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Calcium in PDB 9kdf: Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in Complex with Res-701-3

Enzymatic activity of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in Complex with Res-701-3

All present enzymatic activity of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in Complex with Res-701-3:
5.2.1.8;

Other elements in 9kdf:

The structure of Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in Complex with Res-701-3 also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in Complex with Res-701-3 (pdb code 9kdf). 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 Complex with Res-701-3, PDB code: 9kdf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 9kdf

Go back to Calcium Binding Sites List in 9kdf
Calcium binding site 1 out of 4 in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in Complex with Res-701-3


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 Complex with Res-701-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca1501

b:88.7
occ:1.00
 O R:SER326 2.5 84.5 1.0
OD2 R:ASP322 2.6 88.8 1.0
OG R:SER324 2.6 88.4 1.0
OD1 R:ASP322 2.9 88.8 1.0
CG R:ASP322 3.1 88.8 1.0
OE1 R:GLU331 3.2 85.2 1.0
OE1 R:GLU358 3.4 79.8 1.0
C R:SER326 3.5 84.5 1.0
OD1 R:ASP320 3.6 86.8 1.0
OG R:SER326 3.6 84.5 1.0
CD R:GLU331 3.7 85.2 1.0
CB R:SER324 3.7 88.4 1.0
OE2 R:GLU331 3.7 85.2 1.0
N R:SER328 4.2 85.1 1.0
N R:LEU327 4.3 82.3 1.0
CD R:GLU358 4.4 79.8 1.0
CA R:SER326 4.4 84.5 1.0
N R:SER326 4.4 84.5 1.0
CA R:LEU327 4.5 82.3 1.0
OG R:SER328 4.6 85.1 1.0
OE2 R:GLU358 4.6 79.8 1.0
CB R:ASP322 4.6 88.8 1.0
CB R:SER326 4.6 84.5 1.0
CB R:SER328 4.6 85.1 1.0
C R:LEU327 4.7 82.3 1.0
CG R:ASP320 4.7 86.8 1.0
CA R:SER324 4.7 88.4 1.0
N R:SER324 4.8 88.4 1.0
CG R:GLU331 4.9 85.2 1.0

Calcium binding site 2 out of 4 in 9kdf

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Calcium binding site 2 out of 4 in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in Complex with Res-701-3


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 Complex with Res-701-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca1502

b:68.9
occ:1.00
 OE1 R:GLU363 2.4 76.1 1.0
OD1 R:ASP354 2.4 73.9 1.0
OD1 R:ASN356 2.4 73.1 1.0
ND2 R:ASN356 2.6 73.1 1.0
OE2 R:GLU363 2.6 76.1 1.0
O R:GLU358 2.7 79.8 1.0
CG R:ASN356 2.8 73.1 1.0
CD R:GLU363 2.8 76.1 1.0
CG R:ASP354 3.0 73.9 1.0
OD2 R:ASP354 3.0 73.9 1.0
OD2 R:ASP352 3.8 72.6 1.0
C R:GLU358 3.9 79.8 1.0
OD1 R:ASP352 4.0 72.6 1.0
CG R:ASP352 4.0 72.6 1.0
OD2 R:ASP360 4.1 81.0 1.0
CB R:ASN356 4.2 73.1 1.0
CG R:GLU363 4.3 76.1 1.0
CB R:ASP354 4.3 73.9 1.0
CG R:ASP360 4.5 81.0 1.0
N R:ASP360 4.5 81.0 1.0
CA R:VAL359 4.6 77.1 1.0
N R:ASN356 4.7 73.1 1.0
N R:VAL359 4.7 77.1 1.0
N R:ASP354 4.8 73.9 1.0
N R:GLU358 4.8 79.8 1.0
OD1 R:ASP360 4.9 81.0 1.0
CA R:GLU358 4.9 79.8 1.0
CA R:ASN356 5.0 73.1 1.0
C R:VAL359 5.0 77.1 1.0

Calcium binding site 3 out of 4 in 9kdf

Go back to Calcium Binding Sites List in 9kdf
Calcium binding site 3 out of 4 in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in Complex with Res-701-3


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 Complex with Res-701-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca1503

b:65.3
occ:1.00
 O R:TYR395 2.4 72.1 1.0
OE2 R:GLU400 2.4 69.0 1.0
OD2 R:ASP393 2.4 70.5 1.0
OD1 R:ASP393 2.5 70.5 1.0
OE1 R:GLU400 2.5 69.0 1.0
CG R:ASP393 2.7 70.5 1.0
OD1 R:ASP391 2.7 69.7 1.0
CD R:GLU400 2.7 69.0 1.0
OD1 R:ASP389 3.0 70.2 1.0
C R:TYR395 3.6 72.1 1.0
CG R:ASP391 3.7 69.7 1.0
CG R:ASP389 3.9 70.2 1.0
OD2 R:ASP391 3.9 69.7 1.0
CB R:ASP393 4.1 70.5 1.0
CG R:GLU400 4.2 69.0 1.0
N R:TYR395 4.3 72.1 1.0
N R:ASP393 4.3 70.5 1.0
CA R:TYR395 4.4 72.1 1.0
N R:ILE396 4.5 69.0 1.0
OD2 R:ASP389 4.6 70.2 1.0
N R:SER397 4.6 68.3 1.0
CA R:ILE396 4.6 69.0 1.0
OG R:SER397 4.6 68.3 1.0
CA R:ASP389 4.7 70.2 1.0
CA R:ASP393 4.7 70.5 1.0
CB R:TYR395 4.8 72.1 1.0
N R:ASP391 4.8 69.7 1.0
CB R:ASP389 4.8 70.2 1.0
N R:MET390 4.9 68.3 1.0
N R:LYS392 4.9 71.8 1.0
C R:ILE396 5.0 69.0 1.0
N R:GLY394 5.0 71.7 1.0

Calcium binding site 4 out of 4 in 9kdf

Go back to Calcium Binding Sites List in 9kdf
Calcium binding site 4 out of 4 in the Cryoem Structure of Calcineurin-Fusion Human Endothelin Receptor Type- B in Complex with Res-701-3


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 Complex with Res-701-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca1504

b:73.7
occ:1.00
 OE2 R:GLU441 2.5 68.3 1.0
O R:ARG436 2.5 69.5 1.0
OD1 R:ASP434 2.6 69.7 1.0
OD1 R:ASP432 2.7 68.3 1.0
OE1 R:GLU441 2.8 68.3 1.0
OD2 R:ASP432 3.0 68.3 1.0
OD2 R:ASP434 3.0 69.7 1.0
CD R:GLU441 3.0 68.3 1.0
OD1 R:ASP430 3.0 68.3 1.0
CG R:ASP434 3.1 69.7 1.0
CG R:ASP432 3.1 68.3 1.0
C R:ARG436 3.7 69.5 1.0
CG R:ASP430 4.0 68.3 1.0
OG R:SER438 4.3 70.6 1.0
N R:SER438 4.3 70.6 1.0
CA R:ILE437 4.4 70.2 1.0
CB R:ASP434 4.4 69.7 1.0
CB R:ASP432 4.5 68.3 1.0
CG R:GLU441 4.5 68.3 1.0
N R:ILE437 4.5 70.2 1.0
N R:ASP432 4.6 68.3 1.0
OD2 R:ASP430 4.6 68.3 1.0
CA R:ASP430 4.6 68.3 1.0
N R:ARG436 4.7 69.5 1.0
N R:ASP434 4.7 69.7 1.0
N R:LYS431 4.8 68.3 1.0
CA R:ARG436 4.8 69.5 1.0
CB R:ASP430 4.8 68.3 1.0
CG R:ARG436 4.8 69.5 1.0
C R:ILE437 4.8 70.2 1.0
CB R:SER438 5.0 70.6 1.0
CA R:ASP432 5.0 68.3 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 10:09:53 2025

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