Calcium in PDB 6q2r: Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
Enzymatic activity of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
All present enzymatic activity of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form:
2.7.10.1;
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
(pdb code 6q2r). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the
Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form, PDB code: 6q2r:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 1 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca2001
b:0.2
occ:1.00
|
OD1
|
E:ASP230
|
2.2
|
0.3
|
1.0
|
|
OD2
|
E:ASP267
|
2.2
|
0.4
|
1.0
|
|
CD
|
E:GLU178
|
2.3
|
0.4
|
1.0
|
|
OD1
|
E:ASN179
|
2.3
|
1.0
|
1.0
|
|
OE1
|
E:GLU178
|
2.3
|
0.4
|
1.0
|
|
OD2
|
E:ASP230
|
2.4
|
0.3
|
1.0
|
|
OE2
|
E:GLU178
|
2.4
|
0.4
|
1.0
|
|
CG
|
E:ASP230
|
2.4
|
0.3
|
1.0
|
|
OE1
|
E:GLU232
|
2.4
|
0.7
|
1.0
|
|
CG
|
E:GLU178
|
3.3
|
0.4
|
1.0
|
|
CG
|
E:ASP267
|
3.3
|
0.4
|
1.0
|
|
CD
|
E:GLU232
|
3.3
|
0.7
|
1.0
|
|
CG
|
E:ASN179
|
3.5
|
1.0
|
1.0
|
|
CB
|
E:ASP230
|
3.7
|
0.3
|
1.0
|
|
OE2
|
E:GLU232
|
3.8
|
0.7
|
1.0
|
|
CB
|
E:GLU178
|
3.9
|
0.4
|
1.0
|
|
ND2
|
E:ASN179
|
4.0
|
1.0
|
1.0
|
|
CB
|
E:ASP267
|
4.2
|
0.4
|
1.0
|
|
OD1
|
E:ASP267
|
4.2
|
0.4
|
1.0
|
|
CA
|
E:ASP230
|
4.4
|
0.3
|
1.0
|
|
CG
|
E:GLU232
|
4.4
|
0.7
|
1.0
|
|
CB
|
E:GLU232
|
4.7
|
0.7
|
1.0
|
|
CB
|
E:ASN179
|
4.7
|
1.0
|
1.0
|
|
OD1
|
E:ASP264
|
4.7
|
0.3
|
1.0
|
|
N
|
E:ARG231
|
4.8
|
0.0
|
1.0
|
|
N
|
E:GLU232
|
4.9
|
0.7
|
1.0
|
|
Calcium binding site 2 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 2 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca2002
b:0.9
occ:1.00
|
OD1
|
E:ASP264
|
2.3
|
0.3
|
1.0
|
|
OD1
|
E:ASP267
|
2.3
|
0.4
|
1.0
|
|
OD1
|
E:ASP302
|
2.4
|
0.1
|
1.0
|
|
OE2
|
E:GLU232
|
2.4
|
0.7
|
1.0
|
|
OD2
|
E:ASP264
|
2.4
|
0.3
|
1.0
|
|
O
|
E:GLU265
|
2.4
|
0.1
|
1.0
|
|
CG
|
E:ASP264
|
2.7
|
0.3
|
1.0
|
|
O
|
E:ALA301
|
3.4
|
0.2
|
1.0
|
|
CA
|
E:ASP302
|
3.5
|
0.1
|
1.0
|
|
CG
|
E:ASP302
|
3.5
|
0.1
|
1.0
|
|
CG
|
E:ASP267
|
3.5
|
0.4
|
1.0
|
|
CD
|
E:GLU232
|
3.6
|
0.7
|
1.0
|
|
C
|
E:GLU265
|
3.6
|
0.1
|
1.0
|
|
N
|
E:ASP267
|
3.8
|
0.4
|
1.0
|
|
C
|
E:ALA301
|
3.9
|
0.2
|
1.0
|
|
N
|
E:ASP302
|
4.0
|
0.1
|
1.0
|
|
CB
|
E:ASP302
|
4.0
|
0.1
|
1.0
|
|
OD2
|
E:ASP267
|
4.1
|
0.4
|
1.0
|
|
CB
|
E:ASP264
|
4.1
|
0.3
|
1.0
|
|
OE2
|
E:GLU178
|
4.2
|
0.4
|
1.0
|
|
NH2
|
E:ARG231
|
4.2
|
0.0
|
1.0
|
|
OG
|
E:SER268
|
4.3
|
0.4
|
1.0
|
|
N
|
E:GLU265
|
4.3
|
0.1
|
1.0
|
|
CG
|
E:GLU232
|
4.4
|
0.7
|
1.0
|
|
CA
|
E:ASP266
|
4.4
|
0.0
|
1.0
|
|
N
|
E:ASP266
|
4.5
|
0.0
|
1.0
|
|
OE1
|
E:GLU232
|
4.5
|
0.7
|
1.0
|
|
N
|
E:VAL303
|
4.5
|
0.6
|
1.0
|
|
OD2
|
E:ASP302
|
4.5
|
0.1
|
1.0
|
|
C
|
E:ASP302
|
4.5
|
0.1
|
1.0
|
|
CB
|
E:ASP267
|
4.6
|
0.4
|
1.0
|
|
CA
|
E:ASP267
|
4.6
|
0.4
|
1.0
|
|
CA
|
E:GLU265
|
4.6
|
0.1
|
1.0
|
|
C
|
E:ASP266
|
4.6
|
0.0
|
1.0
|
|
CG2
|
E:VAL304
|
4.8
|
0.2
|
1.0
|
|
N
|
E:SER268
|
4.8
|
0.4
|
1.0
|
|
CB
|
E:SER268
|
4.8
|
0.4
|
1.0
|
|
C
|
E:ASP267
|
4.8
|
0.4
|
1.0
|
|
CA
|
E:ASP264
|
4.9
|
0.3
|
1.0
|
|
CD
|
E:GLU178
|
4.9
|
0.4
|
1.0
|
|
C
|
E:ASP264
|
5.0
|
0.3
|
1.0
|
|
Calcium binding site 3 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 3 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca2003
b:0.0
occ:1.00
|
OD2
|
E:ASP302
|
2.2
|
0.1
|
1.0
|
|
OD2
|
E:ASP378
|
2.3
|
0.1
|
1.0
|
|
OD2
|
E:ASP300
|
2.3
|
0.9
|
1.0
|
|
OH
|
E:TYR314
|
2.4
|
0.4
|
1.0
|
|
CB
|
E:ASP302
|
2.5
|
0.1
|
1.0
|
|
O
|
E:SER268
|
2.6
|
0.4
|
1.0
|
|
OD1
|
E:ASP266
|
2.6
|
0.0
|
1.0
|
|
OD1
|
E:ASP300
|
2.7
|
0.9
|
1.0
|
|
CG
|
E:ASP302
|
2.7
|
0.1
|
1.0
|
|
OD1
|
E:ASP378
|
2.8
|
0.1
|
1.0
|
|
CG
|
E:ASP300
|
2.8
|
0.9
|
1.0
|
|
CG
|
E:ASP378
|
2.9
|
0.1
|
1.0
|
|
CZ
|
E:TYR314
|
3.6
|
0.4
|
1.0
|
|
CG
|
E:ASP266
|
3.7
|
0.0
|
1.0
|
|
C
|
E:SER268
|
3.8
|
0.4
|
1.0
|
|
CA
|
E:ASP302
|
3.9
|
0.1
|
1.0
|
|
OD1
|
E:ASP302
|
3.9
|
0.1
|
1.0
|
|
OD2
|
E:ASP266
|
4.1
|
0.0
|
1.0
|
|
N
|
E:ASP302
|
4.1
|
0.1
|
1.0
|
|
CB
|
E:ASP300
|
4.3
|
0.9
|
1.0
|
|
CB
|
E:ASP378
|
4.4
|
0.1
|
1.0
|
|
CE2
|
E:TYR314
|
4.4
|
0.4
|
1.0
|
|
CE1
|
E:TYR314
|
4.5
|
0.4
|
1.0
|
|
CA
|
E:SER268
|
4.5
|
0.4
|
1.0
|
|
N
|
E:SER268
|
4.6
|
0.4
|
1.0
|
|
C
|
E:ASP302
|
4.6
|
0.1
|
1.0
|
|
CB
|
E:SER268
|
4.6
|
0.4
|
1.0
|
|
O
|
E:ASP302
|
4.6
|
0.1
|
1.0
|
|
N
|
E:ALA269
|
4.8
|
0.5
|
1.0
|
|
CB
|
E:ASP266
|
4.9
|
0.0
|
1.0
|
|
CA
|
E:ALA269
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 4 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 4 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca2004
b:0.6
occ:1.00
|
OD1
|
E:ASP567
|
2.3
|
0.6
|
1.0
|
|
OE1
|
E:GLU574
|
2.4
|
0.8
|
1.0
|
|
OD2
|
E:ASP567
|
2.4
|
0.6
|
1.0
|
|
O
|
E:THR564
|
2.4
|
96.2
|
1.0
|
|
OE2
|
E:GLU574
|
2.4
|
0.8
|
1.0
|
|
OD2
|
E:ASP584
|
2.4
|
96.5
|
1.0
|
|
O
|
E:HIS569
|
2.4
|
0.4
|
1.0
|
|
CG
|
E:ASP567
|
2.6
|
0.6
|
1.0
|
|
CD
|
E:GLU574
|
2.7
|
0.8
|
1.0
|
|
O
|
E:CYS565
|
3.5
|
0.2
|
1.0
|
|
CG
|
E:ASP584
|
3.5
|
96.5
|
1.0
|
|
C
|
E:THR564
|
3.5
|
96.2
|
1.0
|
|
C
|
E:HIS569
|
3.7
|
0.4
|
1.0
|
|
CA
|
E:CYS565
|
3.9
|
0.2
|
1.0
|
|
CB
|
E:ASP584
|
3.9
|
96.5
|
1.0
|
|
CB
|
E:ASP567
|
4.0
|
0.6
|
1.0
|
|
C
|
E:CYS565
|
4.0
|
0.2
|
1.0
|
|
CG
|
E:GLU574
|
4.1
|
0.8
|
1.0
|
|
N
|
E:CYS565
|
4.2
|
0.2
|
1.0
|
|
OD1
|
E:ASP571
|
4.3
|
0.7
|
1.0
|
|
CA
|
E:CYS570
|
4.5
|
0.3
|
1.0
|
|
N
|
E:ASP567
|
4.5
|
0.6
|
1.0
|
|
N
|
E:CYS570
|
4.5
|
0.3
|
1.0
|
|
SG
|
E:CYS581
|
4.5
|
97.9
|
1.0
|
|
N
|
E:HIS569
|
4.6
|
0.4
|
1.0
|
|
OD1
|
E:ASP584
|
4.6
|
96.5
|
1.0
|
|
CG2
|
E:THR564
|
4.6
|
96.2
|
1.0
|
|
CA
|
E:THR564
|
4.6
|
96.2
|
1.0
|
|
CA
|
E:HIS569
|
4.7
|
0.4
|
1.0
|
|
N
|
E:ASP571
|
4.7
|
0.7
|
1.0
|
|
CG
|
E:ASP571
|
4.8
|
0.7
|
1.0
|
|
CA
|
E:ASP567
|
4.8
|
0.6
|
1.0
|
|
CB
|
E:GLU574
|
4.9
|
0.8
|
1.0
|
|
Calcium binding site 5 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 5 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca2001
b:0.2
occ:1.00
|
OD1
|
F:ASP230
|
2.2
|
0.3
|
1.0
|
|
OD2
|
F:ASP267
|
2.2
|
0.4
|
1.0
|
|
CD
|
F:GLU178
|
2.3
|
0.4
|
1.0
|
|
OD1
|
F:ASN179
|
2.3
|
1.0
|
1.0
|
|
OE1
|
F:GLU178
|
2.4
|
0.4
|
1.0
|
|
OE2
|
F:GLU178
|
2.4
|
0.4
|
1.0
|
|
OD2
|
F:ASP230
|
2.4
|
0.3
|
1.0
|
|
CG
|
F:ASP230
|
2.4
|
0.3
|
1.0
|
|
OE1
|
F:GLU232
|
2.4
|
0.7
|
1.0
|
|
CG
|
F:GLU178
|
3.3
|
0.4
|
1.0
|
|
CG
|
F:ASP267
|
3.3
|
0.4
|
1.0
|
|
CD
|
F:GLU232
|
3.3
|
0.7
|
1.0
|
|
CG
|
F:ASN179
|
3.5
|
1.0
|
1.0
|
|
CB
|
F:ASP230
|
3.7
|
0.3
|
1.0
|
|
OE2
|
F:GLU232
|
3.8
|
0.7
|
1.0
|
|
CB
|
F:GLU178
|
3.9
|
0.4
|
1.0
|
|
ND2
|
F:ASN179
|
4.0
|
1.0
|
1.0
|
|
CB
|
F:ASP267
|
4.2
|
0.4
|
1.0
|
|
OD1
|
F:ASP267
|
4.2
|
0.4
|
1.0
|
|
CA
|
F:ASP230
|
4.4
|
0.3
|
1.0
|
|
CG
|
F:GLU232
|
4.4
|
0.7
|
1.0
|
|
CB
|
F:GLU232
|
4.7
|
0.7
|
1.0
|
|
CB
|
F:ASN179
|
4.7
|
1.0
|
1.0
|
|
OD1
|
F:ASP264
|
4.7
|
0.3
|
1.0
|
|
N
|
F:ARG231
|
4.8
|
0.0
|
1.0
|
|
N
|
F:GLU232
|
4.9
|
0.7
|
1.0
|
|
Calcium binding site 6 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 6 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca2002
b:0.9
occ:1.00
|
OD1
|
F:ASP264
|
2.3
|
0.3
|
1.0
|
|
OD1
|
F:ASP267
|
2.3
|
0.4
|
1.0
|
|
OD1
|
F:ASP302
|
2.4
|
0.1
|
1.0
|
|
OE2
|
F:GLU232
|
2.4
|
0.7
|
1.0
|
|
OD2
|
F:ASP264
|
2.4
|
0.3
|
1.0
|
|
O
|
F:GLU265
|
2.4
|
0.1
|
1.0
|
|
CG
|
F:ASP264
|
2.7
|
0.3
|
1.0
|
|
O
|
F:ALA301
|
3.4
|
0.2
|
1.0
|
|
CA
|
F:ASP302
|
3.5
|
0.1
|
1.0
|
|
CG
|
F:ASP267
|
3.5
|
0.4
|
1.0
|
|
CG
|
F:ASP302
|
3.5
|
0.1
|
1.0
|
|
CD
|
F:GLU232
|
3.6
|
0.7
|
1.0
|
|
C
|
F:GLU265
|
3.6
|
0.1
|
1.0
|
|
N
|
F:ASP267
|
3.8
|
0.4
|
1.0
|
|
C
|
F:ALA301
|
3.9
|
0.2
|
1.0
|
|
N
|
F:ASP302
|
4.0
|
0.1
|
1.0
|
|
CB
|
F:ASP302
|
4.0
|
0.1
|
1.0
|
|
OD2
|
F:ASP267
|
4.1
|
0.4
|
1.0
|
|
CB
|
F:ASP264
|
4.1
|
0.3
|
1.0
|
|
OE2
|
F:GLU178
|
4.2
|
0.4
|
1.0
|
|
NH2
|
F:ARG231
|
4.2
|
0.0
|
1.0
|
|
OG
|
F:SER268
|
4.3
|
0.4
|
1.0
|
|
N
|
F:GLU265
|
4.3
|
0.1
|
1.0
|
|
CG
|
F:GLU232
|
4.4
|
0.7
|
1.0
|
|
CA
|
F:ASP266
|
4.4
|
0.0
|
1.0
|
|
N
|
F:ASP266
|
4.5
|
0.0
|
1.0
|
|
OE1
|
F:GLU232
|
4.5
|
0.7
|
1.0
|
|
N
|
F:VAL303
|
4.5
|
0.6
|
1.0
|
|
OD2
|
F:ASP302
|
4.5
|
0.1
|
1.0
|
|
C
|
F:ASP302
|
4.5
|
0.1
|
1.0
|
|
CB
|
F:ASP267
|
4.6
|
0.4
|
1.0
|
|
CA
|
F:ASP267
|
4.6
|
0.4
|
1.0
|
|
CA
|
F:GLU265
|
4.6
|
0.1
|
1.0
|
|
C
|
F:ASP266
|
4.6
|
0.0
|
1.0
|
|
CG2
|
F:VAL304
|
4.8
|
0.2
|
1.0
|
|
N
|
F:SER268
|
4.8
|
0.4
|
1.0
|
|
CB
|
F:SER268
|
4.8
|
0.4
|
1.0
|
|
C
|
F:ASP267
|
4.8
|
0.4
|
1.0
|
|
CA
|
F:ASP264
|
4.9
|
0.3
|
1.0
|
|
CD
|
F:GLU178
|
4.9
|
0.4
|
1.0
|
|
C
|
F:ASP264
|
5.0
|
0.3
|
1.0
|
|
Calcium binding site 7 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 7 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca2003
b:0.0
occ:1.00
|
OD2
|
F:ASP302
|
2.2
|
0.1
|
1.0
|
|
OD2
|
F:ASP378
|
2.3
|
0.1
|
1.0
|
|
OD2
|
F:ASP300
|
2.3
|
0.9
|
1.0
|
|
OH
|
F:TYR314
|
2.4
|
0.4
|
1.0
|
|
CB
|
F:ASP302
|
2.5
|
0.1
|
1.0
|
|
O
|
F:SER268
|
2.6
|
0.4
|
1.0
|
|
OD1
|
F:ASP266
|
2.6
|
0.0
|
1.0
|
|
OD1
|
F:ASP300
|
2.7
|
0.9
|
1.0
|
|
CG
|
F:ASP302
|
2.7
|
0.1
|
1.0
|
|
OD1
|
F:ASP378
|
2.8
|
0.1
|
1.0
|
|
CG
|
F:ASP300
|
2.8
|
0.9
|
1.0
|
|
CG
|
F:ASP378
|
2.9
|
0.1
|
1.0
|
|
CZ
|
F:TYR314
|
3.6
|
0.4
|
1.0
|
|
CG
|
F:ASP266
|
3.7
|
0.0
|
1.0
|
|
C
|
F:SER268
|
3.8
|
0.4
|
1.0
|
|
CA
|
F:ASP302
|
3.9
|
0.1
|
1.0
|
|
OD1
|
F:ASP302
|
3.9
|
0.1
|
1.0
|
|
OD2
|
F:ASP266
|
4.1
|
0.0
|
1.0
|
|
N
|
F:ASP302
|
4.1
|
0.1
|
1.0
|
|
CB
|
F:ASP300
|
4.3
|
0.9
|
1.0
|
|
CB
|
F:ASP378
|
4.4
|
0.1
|
1.0
|
|
CE2
|
F:TYR314
|
4.4
|
0.4
|
1.0
|
|
CE1
|
F:TYR314
|
4.5
|
0.4
|
1.0
|
|
CA
|
F:SER268
|
4.5
|
0.4
|
1.0
|
|
N
|
F:SER268
|
4.6
|
0.4
|
1.0
|
|
C
|
F:ASP302
|
4.6
|
0.1
|
1.0
|
|
CB
|
F:SER268
|
4.6
|
0.4
|
1.0
|
|
O
|
F:ASP302
|
4.6
|
0.1
|
1.0
|
|
N
|
F:ALA269
|
4.8
|
0.5
|
1.0
|
|
CB
|
F:ASP266
|
4.9
|
0.0
|
1.0
|
|
CA
|
F:ALA269
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 8 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 8 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca2004
b:0.6
occ:1.00
|
OD1
|
F:ASP567
|
2.3
|
0.6
|
1.0
|
|
OE1
|
F:GLU574
|
2.4
|
0.8
|
1.0
|
|
OD2
|
F:ASP567
|
2.4
|
0.6
|
1.0
|
|
O
|
F:THR564
|
2.4
|
96.2
|
1.0
|
|
OE2
|
F:GLU574
|
2.4
|
0.8
|
1.0
|
|
OD2
|
F:ASP584
|
2.4
|
96.5
|
1.0
|
|
O
|
F:HIS569
|
2.4
|
0.4
|
1.0
|
|
CG
|
F:ASP567
|
2.6
|
0.6
|
1.0
|
|
CD
|
F:GLU574
|
2.7
|
0.8
|
1.0
|
|
O
|
F:CYS565
|
3.5
|
0.2
|
1.0
|
|
CG
|
F:ASP584
|
3.5
|
96.5
|
1.0
|
|
C
|
F:THR564
|
3.5
|
96.2
|
1.0
|
|
C
|
F:HIS569
|
3.7
|
0.4
|
1.0
|
|
CA
|
F:CYS565
|
3.9
|
0.2
|
1.0
|
|
CB
|
F:ASP584
|
3.9
|
96.5
|
1.0
|
|
CB
|
F:ASP567
|
4.0
|
0.6
|
1.0
|
|
C
|
F:CYS565
|
4.0
|
0.2
|
1.0
|
|
CG
|
F:GLU574
|
4.1
|
0.8
|
1.0
|
|
N
|
F:CYS565
|
4.2
|
0.2
|
1.0
|
|
OD1
|
F:ASP571
|
4.3
|
0.7
|
1.0
|
|
CA
|
F:CYS570
|
4.5
|
0.3
|
1.0
|
|
N
|
F:ASP567
|
4.5
|
0.6
|
1.0
|
|
N
|
F:CYS570
|
4.5
|
0.3
|
1.0
|
|
SG
|
F:CYS581
|
4.5
|
97.9
|
1.0
|
|
N
|
F:HIS569
|
4.6
|
0.4
|
1.0
|
|
OD1
|
F:ASP584
|
4.6
|
96.5
|
1.0
|
|
CG2
|
F:THR564
|
4.6
|
96.2
|
1.0
|
|
CA
|
F:THR564
|
4.6
|
96.2
|
1.0
|
|
CA
|
F:HIS569
|
4.7
|
0.4
|
1.0
|
|
N
|
F:ASP571
|
4.7
|
0.7
|
1.0
|
|
CG
|
F:ASP571
|
4.8
|
0.7
|
1.0
|
|
CA
|
F:ASP567
|
4.8
|
0.6
|
1.0
|
|
CB
|
F:GLU574
|
4.9
|
0.8
|
1.0
|
|
Calcium binding site 9 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 9 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Ca2001
b:0.3
occ:1.00
|
OD1
|
Y:ASP230
|
2.2
|
0.2
|
1.0
|
|
OD2
|
Y:ASP267
|
2.2
|
0.3
|
1.0
|
|
CD
|
Y:GLU178
|
2.3
|
0.5
|
1.0
|
|
OD1
|
Y:ASN179
|
2.3
|
0.1
|
1.0
|
|
OE1
|
Y:GLU178
|
2.4
|
0.5
|
1.0
|
|
OE2
|
Y:GLU178
|
2.4
|
0.5
|
1.0
|
|
OD2
|
Y:ASP230
|
2.4
|
0.2
|
1.0
|
|
CG
|
Y:ASP230
|
2.4
|
0.2
|
1.0
|
|
OE1
|
Y:GLU232
|
2.4
|
0.7
|
1.0
|
|
CG
|
Y:GLU178
|
3.3
|
0.5
|
1.0
|
|
CG
|
Y:ASP267
|
3.3
|
0.3
|
1.0
|
|
CD
|
Y:GLU232
|
3.3
|
0.7
|
1.0
|
|
CG
|
Y:ASN179
|
3.5
|
0.1
|
1.0
|
|
CB
|
Y:ASP230
|
3.7
|
0.2
|
1.0
|
|
OE2
|
Y:GLU232
|
3.8
|
0.7
|
1.0
|
|
CB
|
Y:GLU178
|
3.9
|
0.5
|
1.0
|
|
ND2
|
Y:ASN179
|
4.0
|
0.1
|
1.0
|
|
CB
|
Y:ASP267
|
4.2
|
0.3
|
1.0
|
|
OD1
|
Y:ASP267
|
4.2
|
0.3
|
1.0
|
|
CA
|
Y:ASP230
|
4.4
|
0.2
|
1.0
|
|
CG
|
Y:GLU232
|
4.4
|
0.7
|
1.0
|
|
CB
|
Y:GLU232
|
4.7
|
0.7
|
1.0
|
|
CB
|
Y:ASN179
|
4.7
|
0.1
|
1.0
|
|
OD1
|
Y:ASP264
|
4.7
|
0.6
|
1.0
|
|
N
|
Y:ARG231
|
4.8
|
0.9
|
1.0
|
|
N
|
Y:GLU232
|
4.9
|
0.7
|
1.0
|
|
Calcium binding site 10 out
of 16 in 6q2r
Go back to
Calcium Binding Sites List in 6q2r
Calcium binding site 10 out
of 16 in the Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex in the Tetrameric Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Ca2002
b:0.1
occ:1.00
|
OD1
|
Y:ASP264
|
2.3
|
0.6
|
1.0
|
|
OD1
|
Y:ASP267
|
2.3
|
0.3
|
1.0
|
|
OD1
|
Y:ASP302
|
2.4
|
0.6
|
1.0
|
|
OE2
|
Y:GLU232
|
2.4
|
0.7
|
1.0
|
|
OD2
|
Y:ASP264
|
2.4
|
0.6
|
1.0
|
|
O
|
Y:GLU265
|
2.4
|
0.9
|
1.0
|
|
CG
|
Y:ASP264
|
2.7
|
0.6
|
1.0
|
|
O
|
Y:ALA301
|
3.4
|
0.7
|
1.0
|
|
CA
|
Y:ASP302
|
3.5
|
0.6
|
1.0
|
|
CG
|
Y:ASP267
|
3.5
|
0.3
|
1.0
|
|
CG
|
Y:ASP302
|
3.5
|
0.6
|
1.0
|
|
CD
|
Y:GLU232
|
3.6
|
0.7
|
1.0
|
|
C
|
Y:GLU265
|
3.6
|
0.9
|
1.0
|
|
N
|
Y:ASP267
|
3.8
|
0.3
|
1.0
|
|
C
|
Y:ALA301
|
3.9
|
0.7
|
1.0
|
|
N
|
Y:ASP302
|
4.0
|
0.6
|
1.0
|
|
CB
|
Y:ASP302
|
4.0
|
0.6
|
1.0
|
|
OD2
|
Y:ASP267
|
4.1
|
0.3
|
1.0
|
|
CB
|
Y:ASP264
|
4.1
|
0.6
|
1.0
|
|
OE2
|
Y:GLU178
|
4.2
|
0.5
|
1.0
|
|
NH2
|
Y:ARG231
|
4.2
|
0.9
|
1.0
|
|
OG
|
Y:SER268
|
4.3
|
0.7
|
1.0
|
|
N
|
Y:GLU265
|
4.3
|
0.9
|
1.0
|
|
CG
|
Y:GLU232
|
4.4
|
0.7
|
1.0
|
|
CA
|
Y:ASP266
|
4.4
|
0.9
|
1.0
|
|
N
|
Y:ASP266
|
4.5
|
0.9
|
1.0
|
|
OE1
|
Y:GLU232
|
4.5
|
0.7
|
1.0
|
|
N
|
Y:VAL303
|
4.5
|
0.2
|
1.0
|
|
OD2
|
Y:ASP302
|
4.5
|
0.6
|
1.0
|
|
C
|
Y:ASP302
|
4.5
|
0.6
|
1.0
|
|
CB
|
Y:ASP267
|
4.6
|
0.3
|
1.0
|
|
CA
|
Y:ASP267
|
4.6
|
0.3
|
1.0
|
|
CA
|
Y:GLU265
|
4.6
|
0.9
|
1.0
|
|
C
|
Y:ASP266
|
4.6
|
0.9
|
1.0
|
|
CG2
|
Y:VAL304
|
4.8
|
0.8
|
1.0
|
|
N
|
Y:SER268
|
4.8
|
0.7
|
1.0
|
|
CB
|
Y:SER268
|
4.8
|
0.7
|
1.0
|
|
C
|
Y:ASP267
|
4.8
|
0.3
|
1.0
|
|
CA
|
Y:ASP264
|
4.9
|
0.6
|
1.0
|
|
CD
|
Y:GLU178
|
4.9
|
0.5
|
1.0
|
|
C
|
Y:ASP264
|
5.0
|
0.6
|
1.0
|
|
Reference:
J.Li,
G.Shang,
Y.J.Chen,
C.A.Brautigam,
J.Liou,
X.Zhang,
X.C.Bai.
Cryo-Em Analyses Reveal the Common Mechanism and Diversification in the Activation of Ret By Different Ligands. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31535977
DOI: 10.7554/ELIFE.47650
Page generated: Sat Dec 12 07:26:51 2020
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