Zinc in PDB 8tr8: Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056

The structure of Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056 also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056 (pdb code 8tr8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056, PDB code: 8tr8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:72.6 occ:1.00 SG A:CYS506 2.3 55.8 1.0 SG A:CYS499 2.3 51.6 1.0 SG A:CYS572 2.3 52.3 1.0 SG A:CYS479 2.3 56.7 1.0 HB2 A:CYS479 3.0 56.7 1.0 CB A:CYS479 3.1 56.7 1.0 HB3 A:CYS479 3.1 56.7 1.0 HB3 A:CYS572 3.1 52.3 1.0 CB A:CYS572 3.2 52.3 1.0 HB2 A:CYS506 3.2 55.8 1.0 HB2 A:CYS572 3.2 52.3 1.0 HB3 A:CYS499 3.3 51.6 1.0 CB A:CYS506 3.3 55.8 1.0 H A:CYS499 3.4 51.6 1.0 HA A:CYS506 3.4 55.8 1.0 CB A:CYS499 3.5 51.6 1.0 ZN A:ZN604 3.7 69.0 1.0 HB2 A:ASN481 3.7 56.5 1.0 H A:ILE507 3.8 52.7 1.0 CA A:CYS506 3.9 55.8 1.0 HG22 A:ILE507 3.9 52.7 1.0 HB2 A:CYS499 4.1 51.6 1.0 HB3 A:CYS506 4.2 55.8 1.0 N A:CYS499 4.2 51.6 1.0 SG A:CYS498 4.3 51.6 1.0 SG A:CYS482 4.3 55.8 1.0 N A:ILE507 4.4 52.7 1.0 HG23 A:THR508 4.4 53.4 1.0 OD1 A:ASN481 4.5 56.5 1.0 CA A:CYS499 4.5 51.6 1.0 H A:ASN481 4.5 56.5 1.0 H A:CYS572 4.5 52.3 1.0 H A:THR508 4.6 53.4 1.0 CA A:CYS479 4.6 56.7 1.0 CB A:ASN481 4.6 56.5 1.0 CA A:CYS572 4.6 52.3 1.0 C A:CYS506 4.7 55.8 1.0 HB2 A:PRO570 4.9 48.3 1.0 CG2 A:ILE507 4.9 52.7 1.0 CG A:ASN481 4.9 56.5 1.0 H A:CYS573 4.9 50.2 1.0 HG2 A:ARG500 4.9 53.8 1.0 H A:CYS482 5.0 55.8 1.0 HA A:CYS498 5.0 51.6 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:69.0 occ:1.00 SG A:CYS482 2.3 55.8 1.0 SG A:CYS479 2.3 56.7 1.0 SG A:CYS498 2.3 51.6 1.0 SG A:CYS477 2.3 56.3 1.0 H A:CYS479 3.0 56.7 1.0 HB2 A:CYS482 3.0 55.8 1.0 HB3 A:CYS479 3.1 56.7 1.0 H A:CYS482 3.1 55.8 1.0 CB A:CYS479 3.2 56.7 1.0 CB A:CYS482 3.3 55.8 1.0 H A:GLN478 3.3 56.0 1.0 HB2 A:CYS498 3.4 51.6 1.0 CB A:CYS477 3.5 56.3 1.0 HA A:CYS477 3.5 56.3 1.0 CB A:CYS498 3.5 51.6 1.0 HB2 A:CYS477 3.5 56.3 1.0 N A:CYS479 3.5 56.7 1.0 H A:ASN481 3.7 56.5 1.0 HA A:CYS498 3.7 51.6 1.0 ZN A:ZN603 3.7 72.6 1.0 H A:GLY480 3.7 57.1 1.0 N A:CYS482 3.8 55.8 1.0 H A:CYS499 3.8 51.6 1.0 CA A:CYS479 3.8 56.7 1.0 N A:GLN478 3.9 56.0 1.0 CA A:CYS477 3.9 56.3 1.0 HB3 A:CYS482 4.0 55.8 1.0 HB3 A:CYS572 4.1 52.3 1.0 HB2 A:CYS479 4.1 56.7 1.0 CA A:CYS482 4.1 55.8 1.0 CA A:CYS498 4.1 51.6 1.0 N A:GLY480 4.2 57.1 1.0 HZ3 A:TRP476 4.2 55.4 1.0 SG A:CYS572 4.2 52.3 1.0 C A:CYS479 4.3 56.7 1.0 HB3 A:CYS498 4.3 51.6 1.0 HB3 A:CYS477 4.3 56.3 1.0 C A:CYS477 4.3 56.3 1.0 N A:ASN481 4.4 56.5 1.0 C A:GLN478 4.5 56.0 1.0 HA A:CYS482 4.5 55.8 1.0 SG A:CYS499 4.5 51.6 1.0 N A:CYS499 4.5 51.6 1.0 CB A:CYS572 4.7 52.3 1.0 H A:CYS572 4.7 52.3 1.0 HA A:CYS479 4.7 56.7 1.0 C A:ASN481 4.8 56.5 1.0 HB2 A:ASN481 4.8 56.5 1.0 CA A:GLN478 4.8 56.0 1.0 C A:CYS498 4.9 51.6 1.0 CZ3 A:TRP476 4.9 55.4 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:72.6 occ:1.00 SG B:CYS506 2.3 55.8 1.0 SG B:CYS572 2.3 52.3 1.0 SG B:CYS499 2.3 51.6 1.0 SG B:CYS479 2.3 56.7 1.0 HB2 B:CYS479 3.0 56.7 1.0 CB B:CYS479 3.1 56.7 1.0 HB3 B:CYS479 3.1 56.7 1.0 HB3 B:CYS572 3.1 52.3 1.0 CB B:CYS572 3.2 52.3 1.0 HB2 B:CYS506 3.2 55.8 1.0 HB2 B:CYS572 3.2 52.3 1.0 HB3 B:CYS499 3.3 51.6 1.0 CB B:CYS506 3.3 55.8 1.0 H B:CYS499 3.4 51.6 1.0 HA B:CYS506 3.4 55.8 1.0 CB B:CYS499 3.5 51.6 1.0 ZN B:ZN604 3.7 69.0 1.0 HB2 B:ASN481 3.7 56.5 1.0 H B:ILE507 3.8 52.7 1.0 CA B:CYS506 3.9 55.8 1.0 HG22 B:ILE507 3.9 52.7 1.0 HB2 B:CYS499 4.1 51.6 1.0 HB3 B:CYS506 4.2 55.8 1.0 N B:CYS499 4.2 51.6 1.0 SG B:CYS498 4.3 51.6 1.0 SG B:CYS482 4.3 55.8 1.0 N B:ILE507 4.4 52.7 1.0 HG23 B:THR508 4.4 53.4 1.0 OD1 B:ASN481 4.5 56.5 1.0 CA B:CYS499 4.5 51.6 1.0 H B:ASN481 4.5 56.5 1.0 H B:CYS572 4.5 52.3 1.0 H B:THR508 4.6 53.4 1.0 CA B:CYS479 4.6 56.7 1.0 CB B:ASN481 4.6 56.5 1.0 CA B:CYS572 4.6 52.3 1.0 C B:CYS506 4.7 55.8 1.0 HB2 B:PRO570 4.9 48.3 1.0 CG2 B:ILE507 4.9 52.7 1.0 CG B:ASN481 4.9 56.5 1.0 H B:CYS573 4.9 50.2 1.0 HG2 B:ARG500 4.9 53.8 1.0 H B:CYS482 5.0 55.8 1.0 HA B:CYS498 5.0 51.6 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:69.0 occ:1.00 SG B:CYS498 2.3 51.6 1.0 SG B:CYS479 2.3 56.7 1.0 SG B:CYS482 2.3 55.8 1.0 SG B:CYS477 2.3 56.3 1.0 H B:CYS479 3.0 56.7 1.0 HB2 B:CYS482 3.0 55.8 1.0 HB3 B:CYS479 3.1 56.7 1.0 H B:CYS482 3.1 55.8 1.0 CB B:CYS479 3.2 56.7 1.0 CB B:CYS482 3.3 55.8 1.0 H B:GLN478 3.3 56.0 1.0 HB2 B:CYS498 3.4 51.6 1.0 CB B:CYS477 3.5 56.3 1.0 HA B:CYS477 3.5 56.3 1.0 CB B:CYS498 3.5 51.6 1.0 HB2 B:CYS477 3.5 56.3 1.0 N B:CYS479 3.5 56.7 1.0 H B:ASN481 3.7 56.5 1.0 HA B:CYS498 3.7 51.6 1.0 ZN B:ZN603 3.7 72.6 1.0 H B:GLY480 3.7 57.1 1.0 N B:CYS482 3.8 55.8 1.0 H B:CYS499 3.8 51.6 1.0 CA B:CYS479 3.8 56.7 1.0 N B:GLN478 3.9 56.0 1.0 CA B:CYS477 3.9 56.3 1.0 HB3 B:CYS482 4.0 55.8 1.0 HB3 B:CYS572 4.1 52.3 1.0 HB2 B:CYS479 4.1 56.7 1.0 CA B:CYS482 4.1 55.8 1.0 CA B:CYS498 4.1 51.6 1.0 N B:GLY480 4.2 57.1 1.0 SG B:CYS572 4.2 52.3 1.0 HZ3 B:TRP476 4.2 55.4 1.0 C B:CYS479 4.3 56.7 1.0 HB3 B:CYS498 4.3 51.6 1.0 HB3 B:CYS477 4.3 56.3 1.0 C B:CYS477 4.3 56.3 1.0 N B:ASN481 4.4 56.5 1.0 C B:GLN478 4.5 56.0 1.0 SG B:CYS499 4.5 51.6 1.0 HA B:CYS482 4.5 55.8 1.0 N B:CYS499 4.5 51.6 1.0 CB B:CYS572 4.7 52.3 1.0 H B:CYS572 4.7 52.3 1.0 HA B:CYS479 4.7 56.7 1.0 C B:ASN481 4.8 56.5 1.0 HB2 B:ASN481 4.8 56.5 1.0 CA B:GLN478 4.8 56.0 1.0 C B:CYS498 4.9 51.6 1.0 CZ3 B:TRP476 4.9 55.4 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:72.6 occ:1.00 SG C:CYS506 2.3 55.8 1.0 SG C:CYS572 2.3 52.3 1.0 SG C:CYS499 2.3 51.6 1.0 SG C:CYS479 2.3 56.7 1.0 HB2 C:CYS479 3.0 56.7 1.0 CB C:CYS479 3.1 56.7 1.0 HB3 C:CYS479 3.1 56.7 1.0 HB3 C:CYS572 3.1 52.3 1.0 CB C:CYS572 3.2 52.3 1.0 HB2 C:CYS506 3.2 55.8 1.0 HB2 C:CYS572 3.2 52.3 1.0 HB3 C:CYS499 3.3 51.6 1.0 CB C:CYS506 3.3 55.8 1.0 H C:CYS499 3.4 51.6 1.0 HA C:CYS506 3.4 55.8 1.0 CB C:CYS499 3.5 51.6 1.0 ZN C:ZN604 3.7 69.0 1.0 HB2 C:ASN481 3.7 56.5 1.0 H C:ILE507 3.8 52.7 1.0 CA C:CYS506 3.9 55.8 1.0 HG22 C:ILE507 3.9 52.7 1.0 HB2 C:CYS499 4.1 51.6 1.0 HB3 C:CYS506 4.2 55.8 1.0 N C:CYS499 4.2 51.6 1.0 SG C:CYS498 4.3 51.6 1.0 SG C:CYS482 4.3 55.8 1.0 N C:ILE507 4.4 52.7 1.0 HG23 C:THR508 4.4 53.4 1.0 OD1 C:ASN481 4.5 56.5 1.0 CA C:CYS499 4.5 51.6 1.0 H C:ASN481 4.5 56.5 1.0 H C:CYS572 4.5 52.3 1.0 H C:THR508 4.6 53.4 1.0 CA C:CYS479 4.6 56.7 1.0 CB C:ASN481 4.6 56.5 1.0 CA C:CYS572 4.6 52.3 1.0 C C:CYS506 4.7 55.8 1.0 HB2 C:PRO570 4.9 48.3 1.0 CG2 C:ILE507 4.9 52.7 1.0 CG C:ASN481 4.9 56.5 1.0 H C:CYS573 4.9 50.2 1.0 HG2 C:ARG500 4.9 53.8 1.0 H C:CYS482 5.0 55.8 1.0 HA C:CYS498 5.0 51.6 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist AZD9056 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn604 b:69.0 occ:1.00 SG C:CYS498 2.3 51.6 1.0 SG C:CYS479 2.3 56.7 1.0 SG C:CYS482 2.3 55.8 1.0 SG C:CYS477 2.3 56.3 1.0 H C:CYS479 3.0 56.7 1.0 HB2 C:CYS482 3.1 55.8 1.0 HB3 C:CYS479 3.1 56.7 1.0 H C:CYS482 3.1 55.8 1.0 CB C:CYS479 3.2 56.7 1.0 CB C:CYS482 3.3 55.8 1.0 H C:GLN478 3.3 56.0 1.0 HB2 C:CYS498 3.4 51.6 1.0 CB C:CYS477 3.5 56.3 1.0 HA C:CYS477 3.5 56.3 1.0 CB C:CYS498 3.5 51.6 1.0 HB2 C:CYS477 3.5 56.3 1.0 N C:CYS479 3.5 56.7 1.0 H C:ASN481 3.7 56.5 1.0 HA C:CYS498 3.7 51.6 1.0 ZN C:ZN603 3.7 72.6 1.0 H C:GLY480 3.7 57.1 1.0 N C:CYS482 3.8 55.8 1.0 H C:CYS499 3.8 51.6 1.0 CA C:CYS479 3.8 56.7 1.0 N C:GLN478 3.9 56.0 1.0 CA C:CYS477 3.9 56.3 1.0 HB3 C:CYS482 4.0 55.8 1.0 HB3 C:CYS572 4.1 52.3 1.0 HB2 C:CYS479 4.1 56.7 1.0 CA C:CYS482 4.1 55.8 1.0 CA C:CYS498 4.1 51.6 1.0 N C:GLY480 4.2 57.1 1.0 HZ3 C:TRP476 4.2 55.4 1.0 SG C:CYS572 4.2 52.3 1.0 C C:CYS479 4.3 56.7 1.0 HB3 C:CYS498 4.3 51.6 1.0 HB3 C:CYS477 4.3 56.3 1.0 C C:CYS477 4.3 56.3 1.0 N C:ASN481 4.4 56.5 1.0 C C:GLN478 4.5 56.0 1.0 SG C:CYS499 4.5 51.6 1.0 HA C:CYS482 4.5 55.8 1.0 N C:CYS499 4.5 51.6 1.0 CB C:CYS572 4.7 52.3 1.0 H C:CYS572 4.7 52.3 1.0 HA C:CYS479 4.7 56.7 1.0 C C:ASN481 4.8 56.5 1.0 HB2 C:ASN481 4.8 56.5 1.0 CA C:GLN478 4.8 56.0 1.0 C C:CYS498 4.9 51.6 1.0 CZ3 C:TRP476 4.9 55.4 1.0

A.C.Oken, I.A.Ditter, N.E.Lisi, I.Krishnamurthy, M.H.Godsey, S.E.Mansoor. P2X 7 Receptors Exhibit at Least Three Modes of Allosteric Antagonism. Sci Adv V. 10 O5084 2024.
ISSN: ESSN 2375-2548
PubMed: 39365862
DOI: 10.1126/SCIADV.ADO5084