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Calcium in PDB 6q2j: Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15

Enzymatic activity of Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15

All present enzymatic activity of Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15:
2.7.10.1;

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15 (pdb code 6q2j). 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 Extracellular Dimeric Complex of Ret/Gfral/GDF15, PDB code: 6q2j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6q2j

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Calcium binding site 1 out of 8 in the Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15


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 Extracellular Dimeric Complex of Ret/Gfral/GDF15 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca708

b:55.4
occ:1.00
 OD2 E:ASP300 2.3 51.6 1.0
OD2 E:ASP302 2.3 55.6 1.0
OD1 E:ASP266 2.4 56.8 1.0
OD2 E:ASP378 2.4 56.1 1.0
O E:SER268 2.6 55.9 1.0
OD2 E:ASP266 2.6 56.8 1.0
OD1 E:ASP378 2.7 56.1 1.0
OD1 E:ASP300 2.7 51.6 1.0
CG E:ASP266 2.8 56.8 1.0
CG E:ASP378 2.9 56.1 1.0
CG E:ASP300 2.9 51.6 1.0
CG E:ASP302 3.5 55.6 1.0
C E:SER268 3.8 55.9 1.0
CB E:ASP302 4.1 55.6 1.0
CB E:ASP378 4.3 56.1 1.0
CB E:ASP266 4.3 56.8 1.0
CB E:ASP300 4.4 51.6 1.0
OD1 E:ASP302 4.5 55.6 1.0
N E:ALA269 4.7 52.0 1.0
CA E:SER268 4.8 55.9 1.0
OH E:TYR314 4.8 59.1 1.0
N E:SER268 4.8 55.9 1.0
CA E:ALA269 4.9 52.0 1.0
O E:ASP378 4.9 56.1 1.0
CD E:PRO270 4.9 50.4 1.0
CA E:ASP266 5.0 56.8 1.0
CB E:SER268 5.0 55.9 1.0

Calcium binding site 2 out of 8 in 6q2j

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15


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 Extracellular Dimeric Complex of Ret/Gfral/GDF15 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca709

b:59.4
occ:1.00
 OD1 E:ASP267 2.3 60.2 1.0
OD1 E:ASP264 2.4 56.5 1.0
OE2 E:GLU232 2.4 62.1 1.0
O E:GLU265 2.4 62.2 1.0
OD1 E:ASP302 2.4 55.6 1.0
CG E:ASP264 3.2 56.5 1.0
OD2 E:ASP264 3.2 56.5 1.0
CG E:ASP267 3.5 60.2 1.0
CG E:ASP302 3.6 55.6 1.0
CD E:GLU232 3.6 62.1 1.0
C E:GLU265 3.6 62.2 1.0
OE2 E:GLU178 3.6 59.3 1.0
N E:ASP267 3.7 60.2 1.0
O E:ALA301 3.8 56.1 1.0
CA E:ASP302 4.0 55.6 1.0
OD2 E:ASP267 4.1 60.2 1.0
CB E:ASP302 4.2 55.6 1.0
NH2 E:ARG231 4.2 59.9 1.0
CA E:ASP266 4.3 56.8 1.0
N E:GLU265 4.3 62.2 1.0
N E:ASP266 4.4 56.8 1.0
OE1 E:GLU232 4.5 62.1 1.0
CG E:GLU232 4.5 62.1 1.0
OG E:SER268 4.5 55.9 1.0
C E:ASP266 4.5 56.8 1.0
CA E:ASP267 4.5 60.2 1.0
CB E:ASP267 4.5 60.2 1.0
OD2 E:ASP302 4.6 55.6 1.0
C E:ALA301 4.6 56.1 1.0
CB E:ASP264 4.6 56.5 1.0
CD E:GLU178 4.6 59.3 1.0
CA E:GLU265 4.7 62.2 1.0
N E:ASP302 4.7 55.6 1.0
C E:ASP267 4.8 60.2 1.0
N E:SER268 4.9 55.9 1.0
NE E:ARG231 4.9 59.9 1.0
OE1 E:GLU178 4.9 59.3 1.0
CA E:CA710 4.9 77.3 1.0
CB E:SER268 5.0 55.9 1.0

Calcium binding site 3 out of 8 in 6q2j

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Calcium binding site 3 out of 8 in the Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15


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 Extracellular Dimeric Complex of Ret/Gfral/GDF15 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca710

b:77.3
occ:1.00
 OD2 E:ASP267 2.2 60.2 1.0
CD E:GLU178 2.3 59.3 1.0
OE1 E:GLU178 2.3 59.3 1.0
OE1 E:GLU232 2.4 62.1 1.0
OD1 E:ASP230 2.4 63.3 1.0
OE2 E:GLU178 2.4 59.3 1.0
OD1 E:ASN179 2.4 63.6 1.0
CD E:GLU232 3.3 62.1 1.0
CG E:GLU178 3.3 59.3 1.0
CG E:ASP230 3.3 63.3 1.0
CG E:ASP267 3.3 60.2 1.0
OE2 E:GLU232 3.5 62.1 1.0
CG E:ASN179 3.5 63.6 1.0
OD1 E:ASP267 3.9 60.2 1.0
CB E:GLU178 3.9 59.3 1.0
OD2 E:ASP230 3.9 63.3 1.0
ND2 E:ASN179 4.0 63.6 1.0
CA E:ASP230 4.1 63.3 1.0
CB E:ASP230 4.2 63.3 1.0
N E:ARG231 4.2 59.9 1.0
CB E:ASP267 4.5 60.2 1.0
C E:ASP230 4.6 63.3 1.0
CG E:GLU232 4.7 62.1 1.0
CB E:ASN179 4.7 63.6 1.0
O E:LEU229 4.8 63.5 1.0
N E:GLU232 4.9 62.1 1.0
CA E:CA709 4.9 59.4 1.0
N E:ASN179 5.0 63.6 1.0
OD1 E:ASP264 5.0 56.5 1.0

Calcium binding site 4 out of 8 in 6q2j

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Calcium binding site 4 out of 8 in the Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15


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 Extracellular Dimeric Complex of Ret/Gfral/GDF15 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca711

b:41.4
occ:1.00
 OD1 E:ASP567 2.3 47.0 1.0
O E:THR564 2.3 45.9 1.0
OE1 E:GLU574 2.4 44.1 1.0
OD2 E:ASP584 2.4 43.4 1.0
OE2 E:GLU574 2.4 44.1 1.0
OD2 E:ASP567 2.5 47.0 1.0
O E:HIS569 2.6 46.9 1.0
CG E:ASP567 2.7 47.0 1.0
CD E:GLU574 2.7 44.1 1.0
O E:CYS565 2.8 46.6 1.0
C E:THR564 3.4 45.9 1.0
CG E:ASP584 3.5 43.4 1.0
C E:CYS565 3.6 46.6 1.0
CA E:CYS565 3.6 46.6 1.0
C E:HIS569 3.8 46.9 1.0
N E:CYS565 4.0 46.6 1.0
CB E:ASP584 4.1 43.4 1.0
CB E:ASP567 4.2 47.0 1.0
OD1 E:ASP571 4.2 44.7 1.0
CG E:GLU574 4.3 44.1 1.0
CG2 E:THR564 4.3 45.9 1.0
SG E:CYS581 4.3 39.8 1.0
N E:ASP567 4.4 47.0 1.0
CA E:THR564 4.6 45.9 1.0
OD1 E:ASP584 4.6 43.4 1.0
CA E:CYS570 4.6 46.4 1.0
N E:CYS570 4.6 46.4 1.0
N E:HIS569 4.7 46.9 1.0
CA E:HIS569 4.8 46.9 1.0
N E:PRO566 4.8 43.2 1.0
N E:ASP571 4.8 44.7 1.0
CG E:ASP571 4.8 44.7 1.0
CA E:ASP567 4.9 47.0 1.0
CB E:CYS565 4.9 46.6 1.0

Calcium binding site 5 out of 8 in 6q2j

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Calcium binding site 5 out of 8 in the Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15


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 Extracellular Dimeric Complex of Ret/Gfral/GDF15 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca708

b:55.4
occ:1.00
 OD2 F:ASP300 2.3 51.6 1.0
OD2 F:ASP302 2.3 55.6 1.0
OD1 F:ASP266 2.4 56.8 1.0
OD2 F:ASP378 2.4 56.1 1.0
O F:SER268 2.6 55.9 1.0
OD2 F:ASP266 2.6 56.8 1.0
OD1 F:ASP378 2.7 56.1 1.0
OD1 F:ASP300 2.7 51.6 1.0
CG F:ASP266 2.8 56.8 1.0
CG F:ASP378 2.9 56.1 1.0
CG F:ASP300 2.9 51.6 1.0
CG F:ASP302 3.5 55.6 1.0
C F:SER268 3.8 55.9 1.0
CB F:ASP302 4.1 55.6 1.0
CB F:ASP378 4.3 56.1 1.0
CB F:ASP266 4.3 56.8 1.0
CB F:ASP300 4.4 51.6 1.0
OD1 F:ASP302 4.5 55.6 1.0
N F:ALA269 4.7 52.0 1.0
OH F:TYR314 4.8 59.1 1.0
CA F:SER268 4.8 55.9 1.0
N F:SER268 4.8 55.9 1.0
CA F:ALA269 4.9 52.0 1.0
O F:ASP378 4.9 56.1 1.0
CD F:PRO270 4.9 50.4 1.0
CA F:ASP266 5.0 56.8 1.0
CB F:SER268 5.0 55.9 1.0

Calcium binding site 6 out of 8 in 6q2j

Go back to Calcium Binding Sites List in 6q2j
Calcium binding site 6 out of 8 in the Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15


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 Extracellular Dimeric Complex of Ret/Gfral/GDF15 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca709

b:59.4
occ:1.00
 OD1 F:ASP267 2.3 60.2 1.0
OD1 F:ASP264 2.4 56.5 1.0
OE2 F:GLU232 2.4 62.1 1.0
O F:GLU265 2.4 62.2 1.0
OD1 F:ASP302 2.4 55.6 1.0
CG F:ASP264 3.2 56.5 1.0
OD2 F:ASP264 3.2 56.5 1.0
CG F:ASP267 3.5 60.2 1.0
CG F:ASP302 3.6 55.6 1.0
CD F:GLU232 3.6 62.1 1.0
C F:GLU265 3.6 62.2 1.0
OE2 F:GLU178 3.6 59.3 1.0
N F:ASP267 3.7 60.2 1.0
O F:ALA301 3.8 56.1 1.0
CA F:ASP302 4.0 55.6 1.0
OD2 F:ASP267 4.1 60.2 1.0
CB F:ASP302 4.2 55.6 1.0
NH2 F:ARG231 4.2 59.9 1.0
CA F:ASP266 4.3 56.8 1.0
N F:GLU265 4.3 62.2 1.0
N F:ASP266 4.4 56.8 1.0
OE1 F:GLU232 4.5 62.1 1.0
CG F:GLU232 4.5 62.1 1.0
OG F:SER268 4.5 55.9 1.0
C F:ASP266 4.5 56.8 1.0
CA F:ASP267 4.5 60.2 1.0
CB F:ASP267 4.5 60.2 1.0
OD2 F:ASP302 4.6 55.6 1.0
C F:ALA301 4.6 56.1 1.0
CB F:ASP264 4.6 56.5 1.0
CD F:GLU178 4.6 59.3 1.0
CA F:GLU265 4.7 62.2 1.0
N F:ASP302 4.7 55.6 1.0
C F:ASP267 4.8 60.2 1.0
N F:SER268 4.9 55.9 1.0
NE F:ARG231 4.9 59.9 1.0
OE1 F:GLU178 4.9 59.3 1.0
CA F:CA710 4.9 77.3 1.0
CB F:SER268 5.0 55.9 1.0

Calcium binding site 7 out of 8 in 6q2j

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Calcium binding site 7 out of 8 in the Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15


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 Extracellular Dimeric Complex of Ret/Gfral/GDF15 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca710

b:77.3
occ:1.00
 OD2 F:ASP267 2.2 60.2 1.0
CD F:GLU178 2.3 59.3 1.0
OE1 F:GLU178 2.3 59.3 1.0
OE1 F:GLU232 2.4 62.1 1.0
OD1 F:ASP230 2.4 63.3 1.0
OE2 F:GLU178 2.4 59.3 1.0
OD1 F:ASN179 2.4 63.6 1.0
CD F:GLU232 3.3 62.1 1.0
CG F:GLU178 3.3 59.3 1.0
CG F:ASP230 3.3 63.3 1.0
CG F:ASP267 3.3 60.2 1.0
OE2 F:GLU232 3.5 62.1 1.0
CG F:ASN179 3.5 63.6 1.0
OD1 F:ASP267 3.9 60.2 1.0
CB F:GLU178 3.9 59.3 1.0
OD2 F:ASP230 3.9 63.3 1.0
ND2 F:ASN179 4.0 63.6 1.0
CA F:ASP230 4.1 63.3 1.0
CB F:ASP230 4.2 63.3 1.0
N F:ARG231 4.2 59.9 1.0
CB F:ASP267 4.5 60.2 1.0
C F:ASP230 4.6 63.3 1.0
CG F:GLU232 4.7 62.1 1.0
CB F:ASN179 4.7 63.6 1.0
O F:LEU229 4.8 63.5 1.0
N F:GLU232 4.9 62.1 1.0
CA F:CA709 4.9 59.4 1.0
N F:ASN179 5.0 63.6 1.0
OD1 F:ASP264 5.0 56.5 1.0

Calcium binding site 8 out of 8 in 6q2j

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Calcium binding site 8 out of 8 in the Cryo-Em Structure of Extracellular Dimeric Complex of Ret/Gfral/GDF15


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 Extracellular Dimeric Complex of Ret/Gfral/GDF15 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca711

b:41.4
occ:1.00
 OD1 F:ASP567 2.3 47.0 1.0
O F:THR564 2.3 45.9 1.0
OE1 F:GLU574 2.4 44.1 1.0
OD2 F:ASP584 2.4 43.4 1.0
OE2 F:GLU574 2.4 44.1 1.0
OD2 F:ASP567 2.5 47.0 1.0
O F:HIS569 2.6 46.9 1.0
CG F:ASP567 2.7 47.0 1.0
CD F:GLU574 2.7 44.1 1.0
O F:CYS565 2.8 46.6 1.0
C F:THR564 3.4 45.9 1.0
CG F:ASP584 3.5 43.4 1.0
C F:CYS565 3.6 46.6 1.0
CA F:CYS565 3.6 46.6 1.0
C F:HIS569 3.8 46.9 1.0
N F:CYS565 4.0 46.6 1.0
CB F:ASP584 4.1 43.4 1.0
CB F:ASP567 4.2 47.0 1.0
OD1 F:ASP571 4.2 44.7 1.0
CG F:GLU574 4.3 44.1 1.0
CG2 F:THR564 4.3 45.9 1.0
SG F:CYS581 4.3 39.8 1.0
N F:ASP567 4.4 47.0 1.0
CA F:THR564 4.6 45.9 1.0
OD1 F:ASP584 4.6 43.4 1.0
CA F:CYS570 4.6 46.4 1.0
N F:CYS570 4.6 46.4 1.0
N F:HIS569 4.7 46.9 1.0
CA F:HIS569 4.8 46.9 1.0
N F:PRO566 4.8 43.2 1.0
N F:ASP571 4.8 44.7 1.0
CG F:ASP571 4.8 44.7 1.0
CA F:ASP567 4.9 47.0 1.0
CB F:CYS565 4.9 46.6 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 13:10:30 2024

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