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:
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
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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
|