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Calcium in PDB 6q2o: Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.

Enzymatic activity of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.

All present enzymatic activity of Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. (pdb code 6q2o). 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry., PDB code: 6q2o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 1 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2001

b:76.5
occ:1.00
 OD1 E:ASP230 2.1 61.1 1.0
OD2 E:ASP267 2.3 55.3 1.0
CG E:ASP230 2.4 61.1 1.0
OE2 E:GLU178 2.4 58.5 1.0
CD E:GLU178 2.5 58.5 1.0
OD1 E:ASN179 2.5 64.8 1.0
OE1 E:GLU178 2.5 58.5 1.0
OD2 E:ASP230 2.6 61.1 1.0
OE1 E:GLU232 2.6 58.3 1.0
CB E:ASP230 3.4 61.1 1.0
CG E:ASP267 3.5 55.3 1.0
CG E:GLU178 3.5 58.5 1.0
CG E:ASN179 3.5 64.8 1.0
CD E:GLU232 3.6 58.3 1.0
CA E:ASP230 3.9 61.1 1.0
OE2 E:GLU232 3.9 58.3 1.0
ND2 E:ASN179 3.9 64.8 1.0
CB E:GLU178 4.2 58.5 1.0
OD1 E:ASP267 4.2 55.3 1.0
N E:ARG231 4.4 56.1 1.0
CB E:ASP267 4.5 55.3 1.0
C E:ASP230 4.6 61.1 1.0
CB E:ASN179 4.8 64.8 1.0
O E:LEU229 4.8 64.4 1.0
CG E:GLU232 4.9 58.3 1.0
OD1 E:ASP264 5.0 53.5 1.0

Calcium binding site 2 out of 8 in 6q2o

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2002

b:54.7
occ:1.00
 OD1 E:ASP264 2.3 53.5 1.0
OD1 E:ASP267 2.3 55.3 1.0
O E:GLU265 2.4 57.4 1.0
OE2 E:GLU232 2.4 58.3 1.0
OD2 E:ASP264 2.5 53.5 1.0
OD1 E:ASP302 2.5 52.5 1.0
CG E:ASP264 2.7 53.5 1.0
CG E:ASP267 3.5 55.3 1.0
CG E:ASP302 3.6 52.5 1.0
C E:GLU265 3.6 57.4 1.0
CD E:GLU232 3.7 58.3 1.0
CA E:ASP302 3.7 52.5 1.0
N E:ASP267 3.8 55.3 1.0
OE2 E:GLU178 4.0 58.5 1.0
OD2 E:ASP267 4.1 55.3 1.0
O E:ALA301 4.2 48.8 1.0
CB E:ASP302 4.2 52.5 1.0
CB E:ASP264 4.2 53.5 1.0
NH2 E:ARG231 4.3 56.1 1.0
N E:GLU265 4.3 57.4 1.0
N E:ASP302 4.3 52.5 1.0
CA E:ASP266 4.4 54.5 1.0
N E:ASP266 4.5 54.5 1.0
C E:ALA301 4.5 48.8 1.0
OG E:SER268 4.5 51.2 1.0
OE1 E:GLU232 4.5 58.3 1.0
CG E:GLU232 4.5 58.3 1.0
N E:VAL303 4.5 46.1 1.0
CA E:ASP267 4.6 55.3 1.0
CB E:ASP267 4.6 55.3 1.0
C E:ASP266 4.6 54.5 1.0
OD2 E:ASP302 4.6 52.5 1.0
CA E:GLU265 4.6 57.4 1.0
C E:ASP302 4.7 52.5 1.0
N E:SER268 4.8 51.2 1.0
NE E:ARG231 4.8 56.1 1.0
C E:ASP267 4.8 55.3 1.0
CD E:GLU178 4.9 58.5 1.0
CA E:ASP264 5.0 53.5 1.0
CG2 E:VAL304 5.0 48.2 1.0
CB E:SER268 5.0 51.2 1.0

Calcium binding site 3 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 3 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2003

b:48.9
occ:1.00
 OD2 E:ASP302 2.3 52.5 1.0
OD2 E:ASP300 2.3 47.9 1.0
OD2 E:ASP378 2.4 59.5 1.0
OH E:TYR314 2.5 58.3 1.0
CB E:ASP302 2.5 52.5 1.0
OD1 E:ASP266 2.6 54.5 1.0
OD1 E:ASP300 2.7 47.9 1.0
O E:SER268 2.7 51.2 1.0
CG E:ASP302 2.7 52.5 1.0
OD1 E:ASP378 2.9 59.5 1.0
CG E:ASP300 2.9 47.9 1.0
CG E:ASP378 3.0 59.5 1.0
CG E:ASP266 3.6 54.5 1.0
CZ E:TYR314 3.7 58.3 1.0
CA E:ASP302 3.9 52.5 1.0
C E:SER268 3.9 51.2 1.0
OD2 E:ASP266 3.9 54.5 1.0
OD1 E:ASP302 4.0 52.5 1.0
N E:ASP302 4.2 52.5 1.0
CB E:ASP300 4.4 47.9 1.0
CE1 E:TYR314 4.4 58.3 1.0
CB E:ASP378 4.5 59.5 1.0
CE2 E:TYR314 4.6 58.3 1.0
C E:ASP302 4.6 52.5 1.0
CA E:SER268 4.7 51.2 1.0
CB E:SER268 4.7 51.2 1.0
N E:SER268 4.7 51.2 1.0
O E:ASP302 4.8 52.5 1.0
N E:ALA269 4.9 47.4 1.0
CB E:ASP266 4.9 54.5 1.0

Calcium binding site 4 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 4 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2004

b:47.7
occ:1.00
 O E:THR564 2.3 48.3 1.0
O E:HIS569 2.4 49.5 1.0
OD1 E:ASP567 2.4 48.9 1.0
OE1 E:GLU574 2.4 47.0 1.0
OD2 E:ASP567 2.4 48.9 1.0
OD2 E:ASP584 2.4 43.6 1.0
OE2 E:GLU574 2.5 47.0 1.0
CG E:ASP567 2.7 48.9 1.0
CD E:GLU574 2.7 47.0 1.0
C E:THR564 3.5 48.3 1.0
O E:CYS565 3.5 48.0 1.0
CG E:ASP584 3.6 43.6 1.0
C E:HIS569 3.6 49.5 1.0
CA E:CYS565 4.0 48.0 1.0
C E:CYS565 4.1 48.0 1.0
CB E:ASP584 4.1 43.6 1.0
CB E:ASP567 4.2 48.9 1.0
N E:CYS565 4.2 48.0 1.0
OD1 E:ASP571 4.2 47.9 1.0
CG E:GLU574 4.2 47.0 1.0
CG2 E:THR564 4.4 48.3 1.0
N E:CYS570 4.5 48.1 1.0
CA E:CYS570 4.5 48.1 1.0
N E:HIS569 4.5 49.5 1.0
CA E:THR564 4.6 48.3 1.0
CA E:HIS569 4.6 49.5 1.0
OD1 E:ASP584 4.6 43.6 1.0
N E:ASP571 4.7 47.9 1.0
N E:ASP567 4.7 48.9 1.0
CG E:ASP571 4.8 47.9 1.0
SG E:CYS581 4.9 42.5 1.0
CA E:ASP567 5.0 48.9 1.0
CB E:GLU574 5.0 47.0 1.0

Calcium binding site 5 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 5 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2001

b:76.5
occ:1.00
 OD1 F:ASP230 2.1 61.1 1.0
OD2 F:ASP267 2.3 55.3 1.0
CG F:ASP230 2.4 61.1 1.0
OE2 F:GLU178 2.4 58.5 1.0
CD F:GLU178 2.5 58.5 1.0
OD1 F:ASN179 2.5 64.8 1.0
OE1 F:GLU178 2.5 58.5 1.0
OD2 F:ASP230 2.6 61.1 1.0
OE1 F:GLU232 2.6 58.3 1.0
CB F:ASP230 3.4 61.1 1.0
CG F:ASP267 3.5 55.3 1.0
CG F:GLU178 3.5 58.5 1.0
CG F:ASN179 3.5 64.8 1.0
CD F:GLU232 3.6 58.3 1.0
CA F:ASP230 3.9 61.1 1.0
OE2 F:GLU232 3.9 58.3 1.0
ND2 F:ASN179 3.9 64.8 1.0
CB F:GLU178 4.2 58.5 1.0
OD1 F:ASP267 4.2 55.3 1.0
N F:ARG231 4.4 56.1 1.0
CB F:ASP267 4.5 55.3 1.0
C F:ASP230 4.6 61.1 1.0
CB F:ASN179 4.8 64.8 1.0
O F:LEU229 4.8 64.4 1.0
CG F:GLU232 4.9 58.3 1.0
OD1 F:ASP264 5.0 53.5 1.0

Calcium binding site 6 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 6 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2002

b:54.7
occ:1.00
 OD1 F:ASP264 2.3 53.5 1.0
OD1 F:ASP267 2.3 55.3 1.0
O F:GLU265 2.4 57.4 1.0
OE2 F:GLU232 2.4 58.3 1.0
OD2 F:ASP264 2.5 53.5 1.0
OD1 F:ASP302 2.5 52.5 1.0
CG F:ASP264 2.7 53.5 1.0
CG F:ASP267 3.5 55.3 1.0
CG F:ASP302 3.6 52.5 1.0
C F:GLU265 3.6 57.4 1.0
CD F:GLU232 3.7 58.3 1.0
CA F:ASP302 3.7 52.5 1.0
N F:ASP267 3.8 55.3 1.0
OE2 F:GLU178 4.0 58.5 1.0
OD2 F:ASP267 4.1 55.3 1.0
O F:ALA301 4.2 48.8 1.0
CB F:ASP302 4.2 52.5 1.0
CB F:ASP264 4.2 53.5 1.0
NH2 F:ARG231 4.3 56.1 1.0
N F:GLU265 4.3 57.4 1.0
N F:ASP302 4.3 52.5 1.0
CA F:ASP266 4.4 54.5 1.0
N F:ASP266 4.5 54.5 1.0
C F:ALA301 4.5 48.8 1.0
OG F:SER268 4.5 51.2 1.0
OE1 F:GLU232 4.5 58.3 1.0
CG F:GLU232 4.5 58.3 1.0
N F:VAL303 4.5 46.1 1.0
CA F:ASP267 4.6 55.3 1.0
CB F:ASP267 4.6 55.3 1.0
C F:ASP266 4.6 54.5 1.0
OD2 F:ASP302 4.6 52.5 1.0
CA F:GLU265 4.6 57.4 1.0
C F:ASP302 4.7 52.5 1.0
N F:SER268 4.8 51.2 1.0
NE F:ARG231 4.8 56.1 1.0
C F:ASP267 4.8 55.3 1.0
CD F:GLU178 4.9 58.5 1.0
CA F:ASP264 5.0 53.5 1.0
CG2 F:VAL304 5.0 48.2 1.0
CB F:SER268 5.0 51.2 1.0

Calcium binding site 7 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 7 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2003

b:48.9
occ:1.00
 OD2 F:ASP302 2.3 52.5 1.0
OD2 F:ASP300 2.3 47.9 1.0
OD2 F:ASP378 2.4 59.5 1.0
OH F:TYR314 2.5 58.3 1.0
CB F:ASP302 2.5 52.5 1.0
OD1 F:ASP266 2.6 54.5 1.0
OD1 F:ASP300 2.7 47.9 1.0
O F:SER268 2.7 51.2 1.0
CG F:ASP302 2.7 52.5 1.0
OD1 F:ASP378 2.9 59.5 1.0
CG F:ASP300 2.9 47.9 1.0
CG F:ASP378 3.0 59.5 1.0
CG F:ASP266 3.6 54.5 1.0
CZ F:TYR314 3.7 58.3 1.0
CA F:ASP302 3.9 52.5 1.0
C F:SER268 3.9 51.2 1.0
OD2 F:ASP266 3.9 54.5 1.0
OD1 F:ASP302 4.0 52.5 1.0
N F:ASP302 4.2 52.5 1.0
CB F:ASP300 4.4 47.9 1.0
CE1 F:TYR314 4.4 58.3 1.0
CB F:ASP378 4.5 59.5 1.0
CE2 F:TYR314 4.6 58.3 1.0
C F:ASP302 4.6 52.5 1.0
CA F:SER268 4.7 51.2 1.0
CB F:SER268 4.7 51.2 1.0
N F:SER268 4.7 51.2 1.0
O F:ASP302 4.8 52.5 1.0
N F:ALA269 4.9 47.4 1.0
CB F:ASP266 4.9 54.5 1.0

Calcium binding site 8 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 8 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2004

b:47.7
occ:1.00
 O F:THR564 2.3 48.3 1.0
O F:HIS569 2.4 49.5 1.0
OD1 F:ASP567 2.4 48.9 1.0
OE1 F:GLU574 2.4 47.0 1.0
OD2 F:ASP567 2.4 48.9 1.0
OD2 F:ASP584 2.4 43.6 1.0
OE2 F:GLU574 2.5 47.0 1.0
CG F:ASP567 2.7 48.9 1.0
CD F:GLU574 2.7 47.0 1.0
C F:THR564 3.5 48.3 1.0
O F:CYS565 3.5 48.0 1.0
CG F:ASP584 3.6 43.6 1.0
C F:HIS569 3.6 49.5 1.0
CA F:CYS565 4.0 48.0 1.0
C F:CYS565 4.1 48.0 1.0
CB F:ASP584 4.1 43.6 1.0
CB F:ASP567 4.2 48.9 1.0
N F:CYS565 4.2 48.0 1.0
OD1 F:ASP571 4.2 47.9 1.0
CG F:GLU574 4.2 47.0 1.0
CG2 F:THR564 4.4 48.3 1.0
N F:CYS570 4.5 48.1 1.0
CA F:CYS570 4.5 48.1 1.0
N F:HIS569 4.5 49.5 1.0
CA F:THR564 4.6 48.3 1.0
CA F:HIS569 4.6 49.5 1.0
OD1 F:ASP584 4.6 43.6 1.0
N F:ASP571 4.7 47.9 1.0
N F:ASP567 4.7 48.9 1.0
CG F:ASP571 4.8 47.9 1.0
SG F:CYS581 4.9 42.5 1.0
CA F:ASP567 5.0 48.9 1.0
CB F:GLU574 5.0 47.0 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: Wed Jul 9 16:59:53 2025

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