Atomistry » Calcium » PDB 6pu5-6q77 » 6q2s
Atomistry »
  Calcium »
    PDB 6pu5-6q77 »
      6q2s »

Calcium in PDB 6q2s: Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.

Enzymatic activity of Cryo-Em Structure of Ret/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.

All present enzymatic activity of Cryo-Em Structure of Ret/GFRA3/Artn 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. (pdb code 6q2s). 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry., PDB code: 6q2s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 1 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca707

b:73.4
occ:1.00
OD2 E:ASP300 2.2 69.6 1.0
OD2 E:ASP302 2.3 69.9 1.0
OD2 E:ASP378 2.4 79.1 1.0
OH E:TYR314 2.5 76.1 1.0
OD1 E:ASP266 2.6 70.8 1.0
OD1 E:ASP378 2.6 79.1 1.0
OD1 E:ASP300 2.7 69.6 1.0
O E:SER268 2.7 73.9 1.0
CG E:ASP300 2.8 69.6 1.0
CG E:ASP378 2.9 79.1 1.0
CG E:ASP302 3.3 69.9 1.0
CG E:ASP266 3.6 70.8 1.0
CZ E:TYR314 3.7 76.1 1.0
C E:SER268 3.8 73.9 1.0
CB E:ASP302 3.9 69.9 1.0
OD2 E:ASP266 4.0 70.8 1.0
CB E:ASP300 4.3 69.6 1.0
CE2 E:TYR314 4.4 76.1 1.0
OD1 E:ASP302 4.4 69.9 1.0
CB E:ASP378 4.4 79.1 1.0
N E:ALA269 4.6 74.9 1.0
CE1 E:TYR314 4.7 76.1 1.0
CB E:ASP266 4.7 70.8 1.0
CA E:SER268 4.8 73.9 1.0
CB E:SER268 4.8 73.9 1.0
N E:ASP302 4.9 69.9 1.0
CA E:ALA269 4.9 74.9 1.0
N E:SER268 5.0 73.9 1.0

Calcium binding site 2 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 2 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca708

b:75.8
occ:1.00
OE2 E:GLU232 2.2 76.5 1.0
O E:GLU265 2.2 70.4 1.0
OD1 E:ASP264 2.5 67.8 1.0
OD1 E:ASP267 2.5 75.5 1.0
OD1 E:ASP302 2.5 69.9 1.0
CD E:GLU232 3.4 76.5 1.0
CG E:ASP264 3.5 67.8 1.0
C E:GLU265 3.5 70.4 1.0
CG E:ASP302 3.5 69.9 1.0
CG E:ASP267 3.7 75.5 1.0
CA E:ASP302 3.7 69.9 1.0
OD2 E:ASP264 3.7 67.8 1.0
N E:ASP267 3.8 75.5 1.0
OE2 E:GLU178 3.9 74.1 1.0
CA E:CA709 3.9 82.4 1.0
O E:ALA301 3.9 69.0 1.0
CB E:ASP302 4.0 69.9 1.0
N E:GLU265 4.1 70.4 1.0
CG E:GLU232 4.2 76.5 1.0
OE1 E:GLU232 4.3 76.5 1.0
N E:ASP266 4.4 70.8 1.0
NH2 E:ARG231 4.4 74.0 1.0
N E:ASP302 4.4 69.9 1.0
OD2 E:ASP267 4.4 75.5 1.0
CA E:ASP266 4.4 70.8 1.0
CA E:GLU265 4.4 70.4 1.0
C E:ALA301 4.4 69.0 1.0
OG E:SER268 4.5 73.9 1.0
OD2 E:ASP302 4.6 69.9 1.0
C E:ASP266 4.6 70.8 1.0
NE E:ARG231 4.7 74.0 1.0
CA E:ASP267 4.7 75.5 1.0
CB E:ASP267 4.7 75.5 1.0
CB E:ASP264 4.8 67.8 1.0
C E:ASP302 4.9 69.9 1.0
CD E:GLU178 4.9 74.1 1.0
N E:VAL303 4.9 66.8 1.0
C E:ASP267 4.9 75.5 1.0
N E:SER268 5.0 73.9 1.0

Calcium binding site 3 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 3 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca709

b:82.4
occ:1.00
OD2 E:ASP267 2.1 75.5 1.0
OE1 E:GLU178 2.2 74.1 1.0
OE2 E:GLU178 2.3 74.1 1.0
OD1 E:ASP230 2.3 77.6 1.0
OE1 E:GLU232 2.3 76.5 1.0
CD E:GLU178 2.4 74.1 1.0
CG E:ASP267 2.5 75.5 1.0
OE2 E:GLU232 2.7 76.5 1.0
OD1 E:ASP267 2.8 75.5 1.0
CD E:GLU232 2.9 76.5 1.0
CG E:ASP230 3.5 77.6 1.0
CB E:ASP267 3.7 75.5 1.0
CG E:GLU178 3.8 74.1 1.0
CA E:CA708 3.9 75.8 1.0
ND2 E:ASN179 3.9 76.2 1.0
N E:ARG231 4.0 74.0 1.0
OD2 E:ASP230 4.1 77.6 1.0
O E:GLU265 4.3 70.4 1.0
CG E:GLU232 4.4 76.5 1.0
OD1 E:ASP264 4.5 67.8 1.0
CA E:ASP230 4.5 77.6 1.0
CB E:GLU178 4.5 74.1 1.0
CB E:ASP230 4.6 77.6 1.0
N E:GLU265 4.7 70.4 1.0
CB E:ARG231 4.7 74.0 1.0
N E:GLU232 4.7 76.5 1.0
CG E:ASN179 4.7 76.2 1.0
C E:ASP230 4.7 77.6 1.0
N E:ASP267 4.8 75.5 1.0
CA E:ASP267 4.8 75.5 1.0
OD1 E:ASN179 4.8 76.2 1.0
CA E:ARG231 4.9 74.0 1.0

Calcium binding site 4 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 4 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca710

b:53.2
occ:1.00
O E:CYS565 2.0 48.7 1.0
O E:THR564 2.1 49.8 1.0
OD1 E:ASP567 2.2 49.1 1.0
OE2 E:GLU574 2.2 46.2 1.0
OE1 E:GLU574 2.4 46.2 1.0
CA E:CYS565 2.5 48.7 1.0
C E:CYS565 2.5 48.7 1.0
CD E:GLU574 2.6 46.2 1.0
OD2 E:ASP567 2.6 49.1 1.0
CG E:ASP567 2.6 49.1 1.0
O E:HIS569 3.0 51.7 1.0
C E:THR564 3.0 49.8 1.0
N E:CYS565 3.2 48.7 1.0
OD2 E:ASP584 3.6 45.4 1.0
SG E:CYS581 3.6 40.6 1.0
N E:PRO566 3.8 48.0 1.0
CB E:CYS565 3.8 48.7 1.0
N E:ASP567 3.9 49.1 1.0
CB E:ASP567 4.0 49.1 1.0
CG E:GLU574 4.0 46.2 1.0
C E:HIS569 4.1 51.7 1.0
CG E:ASP584 4.4 45.4 1.0
CB E:ASP584 4.4 45.4 1.0
CA E:THR564 4.4 49.8 1.0
SG E:CYS565 4.4 48.7 1.0
CA E:ASP567 4.5 49.1 1.0
CA E:PRO566 4.5 48.0 1.0
C E:PRO566 4.7 48.0 1.0
CB E:CYS581 4.7 40.6 1.0
N E:GLY568 4.8 45.9 1.0
N E:HIS569 4.8 51.7 1.0
CB E:GLU574 4.8 46.2 1.0
N E:CYS570 5.0 53.9 1.0

Calcium binding site 5 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 5 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca707

b:73.4
occ:1.00
OD2 F:ASP300 2.2 69.6 1.0
OD2 F:ASP302 2.3 69.9 1.0
OD2 F:ASP378 2.4 79.1 1.0
OH F:TYR314 2.5 76.1 1.0
OD1 F:ASP266 2.6 70.8 1.0
OD1 F:ASP378 2.6 79.1 1.0
OD1 F:ASP300 2.7 69.6 1.0
O F:SER268 2.7 73.9 1.0
CG F:ASP300 2.8 69.6 1.0
CG F:ASP378 2.9 79.1 1.0
CG F:ASP302 3.3 69.9 1.0
CG F:ASP266 3.6 70.8 1.0
CZ F:TYR314 3.7 76.1 1.0
C F:SER268 3.8 73.9 1.0
CB F:ASP302 3.9 69.9 1.0
OD2 F:ASP266 4.0 70.8 1.0
CB F:ASP300 4.3 69.6 1.0
CE2 F:TYR314 4.4 76.1 1.0
OD1 F:ASP302 4.4 69.9 1.0
CB F:ASP378 4.4 79.1 1.0
N F:ALA269 4.6 74.9 1.0
CE1 F:TYR314 4.7 76.1 1.0
CB F:ASP266 4.7 70.8 1.0
CA F:SER268 4.8 73.9 1.0
CB F:SER268 4.8 73.9 1.0
N F:ASP302 4.9 69.9 1.0
CA F:ALA269 4.9 74.9 1.0
N F:SER268 5.0 73.9 1.0

Calcium binding site 6 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 6 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca708

b:75.8
occ:1.00
OE2 F:GLU232 2.2 76.5 1.0
O F:GLU265 2.2 70.4 1.0
OD1 F:ASP264 2.5 67.8 1.0
OD1 F:ASP267 2.5 75.5 1.0
OD1 F:ASP302 2.5 69.9 1.0
CD F:GLU232 3.4 76.5 1.0
CG F:ASP264 3.5 67.8 1.0
C F:GLU265 3.5 70.4 1.0
CG F:ASP302 3.5 69.9 1.0
CG F:ASP267 3.7 75.5 1.0
CA F:ASP302 3.7 69.9 1.0
OD2 F:ASP264 3.7 67.8 1.0
N F:ASP267 3.8 75.5 1.0
OE2 F:GLU178 3.9 74.1 1.0
CA F:CA709 3.9 82.4 1.0
O F:ALA301 3.9 69.0 1.0
CB F:ASP302 4.0 69.9 1.0
N F:GLU265 4.1 70.4 1.0
CG F:GLU232 4.2 76.5 1.0
OE1 F:GLU232 4.3 76.5 1.0
N F:ASP266 4.4 70.8 1.0
NH2 F:ARG231 4.4 74.0 1.0
N F:ASP302 4.4 69.9 1.0
OD2 F:ASP267 4.4 75.5 1.0
CA F:ASP266 4.4 70.8 1.0
CA F:GLU265 4.4 70.4 1.0
C F:ALA301 4.4 69.0 1.0
OG F:SER268 4.5 73.9 1.0
OD2 F:ASP302 4.6 69.9 1.0
C F:ASP266 4.6 70.8 1.0
NE F:ARG231 4.7 74.0 1.0
CA F:ASP267 4.7 75.5 1.0
CB F:ASP267 4.7 75.5 1.0
CB F:ASP264 4.8 67.8 1.0
C F:ASP302 4.9 69.9 1.0
CD F:GLU178 4.9 74.1 1.0
N F:VAL303 4.9 66.8 1.0
C F:ASP267 4.9 75.5 1.0
N F:SER268 5.0 73.9 1.0

Calcium binding site 7 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 7 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca709

b:82.4
occ:1.00
OD2 F:ASP267 2.1 75.5 1.0
OE1 F:GLU178 2.2 74.1 1.0
OE2 F:GLU178 2.3 74.1 1.0
OD1 F:ASP230 2.3 77.6 1.0
OE1 F:GLU232 2.3 76.5 1.0
CD F:GLU178 2.4 74.1 1.0
CG F:ASP267 2.5 75.5 1.0
OE2 F:GLU232 2.7 76.5 1.0
OD1 F:ASP267 2.8 75.5 1.0
CD F:GLU232 2.9 76.5 1.0
CG F:ASP230 3.5 77.6 1.0
CB F:ASP267 3.7 75.5 1.0
CG F:GLU178 3.8 74.1 1.0
CA F:CA708 3.9 75.8 1.0
ND2 F:ASN179 3.9 76.2 1.0
N F:ARG231 4.0 74.0 1.0
OD2 F:ASP230 4.1 77.6 1.0
O F:GLU265 4.3 70.4 1.0
CG F:GLU232 4.4 76.5 1.0
OD1 F:ASP264 4.5 67.8 1.0
CA F:ASP230 4.5 77.6 1.0
CB F:GLU178 4.5 74.1 1.0
CB F:ASP230 4.6 77.6 1.0
N F:GLU265 4.7 70.4 1.0
CB F:ARG231 4.7 74.0 1.0
N F:GLU232 4.7 76.5 1.0
CG F:ASN179 4.7 76.2 1.0
C F:ASP230 4.7 77.6 1.0
N F:ASP267 4.8 75.5 1.0
CA F:ASP267 4.8 75.5 1.0
OD1 F:ASN179 4.8 76.2 1.0
CA F:ARG231 4.9 74.0 1.0

Calcium binding site 8 out of 8 in 6q2s

Go back to Calcium Binding Sites List in 6q2s
Calcium binding site 8 out of 8 in the Cryo-Em Structure of Ret/GFRA3/Artn 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/GFRA3/Artn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca710

b:53.2
occ:1.00
O F:CYS565 2.0 48.7 1.0
O F:THR564 2.1 49.8 1.0
OD1 F:ASP567 2.2 49.1 1.0
OE2 F:GLU574 2.2 46.2 1.0
OE1 F:GLU574 2.4 46.2 1.0
CA F:CYS565 2.5 48.7 1.0
C F:CYS565 2.5 48.7 1.0
CD F:GLU574 2.6 46.2 1.0
OD2 F:ASP567 2.6 49.1 1.0
CG F:ASP567 2.6 49.1 1.0
O F:HIS569 3.0 51.7 1.0
C F:THR564 3.0 49.8 1.0
N F:CYS565 3.2 48.7 1.0
OD2 F:ASP584 3.6 45.4 1.0
SG F:CYS581 3.6 40.6 1.0
N F:PRO566 3.8 48.0 1.0
CB F:CYS565 3.8 48.7 1.0
N F:ASP567 3.9 49.1 1.0
CB F:ASP567 4.0 49.1 1.0
CG F:GLU574 4.0 46.2 1.0
C F:HIS569 4.1 51.7 1.0
CG F:ASP584 4.4 45.4 1.0
CB F:ASP584 4.4 45.4 1.0
CA F:THR564 4.4 49.8 1.0
SG F:CYS565 4.4 48.7 1.0
CA F:ASP567 4.5 49.1 1.0
CA F:PRO566 4.5 48.0 1.0
C F:PRO566 4.7 48.0 1.0
CB F:CYS581 4.7 40.6 1.0
N F:GLY568 4.8 45.9 1.0
N F:HIS569 4.8 51.7 1.0
CB F:GLU574 4.8 46.2 1.0
N F:CYS570 5.0 53.9 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 13:15:14 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy