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Calcium in PDB 9kdg: Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form

Enzymatic activity of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form

All present enzymatic activity of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form:
5.2.1.8;

Other elements in 9kdg:

The structure of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form also contains other interesting chemical elements:

Iron (Fe) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form (pdb code 9kdg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form, PDB code: 9kdg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 9kdg

Go back to Calcium Binding Sites List in 9kdg
Calcium binding site 1 out of 4 in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1701

b:83.9
occ:1.00
OD1 A:ASP320 2.5 88.8 1.0
OD1 A:ASP322 2.5 92.5 1.0
O A:SER326 2.5 81.9 1.0
OE1 A:GLU331 2.6 85.4 1.0
OD2 A:ASP322 2.8 92.5 1.0
OG A:SER324 2.8 84.9 1.0
CG A:ASP322 3.1 92.5 1.0
OE2 A:GLU358 3.4 78.5 1.0
CD A:GLU331 3.4 85.4 1.0
OE2 A:GLU331 3.5 85.4 1.0
CG A:ASP320 3.6 88.8 1.0
OG A:SER328 3.7 78.6 1.0
C A:SER326 3.8 81.9 1.0
CB A:SER324 3.8 84.9 1.0
OD2 A:ASP320 4.0 88.8 1.0
N A:SER328 4.2 78.6 1.0
CB A:SER328 4.5 78.6 1.0
CA A:LEU327 4.5 80.0 1.0
OG A:SER326 4.5 81.9 1.0
N A:SER324 4.5 84.9 1.0
CB A:ASP322 4.5 92.5 1.0
N A:LEU327 4.6 80.0 1.0
CD A:GLU358 4.6 78.5 1.0
C A:LEU327 4.7 80.0 1.0
CA A:SER324 4.7 84.9 1.0
N A:SER326 4.7 81.9 1.0
CG A:GLU331 4.8 85.4 1.0
CA A:SER326 4.8 81.9 1.0
CB A:ASP320 4.9 88.8 1.0
N A:ASP322 4.9 92.5 1.0
CA A:SER328 5.0 78.6 1.0

Calcium binding site 2 out of 4 in 9kdg

Go back to Calcium Binding Sites List in 9kdg
Calcium binding site 2 out of 4 in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1702

b:69.1
occ:1.00
OE1 A:GLU363 2.5 72.7 1.0
O A:GLU358 2.5 78.5 1.0
OE2 A:GLU363 2.5 72.7 1.0
OD1 A:ASP352 2.5 72.7 1.0
OD1 A:ASP354 2.6 72.7 1.0
OD1 A:ASN356 2.7 72.9 1.0
CD A:GLU363 2.8 72.7 1.0
CG A:ASP354 3.2 72.7 1.0
OD2 A:ASP354 3.3 72.7 1.0
CG A:ASN356 3.4 72.9 1.0
ND2 A:ASN356 3.5 72.9 1.0
C A:GLU358 3.7 78.5 1.0
CG A:ASP352 3.7 72.7 1.0
CA A:VAL359 4.2 74.9 1.0
CG A:GLU363 4.3 72.7 1.0
N A:VAL359 4.4 74.9 1.0
N A:ASP360 4.4 76.6 1.0
CA A:ASP352 4.5 72.7 1.0
N A:ASP354 4.5 72.7 1.0
CB A:ASP354 4.5 72.7 1.0
OD2 A:ASP352 4.6 72.7 1.0
CB A:ASP352 4.6 72.7 1.0
N A:THR353 4.7 72.7 1.0
CB A:ASN356 4.7 72.9 1.0
OD1 A:ASP360 4.7 76.6 1.0
N A:GLU358 4.7 78.5 1.0
C A:VAL359 4.8 74.9 1.0
CA A:GLU358 4.8 78.5 1.0
C A:ASP352 4.8 72.7 1.0
N A:ASN356 4.8 72.9 1.0
CG A:ASP360 4.9 76.6 1.0

Calcium binding site 3 out of 4 in 9kdg

Go back to Calcium Binding Sites List in 9kdg
Calcium binding site 3 out of 4 in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1703

b:61.9
occ:1.00
OE1 A:GLU400 2.4 72.7 1.0
O A:TYR395 2.4 72.7 1.0
OD1 A:ASP393 2.4 72.7 1.0
OD2 A:ASP393 2.5 72.7 1.0
CG A:ASP393 2.8 72.7 1.0
CD A:GLU400 3.2 72.7 1.0
OE2 A:GLU400 3.2 72.7 1.0
OD1 A:ASP389 3.4 72.7 1.0
C A:TYR395 3.6 72.7 1.0
CB A:ASP393 4.3 72.7 1.0
N A:SER397 4.3 72.7 1.0
CB A:SER397 4.5 72.7 1.0
CA A:TYR395 4.5 72.7 1.0
N A:ILE396 4.5 72.7 1.0
N A:TYR395 4.5 72.7 1.0
CG A:ASP389 4.5 72.7 1.0
CA A:ILE396 4.6 72.7 1.0
OG A:SER397 4.6 72.7 1.0
CG A:GLU400 4.6 72.7 1.0
CB A:TYR395 4.7 72.7 1.0
C A:ILE396 4.7 72.7 1.0
CB A:ASP391 4.7 72.7 1.0
N A:ASP393 4.9 72.7 1.0
N A:ASP391 4.9 72.7 1.0

Calcium binding site 4 out of 4 in 9kdg

Go back to Calcium Binding Sites List in 9kdg
Calcium binding site 4 out of 4 in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in the Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1704

b:59.9
occ:1.00
OE2 A:GLU441 2.4 72.7 1.0
O A:ARG436 2.4 72.7 1.0
OD1 A:ASP434 2.5 72.7 1.0
OD1 A:ASP430 2.6 72.7 1.0
OE1 A:GLU441 2.7 72.7 1.0
CD A:GLU441 2.9 72.7 1.0
CG A:ASP434 3.1 72.7 1.0
OD2 A:ASP434 3.1 72.7 1.0
CG A:ASP430 3.5 72.7 1.0
C A:ARG436 3.6 72.7 1.0
CB A:ASP432 3.8 72.7 1.0
OD2 A:ASP432 4.1 72.7 1.0
OD2 A:ASP430 4.1 72.7 1.0
N A:ASP432 4.2 72.7 1.0
CG A:ASP432 4.3 72.7 1.0
CG A:GLU441 4.3 72.7 1.0
CA A:ILE437 4.4 72.7 1.0
N A:ILE437 4.4 72.7 1.0
CB A:ASP434 4.4 72.7 1.0
N A:ARG436 4.5 72.7 1.0
CB A:ASP430 4.5 72.7 1.0
CA A:ASP430 4.5 72.7 1.0
CA A:ASP432 4.5 72.7 1.0
N A:ASP434 4.5 72.7 1.0
N A:SER438 4.5 72.7 1.0
CA A:ARG436 4.7 72.7 1.0
N A:GLY433 4.7 72.7 1.0
N A:LYS431 4.8 72.7 1.0
C A:ILE437 4.8 72.7 1.0
CG A:ARG436 4.8 72.7 1.0
C A:ASP432 4.9 72.7 1.0
C A:ASP430 4.9 72.7 1.0
CA A:ASP434 4.9 72.7 1.0

Reference:

W.Shihoya, H.Akasaka, P.A.Jordan, A.Lechner, B.K.Okada, G.Costa Machado Da Cruz, F.K.Sano, T.Tanaka, R.Kawahara, R.Chaudhari, H.Masamune, M.J.Burk, O.Nureki. Structure of A Lasso Peptide Bound Et B Receptor Provides Insights Into the Mechanism of Gpcr Inverse Agonism. Nat Commun V. 16 3446 2025.
ISSN: ESSN 2041-1723
PubMed: 40263271
DOI: 10.1038/S41467-025-57960-X
Page generated: Thu Jul 10 10:10:37 2025

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