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Calcium in PDB 7t3u: IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State

Other elements in 7t3u:

The structure of IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State (pdb code 7t3u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State, PDB code: 7t3u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7t3u

Go back to Calcium Binding Sites List in 7t3u
Calcium binding site 1 out of 4 in the IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2704

b:66.3
occ:1.00
OE2 A:GLU1946 2.3 69.3 1.0
O A:THR2581 2.8 63.2 1.0
OE2 A:GLU1882 3.0 90.8 1.0
CD A:GLU1946 3.1 69.3 1.0
OE1 A:GLU1946 3.2 69.3 1.0
OE1 A:GLU1882 3.4 90.8 1.0
CD A:GLU1882 3.5 90.8 1.0
C A:THR2581 3.6 63.2 1.0
O A:TYR2583 4.0 56.9 1.0
N A:ASN1883 4.1 91.2 1.0
NE2 A:HIS1884 4.2 94.1 1.0
CE1 A:HIS1884 4.2 94.1 1.0
OE1 A:GLN1949 4.3 69.7 1.0
CA A:THR2581 4.3 63.2 1.0
N A:ASP2582 4.4 54.9 1.0
CG A:GLU1946 4.4 69.3 1.0
CA A:ASN1883 4.6 91.2 1.0
CA A:ASP2582 4.6 54.9 1.0
C A:ASP2582 4.8 54.9 1.0
N A:TYR2583 4.8 56.9 1.0
CG A:GLU1882 4.9 90.8 1.0
OD1 A:ASN1883 4.9 91.2 1.0
ND1 A:HIS1884 4.9 94.1 1.0
CD2 A:HIS1884 4.9 94.1 1.0

Calcium binding site 2 out of 4 in 7t3u

Go back to Calcium Binding Sites List in 7t3u
Calcium binding site 2 out of 4 in the IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2703

b:101.5
occ:1.00
OE2 B:GLU1946 2.3 104.7 1.0
O B:THR2581 2.4 122.1 1.0
OE1 B:GLU1946 2.5 104.7 1.0
OE2 B:GLU1882 2.6 123.6 1.0
CD B:GLU1946 2.7 104.7 1.0
CD B:GLU1882 3.4 123.6 1.0
C B:THR2581 3.6 122.1 1.0
OE1 B:GLU1882 3.7 123.6 1.0
OE1 B:GLN1949 4.0 115.2 1.0
CG B:GLU1946 4.0 104.7 1.0
N B:ASN1883 4.3 135.5 1.0
CA B:THR2581 4.4 122.1 1.0
O B:TYR2583 4.4 91.9 1.0
CG B:GLU1882 4.5 123.6 1.0
N B:ASP2582 4.6 103.6 1.0
CA B:ASP2582 4.7 103.6 1.0
CB B:THR2581 4.8 122.1 1.0
CA B:GLU1882 4.9 123.6 1.0

Calcium binding site 3 out of 4 in 7t3u

Go back to Calcium Binding Sites List in 7t3u
Calcium binding site 3 out of 4 in the IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2703

b:57.2
occ:1.00
OE2 C:GLU1946 2.3 52.0 1.0
O C:THR2581 2.5 51.5 1.0
OE1 C:GLU1946 2.9 52.0 1.0
CD C:GLU1946 3.0 52.0 1.0
OE2 C:GLU1882 3.5 55.1 1.0
O C:TYR2583 3.7 46.2 1.0
NE2 C:HIS1884 3.7 55.0 1.0
C C:THR2581 3.7 51.5 1.0
OE1 C:GLN1949 3.8 52.5 1.0
CD C:GLU1882 4.1 55.1 1.0
N C:ASN1883 4.2 54.6 1.0
CD2 C:HIS1884 4.3 55.0 1.0
CE1 C:HIS1884 4.3 55.0 1.0
CG C:GLU1946 4.4 52.0 1.0
OE1 C:GLU1882 4.5 55.1 1.0
N C:ASP2582 4.6 49.1 1.0
CA C:THR2581 4.6 51.5 1.0
CA C:ASP2582 4.6 49.1 1.0
N C:TYR2583 4.7 46.2 1.0
C C:ASP2582 4.7 49.1 1.0
CA C:ASN1883 4.7 54.6 1.0
C C:TYR2583 4.8 46.2 1.0
CD C:GLN1949 4.9 52.5 1.0

Calcium binding site 4 out of 4 in 7t3u

Go back to Calcium Binding Sites List in 7t3u
Calcium binding site 4 out of 4 in the IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2704

b:59.4
occ:1.00
OE2 D:GLU1946 2.3 65.6 1.0
O D:THR2581 2.5 48.5 1.0
OE2 D:GLU1882 2.6 82.8 1.0
CD D:GLU1946 3.0 65.6 1.0
OE1 D:GLU1946 3.0 65.6 1.0
C D:THR2581 3.6 48.5 1.0
CD D:GLU1882 3.7 82.8 1.0
O D:TYR2583 3.8 38.2 1.0
CE1 D:HIS1884 3.9 71.9 1.0
N D:ASN1883 4.2 79.0 1.0
OE1 D:GLN1949 4.3 54.2 1.0
CG D:GLU1946 4.4 65.6 1.0
CA D:THR2581 4.4 48.5 1.0
NE2 D:HIS1884 4.4 71.9 1.0
N D:ASP2582 4.4 45.7 1.0
CG D:GLU1882 4.5 82.8 1.0
CA D:ASP2582 4.5 45.7 1.0
ND1 D:HIS1884 4.5 71.9 1.0
OE1 D:GLU1882 4.6 82.8 1.0
N D:TYR2583 4.7 38.2 1.0
C D:ASP2582 4.7 45.7 1.0
CA D:ASN1883 4.8 79.0 1.0
C D:TYR2583 4.9 38.2 1.0

Reference:

E.A.Schmitz, H.Takahashi, E.Karakas. Structural Basis For Activation and Gating of Ip 3 Receptors. Nat Commun V. 13 1408 2022.
ISSN: ESSN 2041-1723
PubMed: 35301323
DOI: 10.1038/S41467-022-29073-2
Page generated: Tue Apr 4 18:45:25 2023

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