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

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

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 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 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 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 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

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