Atomistry » Calcium » PDB 6pus-6q79 » 6q2j
Atomistry »
  Calcium »
    PDB 6pus-6q79 »
      6q2j »

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

Go back to Calcium Binding Sites List in 6q2j
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

Go back to Calcium Binding Sites List in 6q2j
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

Go back to Calcium Binding Sites List in 6q2j
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

Go back to Calcium Binding Sites List in 6q2j
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

Go back to Calcium Binding Sites List in 6q2j
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

Go back to Calcium Binding Sites List in 6q2j
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

Go back to Calcium Binding Sites List in 6q2j
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: Wed Jul 9 16:59:25 2025

Last articles

Mg in 4Q02
Mg in 4PYT
Mg in 4PZZ
Mg in 4PZY
Mg in 4PYL
Mg in 4PYO
Mg in 4PYK
Mg in 4PYJ
Mg in 4PY5
Mg in 4PYH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy