Atomistry » Calcium » PDB 6pus-6q79 » 6q2n
Atomistry »
  Calcium »
    PDB 6pus-6q79 »
      6q2n »

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

Go back to Calcium Binding Sites List in 6q2n
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

Go back to Calcium Binding Sites List in 6q2n
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

Go back to Calcium Binding Sites List in 6q2n
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

Go back to Calcium Binding Sites List in 6q2n
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

Go back to Calcium Binding Sites List in 6q2n
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

Go back to Calcium Binding Sites List in 6q2n
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

Go back to Calcium Binding Sites List in 6q2n
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

Go back to Calcium Binding Sites List in 6q2n
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: Wed Jul 9 16:59:48 2025

Last articles

Mg in 4X5C
Mg in 4X5E
Mg in 4X5V
Mg in 4X5B
Mg in 4X59
Mg in 4X58
Mg in 4X4V
Mg in 4X4S
Mg in 4X4R
Mg in 4X4Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy