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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Tue Jul 16 13:11:24 2024

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