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Calcium in PDB 6q2n: Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex

Enzymatic activity of Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex

All present enzymatic activity of Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex:
2.7.10.1;

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex (pdb code 6q2n). 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/GFRA1/Gdnf Extracellular Complex, PDB code: 6q2n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6q2n

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Calcium binding site 1 out of 8 in the Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex


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/GFRA1/Gdnf Extracellular Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2001

b:0.8
occ:1.00
OD2 E:ASP300 2.1 0.2 1.0
OD2 E:ASP302 2.3 0.8 1.0
O E:SER268 2.4 0.9 1.0
OD1 E:ASP266 2.4 0.1 1.0
OD2 E:ASP378 2.4 0.7 1.0
OD1 E:ASP300 2.6 0.2 1.0
OD1 E:ASP378 2.6 0.7 1.0
CG E:ASP300 2.7 0.2 1.0
CG E:ASP378 2.8 0.7 1.0
CG E:ASP266 3.2 0.1 1.0
CG E:ASP302 3.3 0.8 1.0
C E:SER268 3.4 0.9 1.0
OD2 E:ASP266 3.7 0.1 1.0
CB E:ASP302 4.0 0.8 1.0
OH E:TYR314 4.0 0.3 1.0
CB E:ASP378 4.1 0.7 1.0
CB E:ASP266 4.2 0.1 1.0
OD1 E:ASP302 4.2 0.8 1.0
CB E:ASP300 4.2 0.2 1.0
N E:ALA269 4.3 0.2 1.0
CA E:SER268 4.3 0.9 1.0
CB E:SER268 4.3 0.9 1.0
N E:SER268 4.5 0.9 1.0
CA E:ASP266 4.6 0.1 1.0
CA E:ALA269 4.8 0.2 1.0
N E:ASP302 4.9 0.8 1.0
O E:ASP378 5.0 0.7 1.0

Calcium binding site 2 out of 8 in 6q2n

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex


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/GFRA1/Gdnf Extracellular Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2002

b:1.0
occ:1.00
N E:GLU265 2.3 0.8 1.0
OD1 E:ASP264 2.3 0.3 1.0
OD1 E:ASP267 2.4 0.1 1.0
O E:GLU265 2.4 0.8 1.0
OE2 E:GLU178 2.4 0.9 1.0
CA E:GLU265 2.5 0.8 1.0
CB E:GLU265 2.5 0.8 1.0
C E:GLU265 2.6 0.8 1.0
CG E:ASP267 2.7 0.1 1.0
OD2 E:ASP267 2.9 0.1 1.0
CA E:CA2003 2.9 0.3 1.0
C E:ASP264 3.4 0.3 1.0
OE2 E:GLU232 3.5 0.5 1.0
CG E:ASP264 3.6 0.3 1.0
CG E:GLU265 3.6 0.8 1.0
N E:ASP267 3.6 0.1 1.0
CD E:GLU178 3.7 0.9 1.0
N E:ASP266 3.8 0.1 1.0
CB E:ASP267 3.8 0.1 1.0
CA E:ASP264 4.0 0.3 1.0
OE1 E:GLU265 4.0 0.8 1.0
CD E:GLU265 4.2 0.8 1.0
CA E:ASP267 4.4 0.1 1.0
OE1 E:GLU178 4.4 0.9 1.0
CB E:ASP264 4.4 0.3 1.0
O E:ASP264 4.4 0.3 1.0
OD2 E:ASP264 4.4 0.3 1.0
OD1 E:ASP302 4.4 0.8 1.0
C E:ASP266 4.5 0.1 1.0
CA E:ASP266 4.5 0.1 1.0
ND2 E:ASN179 4.6 0.6 1.0
CD E:GLU232 4.6 0.5 1.0
CG E:GLU178 4.7 0.9 1.0
OE1 E:GLU232 4.8 0.5 1.0

Calcium binding site 3 out of 8 in 6q2n

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Calcium binding site 3 out of 8 in the Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex


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/GFRA1/Gdnf Extracellular Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2003

b:0.3
occ:1.00
OE2 E:GLU178 2.2 0.9 1.0
OE1 E:GLU232 2.3 0.5 1.0
OD2 E:ASP267 2.3 0.1 1.0
OD1 E:ASP230 2.3 0.1 1.0
OE2 E:GLU232 2.4 0.5 1.0
OE1 E:GLU178 2.5 0.9 1.0
CD E:GLU178 2.6 0.9 1.0
CD E:GLU232 2.6 0.5 1.0
CA E:CA2002 2.9 1.0 1.0
CG E:ASP230 3.2 0.1 1.0
CG E:ASP267 3.2 0.1 1.0
ND2 E:ASN179 3.3 0.6 1.0
OD1 E:ASP267 3.5 0.1 1.0
OD2 E:ASP230 3.6 0.1 1.0
OD1 E:ASP264 3.6 0.3 1.0
CG E:GLU178 3.9 0.9 1.0
CG E:GLU232 4.1 0.5 1.0
CG E:ASN179 4.4 0.6 1.0
N E:ARG231 4.5 0.2 1.0
CB E:ASP230 4.5 0.1 1.0
N E:GLU265 4.6 0.8 1.0
CB E:ASP267 4.6 0.1 1.0
CG E:ASP264 4.6 0.3 1.0
OD1 E:ASN179 4.7 0.6 1.0
CA E:ASP230 4.8 0.1 1.0
CB E:GLU178 4.8 0.9 1.0
CB E:GLU232 4.8 0.5 1.0
N E:GLU232 4.8 0.5 1.0
CB E:GLU265 5.0 0.8 1.0
CA E:ASP264 5.0 0.3 1.0
OE1 E:GLU265 5.0 0.8 1.0

Calcium binding site 4 out of 8 in 6q2n

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Calcium binding site 4 out of 8 in the Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex


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/GFRA1/Gdnf Extracellular Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2004

b:81.1
occ:1.00
O E:THR564 2.1 69.2 1.0
O E:HIS569 2.3 74.5 1.0
OD2 E:ASP584 2.4 60.8 1.0
OD1 E:ASP567 2.4 66.8 1.0
OE1 E:GLU574 2.5 81.7 1.0
OD2 E:ASP567 2.5 66.8 1.0
OE2 E:GLU574 2.5 81.7 1.0
CG E:ASP567 2.7 66.8 1.0
CD E:GLU574 2.8 81.7 1.0
O E:CYS565 2.9 73.8 1.0
CG E:ASP584 3.0 60.8 1.0
CB E:ASP584 3.1 60.8 1.0
C E:THR564 3.2 69.2 1.0
CA E:CYS565 3.5 73.8 1.0
C E:HIS569 3.5 74.5 1.0
C E:CYS565 3.6 73.8 1.0
N E:CYS565 3.9 73.8 1.0
SG E:CYS581 3.9 70.7 1.0
CB E:ASP567 4.2 66.8 1.0
OD1 E:ASP584 4.2 60.8 1.0
N E:HIS569 4.3 74.5 1.0
N E:CYS570 4.3 79.3 1.0
CG E:GLU574 4.4 81.7 1.0
CA E:CYS570 4.4 79.3 1.0
CG2 E:THR564 4.4 69.2 1.0
CA E:THR564 4.4 69.2 1.0
CA E:HIS569 4.5 74.5 1.0
N E:ASP567 4.5 66.8 1.0
CA E:ASP584 4.5 60.8 1.0
CB E:CYS565 4.8 73.8 1.0
OD1 E:ASP571 4.9 81.7 1.0
SG E:CYS585 4.9 54.6 1.0
N E:PRO566 4.9 65.3 1.0
N E:GLY568 4.9 67.9 1.0
CA E:ASP567 4.9 66.8 1.0
CB E:THR564 4.9 69.2 1.0
CB E:CYS581 5.0 70.7 1.0

Calcium binding site 5 out of 8 in 6q2n

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Calcium binding site 5 out of 8 in the Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex


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/GFRA1/Gdnf Extracellular Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2001

b:0.1
occ:1.00
OD2 F:ASP300 2.1 0.2 1.0
OD2 F:ASP302 2.3 0.4 1.0
O F:SER268 2.4 0.7 1.0
OD1 F:ASP266 2.4 0.3 1.0
OD2 F:ASP378 2.4 0.5 1.0
OD1 F:ASP300 2.6 0.2 1.0
OD1 F:ASP378 2.6 0.5 1.0
CG F:ASP300 2.7 0.2 1.0
CG F:ASP378 2.8 0.5 1.0
CG F:ASP266 3.2 0.3 1.0
CG F:ASP302 3.3 0.4 1.0
C F:SER268 3.4 0.7 1.0
OD2 F:ASP266 3.7 0.3 1.0
CB F:ASP302 4.0 0.4 1.0
OH F:TYR314 4.0 0.7 1.0
CB F:ASP378 4.1 0.5 1.0
CB F:ASP266 4.2 0.3 1.0
OD1 F:ASP302 4.2 0.4 1.0
CB F:ASP300 4.2 0.2 1.0
N F:ALA269 4.3 0.4 1.0
CA F:SER268 4.3 0.7 1.0
CB F:SER268 4.3 0.7 1.0
N F:SER268 4.5 0.7 1.0
CA F:ASP266 4.6 0.3 1.0
CA F:ALA269 4.8 0.4 1.0
N F:ASP302 4.9 0.4 1.0
O F:ASP378 5.0 0.5 1.0

Calcium binding site 6 out of 8 in 6q2n

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Calcium binding site 6 out of 8 in the Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex


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/GFRA1/Gdnf Extracellular Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2002

b:0.8
occ:1.00
N F:GLU265 2.2 0.5 1.0
OD1 F:ASP264 2.3 0.4 1.0
OD1 F:ASP267 2.4 0.9 1.0
O F:GLU265 2.4 0.5 1.0
OE2 F:GLU178 2.4 0.8 1.0
CA F:GLU265 2.5 0.5 1.0
CB F:GLU265 2.5 0.5 1.0
C F:GLU265 2.6 0.5 1.0
CG F:ASP267 2.7 0.9 1.0
OD2 F:ASP267 2.9 0.9 1.0
CA F:CA2003 2.9 0.9 1.0
C F:ASP264 3.4 0.4 1.0
OE2 F:GLU232 3.5 1.0 1.0
CG F:ASP264 3.6 0.4 1.0
CG F:GLU265 3.6 0.5 1.0
N F:ASP267 3.6 0.9 1.0
CD F:GLU178 3.7 0.8 1.0
N F:ASP266 3.8 0.3 1.0
CB F:ASP267 3.8 0.9 1.0
CA F:ASP264 4.0 0.4 1.0
OE1 F:GLU265 4.0 0.5 1.0
CD F:GLU265 4.2 0.5 1.0
CA F:ASP267 4.4 0.9 1.0
OE1 F:GLU178 4.4 0.8 1.0
CB F:ASP264 4.4 0.4 1.0
O F:ASP264 4.4 0.4 1.0
OD2 F:ASP264 4.4 0.4 1.0
OD1 F:ASP302 4.4 0.4 1.0
C F:ASP266 4.5 0.3 1.0
CA F:ASP266 4.5 0.3 1.0
CD F:GLU232 4.6 1.0 1.0
ND2 F:ASN179 4.6 0.9 1.0
CG F:GLU178 4.7 0.8 1.0
OE1 F:GLU232 4.8 1.0 1.0

Calcium binding site 7 out of 8 in 6q2n

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Calcium binding site 7 out of 8 in the Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex


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/GFRA1/Gdnf Extracellular Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2003

b:0.9
occ:1.00
OE2 F:GLU178 2.2 0.8 1.0
OE1 F:GLU232 2.3 1.0 1.0
OD2 F:ASP267 2.3 0.9 1.0
OD1 F:ASP230 2.3 0.4 1.0
OE2 F:GLU232 2.4 1.0 1.0
OE1 F:GLU178 2.5 0.8 1.0
CD F:GLU178 2.6 0.8 1.0
CD F:GLU232 2.6 1.0 1.0
CA F:CA2002 2.9 0.8 1.0
CG F:ASP230 3.2 0.4 1.0
CG F:ASP267 3.2 0.9 1.0
ND2 F:ASN179 3.3 0.9 1.0
OD1 F:ASP267 3.5 0.9 1.0
OD2 F:ASP230 3.6 0.4 1.0
OD1 F:ASP264 3.6 0.4 1.0
CG F:GLU178 3.9 0.8 1.0
CG F:GLU232 4.1 1.0 1.0
CG F:ASN179 4.4 0.9 1.0
N F:ARG231 4.5 0.8 1.0
CB F:ASP230 4.5 0.4 1.0
N F:GLU265 4.6 0.5 1.0
CB F:ASP267 4.6 0.9 1.0
CG F:ASP264 4.6 0.4 1.0
OD1 F:ASN179 4.7 0.9 1.0
CA F:ASP230 4.8 0.4 1.0
CB F:GLU178 4.8 0.8 1.0
CB F:GLU232 4.8 1.0 1.0
N F:GLU232 4.8 1.0 1.0
CB F:GLU265 5.0 0.5 1.0
CA F:ASP264 5.0 0.4 1.0
OE1 F:GLU265 5.0 0.5 1.0

Calcium binding site 8 out of 8 in 6q2n

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Calcium binding site 8 out of 8 in the Cryo-Em Structure of Ret/GFRA1/Gdnf Extracellular Complex


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/GFRA1/Gdnf Extracellular Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2004

b:71.9
occ:1.00
O F:THR564 2.1 64.7 1.0
O F:HIS569 2.3 67.2 1.0
OD2 F:ASP584 2.4 54.5 1.0
OD1 F:ASP567 2.4 61.1 1.0
OE1 F:GLU574 2.5 72.5 1.0
OD2 F:ASP567 2.5 61.1 1.0
OE2 F:GLU574 2.5 72.5 1.0
CG F:ASP567 2.7 61.1 1.0
CD F:GLU574 2.8 72.5 1.0
O F:CYS565 2.9 68.1 1.0
CG F:ASP584 3.0 54.5 1.0
CB F:ASP584 3.1 54.5 1.0
C F:THR564 3.2 64.7 1.0
CA F:CYS565 3.5 68.1 1.0
C F:HIS569 3.5 67.2 1.0
C F:CYS565 3.6 68.1 1.0
N F:CYS565 3.9 68.1 1.0
SG F:CYS581 3.9 62.5 1.0
CB F:ASP567 4.2 61.1 1.0
OD1 F:ASP584 4.2 54.5 1.0
N F:HIS569 4.3 67.2 1.0
N F:CYS570 4.3 69.0 1.0
CG F:GLU574 4.4 72.5 1.0
CA F:CYS570 4.4 69.0 1.0
CG2 F:THR564 4.4 64.7 1.0
CA F:THR564 4.4 64.7 1.0
CA F:HIS569 4.5 67.2 1.0
N F:ASP567 4.5 61.1 1.0
CA F:ASP584 4.5 54.5 1.0
CB F:CYS565 4.8 68.1 1.0
OD1 F:ASP571 4.9 73.7 1.0
SG F:CYS585 4.9 49.1 1.0
N F:PRO566 4.9 59.3 1.0
N F:GLY568 4.9 59.1 1.0
CA F:ASP567 4.9 61.1 1.0
CB F:THR564 4.9 64.7 1.0
CB F:CYS581 5.0 62.5 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 13:11:02 2024

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