.6
|
25.5
|
1.0
|
|
HD21
|
D:ASN299
|
4.7
|
25.5
|
1.0
|
|
HB2
|
D:ASN254
|
4.7
|
28.9
|
1.0
|
|
CA
|
D:SER255
|
4.7
|
25.1
|
1.0
|
|
HB2
|
D:ASP363
|
4.7
|
32.8
|
1.0
|
|
N
|
D:SER255
|
4.7
|
25.1
|
1.0
|
|
ND2
|
D:ASN299
|
4.7
|
25.5
|
1.0
|
|
N
|
D:ASN254
|
4.8
|
28.9
|
1.0
|
|
CA
|
D:ASP252
|
4.8
|
30.7
|
1.0
|
|
CA
|
D:ASN254
|
4.8
|
28.9
|
1.0
|
|
CA
|
D:ASN299
|
5.0
|
25.5
|
1.0
|
|
HA
|
D:ASP285
|
5.0
|
24.6
|
1.0
|
|
N
|
D:ASP287
|
5.0
|
28.3
|
1.0
|
|
Calcium binding site 8 out
of 8 in 7aml
Go back to
Calcium Binding Sites List in 7aml
Calcium binding site 8 out
of 8 in the Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Ret/Gdnf/GFRA1 Extracellular Complex Cryo-Em Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca704
b:21.2
occ:1.00
|
OE2
|
D:GLU569
|
1.8
|
13.9
|
1.0
|
|
O
|
D:THR559
|
2.2
|
13.8
|
1.0
|
|
HA
|
D:CYS565
|
2.6
|
17.0
|
1.0
|
|
CD
|
D:GLU569
|
3.0
|
13.9
|
1.0
|
|
OD1
|
D:ASP566
|
3.2
|
16.2
|
1.0
|
|
HB3
|
D:ASP562
|
3.2
|
16.6
|
1.0
|
|
H
|
D:ASP566
|
3.3
|
16.2
|
1.0
|
|
OD1
|
D:ASP579
|
3.4
|
12.4
|
1.0
|
|
HB
|
D:THR559
|
3.4
|
13.8
|
1.0
|
|
C
|
D:THR559
|
3.4
|
13.8
|
1.0
|
|
OD2
|
D:ASP566
|
3.5
|
16.2
|
1.0
|
|
CG
|
D:ASP566
|
3.5
|
16.2
|
1.0
|
|
O
|
D:TYR564
|
3.5
|
21.8
|
1.0
|
|
CA
|
D:CYS565
|
3.6
|
17.0
|
1.0
|
|
HG3
|
D:GLU569
|
3.7
|
13.9
|
1.0
|
|
OE1
|
D:GLU569
|
3.8
|
13.9
|
1.0
|
|
N
|
D:ASP566
|
3.8
|
16.2
|
1.0
|
|
H
|
D:GLY563
|
3.8
|
16.5
|
1.0
|
|
HB2
|
D:ASP579
|
3.8
|
12.4
|
1.0
|
|
HB3
|
D:ASP579
|
3.8
|
12.4
|
1.0
|
|
HA
|
D:CYS560
|
3.9
|
11.5
|
1.0
|
|
CG
|
D:GLU569
|
4.0
|
13.9
|
1.0
|
|
C
|
D:TYR564
|
4.1
|
21.8
|
1.0
|
|
C
|
D:CYS565
|
4.1
|
17.0
|
1.0
|
|
CB
|
D:THR559
|
4.1
|
13.8
|
1.0
|
|
H
|
D:ASP562
|
4.1
|
16.6
|
1.0
|
|
HB3
|
D:CYS565
|
4.1
|
17.0
|
1.0
|
|
CB
|
D:ASP579
|
4.2
|
12.4
|
1.0
|
|
N
|
D:CYS565
|
4.2
|
17.0
|
1.0
|
|
CA
|
D:THR559
|
4.2
|
13.8
|
1.0
|
|
CG
|
D:ASP579
|
4.2
|
12.4
|
1.0
|
|
CB
|
D:ASP562
|
4.2
|
16.6
|
1.0
|
|
HA
|
D:THR559
|
4.2
|
13.8
|
1.0
|
|
O
|
D:CYS560
|
4.2
|
11.5
|
1.0
|
|
N
|
D:CYS560
|
4.4
|
11.5
|
1.0
|
|
CA
|
D:CYS560
|
4.4
|
11.5
|
1.0
|
|
CB
|
D:CYS565
|
4.5
|
17.0
|
1.0
|
|
OG1
|
D:THR559
|
4.5
|
13.8
|
1.0
|
|
C
|
D:CYS560
|
4.5
|
11.5
|
1.0
|
|
HB2
|
D:ASP562
|
4.5
|
16.6
|
1.0
|
|
CB
|
D:ASP566
|
4.6
|
16.2
|
1.0
|
|
HG2
|
D:GLU569
|
4.6
|
13.9
|
1.0
|
|
N
|
D:GLY563
|
4.6
|
16.5
|
1.0
|
|
HB2
|
D:ASP566
|
4.7
|
16.2
|
1.0
|
|
OD2
|
D:ASP562
|
4.7
|
16.6
|
1.0
|
|
N
|
D:ASP562
|
4.7
|
16.6
|
1.0
|
|
CA
|
D:ASP566
|
4.8
|
16.2
|
1.0
|
|
HB2
|
D:CYS565
|
4.8
|
17.0
|
1.0
|
|
H
|
D:CYS565
|
4.9
|
17.0
|
1.0
|
|
HB2
|
D:GLU569
|
4.9
|
13.9
|
1.0
|
|
HG1
|
D:THR559
|
4.9
|
13.8
|
1.0
|
|
CA
|
D:ASP562
|
5.0
|
16.6
|
1.0
|
|
H
|
D:TYR564
|
5.0
|
21.8
|
1.0
|
|
CG
|
D:ASP562
|
5.0
|
16.6
|
1.0
|
|
Reference:
S.E.Adams,
A.G.Purkiss,
P.K.Knowles,
A.Nans,
D.C.Briggs,
A.Borg,
C.P.Earl,
K.M.Goodman,
A.Narowtek,
P.J.Mcintosh,
F.M.Houghton,
S.Kjaer,
N.Q.Mcdonald.
A Two-Site Flexible Clamp Mechanism For Ret-Gdnf-GFRA1 Assembly Reveals Both Conformational Adaptation and Strict Geometric Spacing Structure V. 29 2021.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2020.12.012
Page generated: Thu Jul 18 22:55:06 2024
|
