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Calcium in PDB 6q2s: Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.

Enzymatic activity of Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.

All present enzymatic activity of Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.:
2.7.10.1;

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. (pdb code 6q2s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry., PDB code: 6q2s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6q2s

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Calcium binding site 1 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.


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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca707

b:73.4
occ:1.00
 OD2 E:ASP300 2.2 69.6 1.0
OD2 E:ASP302 2.3 69.9 1.0
OD2 E:ASP378 2.4 79.1 1.0
OH E:TYR314 2.5 76.1 1.0
OD1 E:ASP266 2.6 70.8 1.0
OD1 E:ASP378 2.6 79.1 1.0
OD1 E:ASP300 2.7 69.6 1.0
O E:SER268 2.7 73.9 1.0
CG E:ASP300 2.8 69.6 1.0
CG E:ASP378 2.9 79.1 1.0
CG E:ASP302 3.3 69.9 1.0
CG E:ASP266 3.6 70.8 1.0
CZ E:TYR314 3.7 76.1 1.0
C E:SER268 3.8 73.9 1.0
CB E:ASP302 3.9 69.9 1.0
OD2 E:ASP266 4.0 70.8 1.0
CB E:ASP300 4.3 69.6 1.0
CE2 E:TYR314 4.4 76.1 1.0
OD1 E:ASP302 4.4 69.9 1.0
CB E:ASP378 4.4 79.1 1.0
N E:ALA269 4.6 74.9 1.0
CE1 E:TYR314 4.7 76.1 1.0
CB E:ASP266 4.7 70.8 1.0
CA E:SER268 4.8 73.9 1.0
CB E:SER268 4.8 73.9 1.0
N E:ASP302 4.9 69.9 1.0
CA E:ALA269 4.9 74.9 1.0
N E:SER268 5.0 73.9 1.0

Calcium binding site 2 out of 8 in 6q2s

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.


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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca708

b:75.8
occ:1.00
 OE2 E:GLU232 2.2 76.5 1.0
O E:GLU265 2.2 70.4 1.0
OD1 E:ASP264 2.5 67.8 1.0
OD1 E:ASP267 2.5 75.5 1.0
OD1 E:ASP302 2.5 69.9 1.0
CD E:GLU232 3.4 76.5 1.0
CG E:ASP264 3.5 67.8 1.0
C E:GLU265 3.5 70.4 1.0
CG E:ASP302 3.5 69.9 1.0
CG E:ASP267 3.7 75.5 1.0
CA E:ASP302 3.7 69.9 1.0
OD2 E:ASP264 3.7 67.8 1.0
N E:ASP267 3.8 75.5 1.0
OE2 E:GLU178 3.9 74.1 1.0
CA E:CA709 3.9 82.4 1.0
O E:ALA301 3.9 69.0 1.0
CB E:ASP302 4.0 69.9 1.0
N E:GLU265 4.1 70.4 1.0
CG E:GLU232 4.2 76.5 1.0
OE1 E:GLU232 4.3 76.5 1.0
N E:ASP266 4.4 70.8 1.0
NH2 E:ARG231 4.4 74.0 1.0
N E:ASP302 4.4 69.9 1.0
OD2 E:ASP267 4.4 75.5 1.0
CA E:ASP266 4.4 70.8 1.0
CA E:GLU265 4.4 70.4 1.0
C E:ALA301 4.4 69.0 1.0
OG E:SER268 4.5 73.9 1.0
OD2 E:ASP302 4.6 69.9 1.0
C E:ASP266 4.6 70.8 1.0
NE E:ARG231 4.7 74.0 1.0
CA E:ASP267 4.7 75.5 1.0
CB E:ASP267 4.7 75.5 1.0
CB E:ASP264 4.8 67.8 1.0
C E:ASP302 4.9 69.9 1.0
CD E:GLU178 4.9 74.1 1.0
N E:VAL303 4.9 66.8 1.0
C E:ASP267 4.9 75.5 1.0
N E:SER268 5.0 73.9 1.0

Calcium binding site 3 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 3 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.


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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca709

b:82.4
occ:1.00
 OD2 E:ASP267 2.1 75.5 1.0
OE1 E:GLU178 2.2 74.1 1.0
OE2 E:GLU178 2.3 74.1 1.0
OD1 E:ASP230 2.3 77.6 1.0
OE1 E:GLU232 2.3 76.5 1.0
CD E:GLU178 2.4 74.1 1.0
CG E:ASP267 2.5 75.5 1.0
OE2 E:GLU232 2.7 76.5 1.0
OD1 E:ASP267 2.8 75.5 1.0
CD E:GLU232 2.9 76.5 1.0
CG E:ASP230 3.5 77.6 1.0
CB E:ASP267 3.7 75.5 1.0
CG E:GLU178 3.8 74.1 1.0
CA E:CA708 3.9 75.8 1.0
ND2 E:ASN179 3.9 76.2 1.0
N E:ARG231 4.0 74.0 1.0
OD2 E:ASP230 4.1 77.6 1.0
O E:GLU265 4.3 70.4 1.0
CG E:GLU232 4.4 76.5 1.0
OD1 E:ASP264 4.5 67.8 1.0
CA E:ASP230 4.5 77.6 1.0
CB E:GLU178 4.5 74.1 1.0
CB E:ASP230 4.6 77.6 1.0
N E:GLU265 4.7 70.4 1.0
CB E:ARG231 4.7 74.0 1.0
N E:GLU232 4.7 76.5 1.0
CG E:ASN179 4.7 76.2 1.0
C E:ASP230 4.7 77.6 1.0
N E:ASP267 4.8 75.5 1.0
CA E:ASP267 4.8 75.5 1.0
OD1 E:ASN179 4.8 76.2 1.0
CA E:ARG231 4.9 74.0 1.0

Calcium binding site 4 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 4 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.


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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca710

b:53.2
occ:1.00
 O E:CYS565 2.0 48.7 1.0
O E:THR564 2.1 49.8 1.0
OD1 E:ASP567 2.2 49.1 1.0
OE2 E:GLU574 2.2 46.2 1.0
OE1 E:GLU574 2.4 46.2 1.0
CA E:CYS565 2.5 48.7 1.0
C E:CYS565 2.5 48.7 1.0
CD E:GLU574 2.6 46.2 1.0
OD2 E:ASP567 2.6 49.1 1.0
CG E:ASP567 2.6 49.1 1.0
O E:HIS569 3.0 51.7 1.0
C E:THR564 3.0 49.8 1.0
N E:CYS565 3.2 48.7 1.0
OD2 E:ASP584 3.6 45.4 1.0
SG E:CYS581 3.6 40.6 1.0
N E:PRO566 3.8 48.0 1.0
CB E:CYS565 3.8 48.7 1.0
N E:ASP567 3.9 49.1 1.0
CB E:ASP567 4.0 49.1 1.0
CG E:GLU574 4.0 46.2 1.0
C E:HIS569 4.1 51.7 1.0
CG E:ASP584 4.4 45.4 1.0
CB E:ASP584 4.4 45.4 1.0
CA E:THR564 4.4 49.8 1.0
SG E:CYS565 4.4 48.7 1.0
CA E:ASP567 4.5 49.1 1.0
CA E:PRO566 4.5 48.0 1.0
C E:PRO566 4.7 48.0 1.0
CB E:CYS581 4.7 40.6 1.0
N E:GLY568 4.8 45.9 1.0
N E:HIS569 4.8 51.7 1.0
CB E:GLU574 4.8 46.2 1.0
N E:CYS570 5.0 53.9 1.0

Calcium binding site 5 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 5 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.


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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca707

b:73.4
occ:1.00
 OD2 F:ASP300 2.2 69.6 1.0
OD2 F:ASP302 2.3 69.9 1.0
OD2 F:ASP378 2.4 79.1 1.0
OH F:TYR314 2.5 76.1 1.0
OD1 F:ASP266 2.6 70.8 1.0
OD1 F:ASP378 2.6 79.1 1.0
OD1 F:ASP300 2.7 69.6 1.0
O F:SER268 2.7 73.9 1.0
CG F:ASP300 2.8 69.6 1.0
CG F:ASP378 2.9 79.1 1.0
CG F:ASP302 3.3 69.9 1.0
CG F:ASP266 3.6 70.8 1.0
CZ F:TYR314 3.7 76.1 1.0
C F:SER268 3.8 73.9 1.0
CB F:ASP302 3.9 69.9 1.0
OD2 F:ASP266 4.0 70.8 1.0
CB F:ASP300 4.3 69.6 1.0
CE2 F:TYR314 4.4 76.1 1.0
OD1 F:ASP302 4.4 69.9 1.0
CB F:ASP378 4.4 79.1 1.0
N F:ALA269 4.6 74.9 1.0
CE1 F:TYR314 4.7 76.1 1.0
CB F:ASP266 4.7 70.8 1.0
CA F:SER268 4.8 73.9 1.0
CB F:SER268 4.8 73.9 1.0
N F:ASP302 4.9 69.9 1.0
CA F:ALA269 4.9 74.9 1.0
N F:SER268 5.0 73.9 1.0

Calcium binding site 6 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 6 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.


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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca708

b:75.8
occ:1.00
 OE2 F:GLU232 2.2 76.5 1.0
O F:GLU265 2.2 70.4 1.0
OD1 F:ASP264 2.5 67.8 1.0
OD1 F:ASP267 2.5 75.5 1.0
OD1 F:ASP302 2.5 69.9 1.0
CD F:GLU232 3.4 76.5 1.0
CG F:ASP264 3.5 67.8 1.0
C F:GLU265 3.5 70.4 1.0
CG F:ASP302 3.5 69.9 1.0
CG F:ASP267 3.7 75.5 1.0
CA F:ASP302 3.7 69.9 1.0
OD2 F:ASP264 3.7 67.8 1.0
N F:ASP267 3.8 75.5 1.0
OE2 F:GLU178 3.9 74.1 1.0
CA F:CA709 3.9 82.4 1.0
O F:ALA301 3.9 69.0 1.0
CB F:ASP302 4.0 69.9 1.0
N F:GLU265 4.1 70.4 1.0
CG F:GLU232 4.2 76.5 1.0
OE1 F:GLU232 4.3 76.5 1.0
N F:ASP266 4.4 70.8 1.0
NH2 F:ARG231 4.4 74.0 1.0
N F:ASP302 4.4 69.9 1.0
OD2 F:ASP267 4.4 75.5 1.0
CA F:ASP266 4.4 70.8 1.0
CA F:GLU265 4.4 70.4 1.0
C F:ALA301 4.4 69.0 1.0
OG F:SER268 4.5 73.9 1.0
OD2 F:ASP302 4.6 69.9 1.0
C F:ASP266 4.6 70.8 1.0
NE F:ARG231 4.7 74.0 1.0
CA F:ASP267 4.7 75.5 1.0
CB F:ASP267 4.7 75.5 1.0
CB F:ASP264 4.8 67.8 1.0
C F:ASP302 4.9 69.9 1.0
CD F:GLU178 4.9 74.1 1.0
N F:VAL303 4.9 66.8 1.0
C F:ASP267 4.9 75.5 1.0
N F:SER268 5.0 73.9 1.0

Calcium binding site 7 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 7 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.


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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca709

b:82.4
occ:1.00
 OD2 F:ASP267 2.1 75.5 1.0
OE1 F:GLU178 2.2 74.1 1.0
OE2 F:GLU178 2.3 74.1 1.0
OD1 F:ASP230 2.3 77.6 1.0
OE1 F:GLU232 2.3 76.5 1.0
CD F:GLU178 2.4 74.1 1.0
CG F:ASP267 2.5 75.5 1.0
OE2 F:GLU232 2.7 76.5 1.0
OD1 F:ASP267 2.8 75.5 1.0
CD F:GLU232 2.9 76.5 1.0
CG F:ASP230 3.5 77.6 1.0
CB F:ASP267 3.7 75.5 1.0
CG F:GLU178 3.8 74.1 1.0
CA F:CA708 3.9 75.8 1.0
ND2 F:ASN179 3.9 76.2 1.0
N F:ARG231 4.0 74.0 1.0
OD2 F:ASP230 4.1 77.6 1.0
O F:GLU265 4.3 70.4 1.0
CG F:GLU232 4.4 76.5 1.0
OD1 F:ASP264 4.5 67.8 1.0
CA F:ASP230 4.5 77.6 1.0
CB F:GLU178 4.5 74.1 1.0
CB F:ASP230 4.6 77.6 1.0
N F:GLU265 4.7 70.4 1.0
CB F:ARG231 4.7 74.0 1.0
N F:GLU232 4.7 76.5 1.0
CG F:ASN179 4.7 76.2 1.0
C F:ASP230 4.7 77.6 1.0
N F:ASP267 4.8 75.5 1.0
CA F:ASP267 4.8 75.5 1.0
OD1 F:ASN179 4.8 76.2 1.0
CA F:ARG231 4.9 74.0 1.0

Calcium binding site 8 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 8 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.


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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca710

b:53.2
occ:1.00
 O F:CYS565 2.0 48.7 1.0
O F:THR564 2.1 49.8 1.0
OD1 F:ASP567 2.2 49.1 1.0
OE2 F:GLU574 2.2 46.2 1.0
OE1 F:GLU574 2.4 46.2 1.0
CA F:CYS565 2.5 48.7 1.0
C F:CYS565 2.5 48.7 1.0
CD F:GLU574 2.6 46.2 1.0
OD2 F:ASP567 2.6 49.1 1.0
CG F:ASP567 2.6 49.1 1.0
O F:HIS569 3.0 51.7 1.0
C F:THR564 3.0 49.8 1.0
N F:CYS565 3.2 48.7 1.0
OD2 F:ASP584 3.6 45.4 1.0
SG F:CYS581 3.6 40.6 1.0
N F:PRO566 3.8 48.0 1.0
CB F:CYS565 3.8 48.7 1.0
N F:ASP567 3.9 49.1 1.0
CB F:ASP567 4.0 49.1 1.0
CG F:GLU574 4.0 46.2 1.0
C F:HIS569 4.1 51.7 1.0
CG F:ASP584 4.4 45.4 1.0
CB F:ASP584 4.4 45.4 1.0
CA F:THR564 4.4 49.8 1.0
SG F:CYS565 4.4 48.7 1.0
CA F:ASP567 4.5 49.1 1.0
CA F:PRO566 4.5 48.0 1.0
C F:PRO566 4.7 48.0 1.0
CB F:CYS581 4.7 40.6 1.0
N F:GLY568 4.8 45.9 1.0
N F:HIS569 4.8 51.7 1.0
CB F:GLU574 4.8 46.2 1.0
N F:CYS570 5.0 53.9 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 13:15:14 2024

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