Atomistry » Calcium » PDB 6pu4-6q6x » 6q2o
Atomistry »
  Calcium »
    PDB 6pu4-6q6x »
      6q2o »

Calcium in PDB 6q2o: Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.

Enzymatic activity of Cryo-Em Structure of Ret/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry.

All present enzymatic activity of Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. (pdb code 6q2o). 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry., PDB code: 6q2o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 1 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2001

b:76.5
occ:1.00
 OD1 E:ASP230 2.1 61.1 1.0
OD2 E:ASP267 2.3 55.3 1.0
CG E:ASP230 2.4 61.1 1.0
OE2 E:GLU178 2.4 58.5 1.0
CD E:GLU178 2.5 58.5 1.0
OD1 E:ASN179 2.5 64.8 1.0
OE1 E:GLU178 2.5 58.5 1.0
OD2 E:ASP230 2.6 61.1 1.0
OE1 E:GLU232 2.6 58.3 1.0
CB E:ASP230 3.4 61.1 1.0
CG E:ASP267 3.5 55.3 1.0
CG E:GLU178 3.5 58.5 1.0
CG E:ASN179 3.5 64.8 1.0
CD E:GLU232 3.6 58.3 1.0
CA E:ASP230 3.9 61.1 1.0
OE2 E:GLU232 3.9 58.3 1.0
ND2 E:ASN179 3.9 64.8 1.0
CB E:GLU178 4.2 58.5 1.0
OD1 E:ASP267 4.2 55.3 1.0
N E:ARG231 4.4 56.1 1.0
CB E:ASP267 4.5 55.3 1.0
C E:ASP230 4.6 61.1 1.0
CB E:ASN179 4.8 64.8 1.0
O E:LEU229 4.8 64.4 1.0
CG E:GLU232 4.9 58.3 1.0
OD1 E:ASP264 5.0 53.5 1.0

Calcium binding site 2 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 2 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2002

b:54.7
occ:1.00
 OD1 E:ASP264 2.3 53.5 1.0
OD1 E:ASP267 2.3 55.3 1.0
O E:GLU265 2.4 57.4 1.0
OE2 E:GLU232 2.4 58.3 1.0
OD2 E:ASP264 2.5 53.5 1.0
OD1 E:ASP302 2.5 52.5 1.0
CG E:ASP264 2.7 53.5 1.0
CG E:ASP267 3.5 55.3 1.0
CG E:ASP302 3.6 52.5 1.0
C E:GLU265 3.6 57.4 1.0
CD E:GLU232 3.7 58.3 1.0
CA E:ASP302 3.7 52.5 1.0
N E:ASP267 3.8 55.3 1.0
OE2 E:GLU178 4.0 58.5 1.0
OD2 E:ASP267 4.1 55.3 1.0
O E:ALA301 4.2 48.8 1.0
CB E:ASP302 4.2 52.5 1.0
CB E:ASP264 4.2 53.5 1.0
NH2 E:ARG231 4.3 56.1 1.0
N E:GLU265 4.3 57.4 1.0
N E:ASP302 4.3 52.5 1.0
CA E:ASP266 4.4 54.5 1.0
N E:ASP266 4.5 54.5 1.0
C E:ALA301 4.5 48.8 1.0
OG E:SER268 4.5 51.2 1.0
OE1 E:GLU232 4.5 58.3 1.0
CG E:GLU232 4.5 58.3 1.0
N E:VAL303 4.5 46.1 1.0
CA E:ASP267 4.6 55.3 1.0
CB E:ASP267 4.6 55.3 1.0
C E:ASP266 4.6 54.5 1.0
OD2 E:ASP302 4.6 52.5 1.0
CA E:GLU265 4.6 57.4 1.0
C E:ASP302 4.7 52.5 1.0
N E:SER268 4.8 51.2 1.0
NE E:ARG231 4.8 56.1 1.0
C E:ASP267 4.8 55.3 1.0
CD E:GLU178 4.9 58.5 1.0
CA E:ASP264 5.0 53.5 1.0
CG2 E:VAL304 5.0 48.2 1.0
CB E:SER268 5.0 51.2 1.0

Calcium binding site 3 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 3 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2003

b:48.9
occ:1.00
 OD2 E:ASP302 2.3 52.5 1.0
OD2 E:ASP300 2.3 47.9 1.0
OD2 E:ASP378 2.4 59.5 1.0
OH E:TYR314 2.5 58.3 1.0
CB E:ASP302 2.5 52.5 1.0
OD1 E:ASP266 2.6 54.5 1.0
OD1 E:ASP300 2.7 47.9 1.0
O E:SER268 2.7 51.2 1.0
CG E:ASP302 2.7 52.5 1.0
OD1 E:ASP378 2.9 59.5 1.0
CG E:ASP300 2.9 47.9 1.0
CG E:ASP378 3.0 59.5 1.0
CG E:ASP266 3.6 54.5 1.0
CZ E:TYR314 3.7 58.3 1.0
CA E:ASP302 3.9 52.5 1.0
C E:SER268 3.9 51.2 1.0
OD2 E:ASP266 3.9 54.5 1.0
OD1 E:ASP302 4.0 52.5 1.0
N E:ASP302 4.2 52.5 1.0
CB E:ASP300 4.4 47.9 1.0
CE1 E:TYR314 4.4 58.3 1.0
CB E:ASP378 4.5 59.5 1.0
CE2 E:TYR314 4.6 58.3 1.0
C E:ASP302 4.6 52.5 1.0
CA E:SER268 4.7 51.2 1.0
CB E:SER268 4.7 51.2 1.0
N E:SER268 4.7 51.2 1.0
O E:ASP302 4.8 52.5 1.0
N E:ALA269 4.9 47.4 1.0
CB E:ASP266 4.9 54.5 1.0

Calcium binding site 4 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 4 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2004

b:47.7
occ:1.00
 O E:THR564 2.3 48.3 1.0
O E:HIS569 2.4 49.5 1.0
OD1 E:ASP567 2.4 48.9 1.0
OE1 E:GLU574 2.4 47.0 1.0
OD2 E:ASP567 2.4 48.9 1.0
OD2 E:ASP584 2.4 43.6 1.0
OE2 E:GLU574 2.5 47.0 1.0
CG E:ASP567 2.7 48.9 1.0
CD E:GLU574 2.7 47.0 1.0
C E:THR564 3.5 48.3 1.0
O E:CYS565 3.5 48.0 1.0
CG E:ASP584 3.6 43.6 1.0
C E:HIS569 3.6 49.5 1.0
CA E:CYS565 4.0 48.0 1.0
C E:CYS565 4.1 48.0 1.0
CB E:ASP584 4.1 43.6 1.0
CB E:ASP567 4.2 48.9 1.0
N E:CYS565 4.2 48.0 1.0
OD1 E:ASP571 4.2 47.9 1.0
CG E:GLU574 4.2 47.0 1.0
CG2 E:THR564 4.4 48.3 1.0
N E:CYS570 4.5 48.1 1.0
CA E:CYS570 4.5 48.1 1.0
N E:HIS569 4.5 49.5 1.0
CA E:THR564 4.6 48.3 1.0
CA E:HIS569 4.6 49.5 1.0
OD1 E:ASP584 4.6 43.6 1.0
N E:ASP571 4.7 47.9 1.0
N E:ASP567 4.7 48.9 1.0
CG E:ASP571 4.8 47.9 1.0
SG E:CYS581 4.9 42.5 1.0
CA E:ASP567 5.0 48.9 1.0
CB E:GLU574 5.0 47.0 1.0

Calcium binding site 5 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 5 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2001

b:76.5
occ:1.00
 OD1 F:ASP230 2.1 61.1 1.0
OD2 F:ASP267 2.3 55.3 1.0
CG F:ASP230 2.4 61.1 1.0
OE2 F:GLU178 2.4 58.5 1.0
CD F:GLU178 2.5 58.5 1.0
OD1 F:ASN179 2.5 64.8 1.0
OE1 F:GLU178 2.5 58.5 1.0
OD2 F:ASP230 2.6 61.1 1.0
OE1 F:GLU232 2.6 58.3 1.0
CB F:ASP230 3.4 61.1 1.0
CG F:ASP267 3.5 55.3 1.0
CG F:GLU178 3.5 58.5 1.0
CG F:ASN179 3.5 64.8 1.0
CD F:GLU232 3.6 58.3 1.0
CA F:ASP230 3.9 61.1 1.0
OE2 F:GLU232 3.9 58.3 1.0
ND2 F:ASN179 3.9 64.8 1.0
CB F:GLU178 4.2 58.5 1.0
OD1 F:ASP267 4.2 55.3 1.0
N F:ARG231 4.4 56.1 1.0
CB F:ASP267 4.5 55.3 1.0
C F:ASP230 4.6 61.1 1.0
CB F:ASN179 4.8 64.8 1.0
O F:LEU229 4.8 64.4 1.0
CG F:GLU232 4.9 58.3 1.0
OD1 F:ASP264 5.0 53.5 1.0

Calcium binding site 6 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 6 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2002

b:54.7
occ:1.00
 OD1 F:ASP264 2.3 53.5 1.0
OD1 F:ASP267 2.3 55.3 1.0
O F:GLU265 2.4 57.4 1.0
OE2 F:GLU232 2.4 58.3 1.0
OD2 F:ASP264 2.5 53.5 1.0
OD1 F:ASP302 2.5 52.5 1.0
CG F:ASP264 2.7 53.5 1.0
CG F:ASP267 3.5 55.3 1.0
CG F:ASP302 3.6 52.5 1.0
C F:GLU265 3.6 57.4 1.0
CD F:GLU232 3.7 58.3 1.0
CA F:ASP302 3.7 52.5 1.0
N F:ASP267 3.8 55.3 1.0
OE2 F:GLU178 4.0 58.5 1.0
OD2 F:ASP267 4.1 55.3 1.0
O F:ALA301 4.2 48.8 1.0
CB F:ASP302 4.2 52.5 1.0
CB F:ASP264 4.2 53.5 1.0
NH2 F:ARG231 4.3 56.1 1.0
N F:GLU265 4.3 57.4 1.0
N F:ASP302 4.3 52.5 1.0
CA F:ASP266 4.4 54.5 1.0
N F:ASP266 4.5 54.5 1.0
C F:ALA301 4.5 48.8 1.0
OG F:SER268 4.5 51.2 1.0
OE1 F:GLU232 4.5 58.3 1.0
CG F:GLU232 4.5 58.3 1.0
N F:VAL303 4.5 46.1 1.0
CA F:ASP267 4.6 55.3 1.0
CB F:ASP267 4.6 55.3 1.0
C F:ASP266 4.6 54.5 1.0
OD2 F:ASP302 4.6 52.5 1.0
CA F:GLU265 4.6 57.4 1.0
C F:ASP302 4.7 52.5 1.0
N F:SER268 4.8 51.2 1.0
NE F:ARG231 4.8 56.1 1.0
C F:ASP267 4.8 55.3 1.0
CD F:GLU178 4.9 58.5 1.0
CA F:ASP264 5.0 53.5 1.0
CG2 F:VAL304 5.0 48.2 1.0
CB F:SER268 5.0 51.2 1.0

Calcium binding site 7 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 7 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2003

b:48.9
occ:1.00
 OD2 F:ASP302 2.3 52.5 1.0
OD2 F:ASP300 2.3 47.9 1.0
OD2 F:ASP378 2.4 59.5 1.0
OH F:TYR314 2.5 58.3 1.0
CB F:ASP302 2.5 52.5 1.0
OD1 F:ASP266 2.6 54.5 1.0
OD1 F:ASP300 2.7 47.9 1.0
O F:SER268 2.7 51.2 1.0
CG F:ASP302 2.7 52.5 1.0
OD1 F:ASP378 2.9 59.5 1.0
CG F:ASP300 2.9 47.9 1.0
CG F:ASP378 3.0 59.5 1.0
CG F:ASP266 3.6 54.5 1.0
CZ F:TYR314 3.7 58.3 1.0
CA F:ASP302 3.9 52.5 1.0
C F:SER268 3.9 51.2 1.0
OD2 F:ASP266 3.9 54.5 1.0
OD1 F:ASP302 4.0 52.5 1.0
N F:ASP302 4.2 52.5 1.0
CB F:ASP300 4.4 47.9 1.0
CE1 F:TYR314 4.4 58.3 1.0
CB F:ASP378 4.5 59.5 1.0
CE2 F:TYR314 4.6 58.3 1.0
C F:ASP302 4.6 52.5 1.0
CA F:SER268 4.7 51.2 1.0
CB F:SER268 4.7 51.2 1.0
N F:SER268 4.7 51.2 1.0
O F:ASP302 4.8 52.5 1.0
N F:ALA269 4.9 47.4 1.0
CB F:ASP266 4.9 54.5 1.0

Calcium binding site 8 out of 8 in 6q2o

Go back to Calcium Binding Sites List in 6q2o
Calcium binding site 8 out of 8 in the Cryo-Em Structure of Ret/GFRA2/Nrtn 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/GFRA2/Nrtn Extracellular Complex. the 3D Refinement Was Applied with C2 Symmetry. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca2004

b:47.7
occ:1.00
 O F:THR564 2.3 48.3 1.0
O F:HIS569 2.4 49.5 1.0
OD1 F:ASP567 2.4 48.9 1.0
OE1 F:GLU574 2.4 47.0 1.0
OD2 F:ASP567 2.4 48.9 1.0
OD2 F:ASP584 2.4 43.6 1.0
OE2 F:GLU574 2.5 47.0 1.0
CG F:ASP567 2.7 48.9 1.0
CD F:GLU574 2.7 47.0 1.0
C F:THR564 3.5 48.3 1.0
O F:CYS565 3.5 48.0 1.0
CG F:ASP584 3.6 43.6 1.0
C F:HIS569 3.6 49.5 1.0
CA F:CYS565 4.0 48.0 1.0
C F:CYS565 4.1 48.0 1.0
CB F:ASP584 4.1 43.6 1.0
CB F:ASP567 4.2 48.9 1.0
N F:CYS565 4.2 48.0 1.0
OD1 F:ASP571 4.2 47.9 1.0
CG F:GLU574 4.2 47.0 1.0
CG2 F:THR564 4.4 48.3 1.0
N F:CYS570 4.5 48.1 1.0
CA F:CYS570 4.5 48.1 1.0
N F:HIS569 4.5 49.5 1.0
CA F:THR564 4.6 48.3 1.0
CA F:HIS569 4.6 49.5 1.0
OD1 F:ASP584 4.6 43.6 1.0
N F:ASP571 4.7 47.9 1.0
N F:ASP567 4.7 48.9 1.0
CG F:ASP571 4.8 47.9 1.0
SG F:CYS581 4.9 42.5 1.0
CA F:ASP567 5.0 48.9 1.0
CB F:GLU574 5.0 47.0 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 13:11:12 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy