Zinc 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:

Calcium

(Ca)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the IP3, Atp, and CA2+ Bound Type 3 IP3 Receptor in the Inactive State, PDB code: 7t3u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc 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 Zinc with other atoms in the Zn 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:Zn2701 b:75.0 occ:1.00 NE2 A:HIS2558 2.0 66.1 1.0 ND1 A:HIS2563 2.0 53.7 1.0 SG A:CYS2541 2.3 56.2 1.0 SG A:CYS2538 2.3 61.1 1.0 CG A:HIS2563 2.7 53.7 1.0 CB A:HIS2563 2.8 53.7 1.0 CE1 A:HIS2558 2.9 66.1 1.0 CD2 A:HIS2558 3.0 66.1 1.0 CB A:CYS2538 3.1 61.1 1.0 CE1 A:HIS2563 3.2 53.7 1.0 CB A:CYS2541 3.8 56.2 1.0 ND1 A:HIS2558 3.9 66.1 1.0 CD2 A:HIS2563 3.9 53.7 1.0 CG A:HIS2558 4.1 66.1 1.0 N A:CYS2541 4.1 56.2 1.0 NE2 A:HIS2563 4.1 53.7 1.0 CA A:HIS2563 4.3 53.7 1.0 O A:HIS2558 4.5 66.1 1.0 CA A:CYS2538 4.5 61.1 1.0 CA A:CYS2541 4.6 56.2 1.0 O A:HIS2563 4.7 53.7 1.0 N A:HIS2563 4.9 53.7 1.0 CB A:ILE2540 5.0 51.5 1.0 N6 A:ATP2703 5.0 59.7 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn2701 b:63.4 occ:1.00 NE2 B:HIS2558 2.0 39.7 1.0 ND1 B:HIS2563 2.0 37.8 1.0 SG B:CYS2541 2.3 40.9 1.0 SG B:CYS2538 2.3 41.0 1.0 CE1 B:HIS2558 2.7 39.7 1.0 CG B:HIS2563 2.8 37.8 1.0 CB B:HIS2563 3.0 37.8 1.0 CB B:CYS2538 3.1 41.0 1.0 CD2 B:HIS2558 3.2 39.7 1.0 CE1 B:HIS2563 3.2 37.8 1.0 CB B:CYS2541 3.5 40.9 1.0 N B:CYS2541 3.9 40.9 1.0 ND1 B:HIS2558 3.9 39.7 1.0 CD2 B:HIS2563 4.0 37.8 1.0 CG B:HIS2558 4.1 39.7 1.0 NE2 B:HIS2563 4.2 37.8 1.0 CA B:CYS2541 4.3 40.9 1.0 CA B:HIS2563 4.5 37.8 1.0 CA B:CYS2538 4.6 41.0 1.0 CB B:ILE2540 4.8 37.2 1.0 O B:HIS2563 4.9 37.8 1.0 N B:ILE2540 5.0 37.2 1.0 O B:HIS2558 5.0 39.7 1.0 C B:CYS2541 5.0 40.9 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn2701 b:72.9 occ:1.00 NE2 C:HIS2558 2.0 41.7 1.0 ND1 C:HIS2563 2.0 47.3 1.0 SG C:CYS2541 2.3 58.2 1.0 SG C:CYS2538 2.3 52.4 1.0 CG C:HIS2563 2.9 47.3 1.0 CE1 C:HIS2558 2.9 41.7 1.0 CB C:HIS2563 3.0 47.3 1.0 CB C:CYS2538 3.1 52.4 1.0 CD2 C:HIS2558 3.1 41.7 1.0 CE1 C:HIS2563 3.1 47.3 1.0 CB C:CYS2541 3.6 58.2 1.0 N C:CYS2541 4.0 58.2 1.0 ND1 C:HIS2558 4.1 41.7 1.0 CD2 C:HIS2563 4.1 47.3 1.0 NE2 C:HIS2563 4.2 47.3 1.0 CG C:HIS2558 4.2 41.7 1.0 CA C:CYS2541 4.4 58.2 1.0 CA C:CYS2538 4.5 52.4 1.0 CA C:HIS2563 4.6 47.3 1.0 CB C:ILE2540 4.9 54.6 1.0 O C:HIS2563 5.0 47.3 1.0 N C:ILE2540 5.0 54.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn2701 b:67.9 occ:1.00 NE2 D:HIS2558 2.0 64.9 1.0 ND1 D:HIS2563 2.0 49.5 1.0 SG D:CYS2541 2.3 57.1 1.0 SG D:CYS2538 2.3 65.8 1.0 CG D:HIS2563 2.9 49.5 1.0 CE1 D:HIS2558 2.9 64.9 1.0 CB D:CYS2538 3.1 65.8 1.0 CB D:HIS2563 3.1 49.5 1.0 CE1 D:HIS2563 3.1 49.5 1.0 CD2 D:HIS2558 3.1 64.9 1.0 CB D:CYS2541 3.7 57.1 1.0 ND1 D:HIS2558 4.0 64.9 1.0 CD2 D:HIS2563 4.1 49.5 1.0 N D:CYS2541 4.1 57.1 1.0 NE2 D:HIS2563 4.1 49.5 1.0 CG D:HIS2558 4.2 64.9 1.0 CA D:CYS2541 4.4 57.1 1.0 CA D:CYS2538 4.5 65.8 1.0 CA D:HIS2563 4.6 49.5 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