Atomistry » Calcium » PDB 6pu4-6q6x » 6q2s
Atomistry »
  Calcium »
    PDB 6pu4-6q6x »
      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 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy