Zinc in PDB 8tra: Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist GSK1482160

The structure of Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist GSK1482160 also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	3 atoms
Fluorine	(F)	9 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist GSK1482160 (pdb code 8tra). 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 GSK1482160, PDB code: 8tra:
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 GSK1482160


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 GSK1482160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:69.2 occ:1.00 SG A:CYS572 2.3 37.7 1.0 SG A:CYS499 2.3 38.4 1.0 SG A:CYS506 2.3 41.3 1.0 SG A:CYS479 2.3 43.9 1.0 HB2 A:CYS479 3.0 43.9 1.0 CB A:CYS479 3.1 43.9 1.0 HB3 A:CYS499 3.1 38.4 1.0 HB3 A:CYS479 3.1 43.9 1.0 HB3 A:CYS572 3.1 37.7 1.0 CB A:CYS572 3.1 37.7 1.0 HB2 A:CYS572 3.1 37.7 1.0 HB2 A:CYS506 3.1 41.3 1.0 CB A:CYS506 3.3 41.3 1.0 HA A:CYS506 3.3 41.3 1.0 CB A:CYS499 3.3 38.4 1.0 H A:CYS499 3.4 38.4 1.0 HB2 A:ASN481 3.6 43.4 1.0 H A:ILE507 3.7 37.3 1.0 ZN A:ZN604 3.8 68.2 1.0 CA A:CYS506 3.8 41.3 1.0 HB2 A:CYS499 4.0 38.4 1.0 HG22 A:ILE507 4.0 37.3 1.0 HB3 A:CYS506 4.1 41.3 1.0 N A:CYS499 4.2 38.4 1.0 N A:ILE507 4.3 37.3 1.0 CA A:CYS499 4.4 38.4 1.0 SG A:CYS482 4.4 41.7 1.0 H A:THR508 4.4 38.4 1.0 HG23 A:THR508 4.5 38.4 1.0 H A:ASN481 4.5 43.4 1.0 SG A:CYS498 4.5 38.1 1.0 H A:CYS572 4.5 37.7 1.0 CA A:CYS479 4.6 43.9 1.0 CB A:ASN481 4.6 43.4 1.0 CA A:CYS572 4.6 37.7 1.0 C A:CYS506 4.6 41.3 1.0 OD1 A:ASN481 4.7 43.4 1.0 HG2 A:ARG500 4.7 40.3 1.0 HB2 A:PRO570 4.9 33.2 1.0 H A:CYS573 4.9 34.8 1.0 CG2 A:ILE507 5.0 37.3 1.0 HG21 A:THR508 5.0 38.4 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 GSK1482160


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 GSK1482160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:68.2 occ:1.00 SG A:CYS482 2.3 41.7 1.0 SG A:CYS479 2.3 43.9 1.0 SG A:CYS477 2.3 42.4 1.0 SG A:CYS498 2.3 38.1 1.0 H A:CYS479 2.8 43.9 1.0 HB2 A:CYS482 3.0 41.7 1.0 H A:CYS482 3.1 41.7 1.0 HB3 A:CYS479 3.2 43.9 1.0 H A:GLN478 3.3 43.8 1.0 CB A:CYS479 3.3 43.9 1.0 CB A:CYS482 3.3 41.7 1.0 N A:CYS479 3.4 43.9 1.0 HA A:CYS477 3.5 42.4 1.0 CB A:CYS477 3.5 42.4 1.0 H A:ASN481 3.5 43.4 1.0 H A:GLY480 3.6 43.3 1.0 HB2 A:CYS477 3.6 42.4 1.0 CB A:CYS498 3.6 38.1 1.0 HB2 A:CYS498 3.6 38.1 1.0 HA A:CYS498 3.6 38.1 1.0 H A:CYS499 3.7 38.4 1.0 N A:CYS482 3.7 41.7 1.0 ZN A:ZN603 3.8 69.2 1.0 CA A:CYS479 3.8 43.9 1.0 N A:GLN478 3.8 43.8 1.0 HB3 A:CYS572 3.9 37.7 1.0 CA A:CYS477 3.9 42.4 1.0 N A:GLY480 4.0 43.3 1.0 HB3 A:CYS482 4.0 41.7 1.0 CA A:CYS482 4.1 41.7 1.0 HZ3 A:TRP476 4.1 41.0 1.0 HB2 A:CYS479 4.1 43.9 1.0 CA A:CYS498 4.2 38.1 1.0 SG A:CYS572 4.2 37.7 1.0 C A:CYS479 4.2 43.9 1.0 C A:CYS477 4.3 42.4 1.0 N A:ASN481 4.3 43.4 1.0 HB3 A:CYS477 4.3 42.4 1.0 HB3 A:CYS498 4.4 38.1 1.0 C A:GLN478 4.4 43.8 1.0 N A:CYS499 4.5 38.4 1.0 HA A:CYS482 4.5 41.7 1.0 CB A:CYS572 4.5 37.7 1.0 H A:CYS572 4.7 37.7 1.0 SG A:CYS499 4.7 38.4 1.0 C A:ASN481 4.7 43.4 1.0 HA A:CYS479 4.7 43.9 1.0 HB2 A:ASN481 4.7 43.4 1.0 CA A:GLN478 4.8 43.8 1.0 CZ3 A:TRP476 4.9 41.0 1.0 C A:CYS498 4.9 38.1 1.0 CA A:ASN481 5.0 43.4 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 GSK1482160


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 GSK1482160 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:69.2 occ:1.00 SG B:CYS572 2.3 37.7 1.0 SG B:CYS506 2.3 41.3 1.0 SG B:CYS499 2.3 38.4 1.0 SG B:CYS479 2.3 43.9 1.0 HB2 B:CYS479 3.0 43.9 1.0 CB B:CYS479 3.1 43.9 1.0 HB3 B:CYS499 3.1 38.4 1.0 HB3 B:CYS479 3.1 43.9 1.0 HB3 B:CYS572 3.1 37.7 1.0 CB B:CYS572 3.1 37.7 1.0 HB2 B:CYS572 3.1 37.7 1.0 HB2 B:CYS506 3.1 41.3 1.0 CB B:CYS506 3.3 41.3 1.0 HA B:CYS506 3.3 41.3 1.0 CB B:CYS499 3.3 38.4 1.0 H B:CYS499 3.4 38.4 1.0 HB2 B:ASN481 3.6 43.4 1.0 H B:ILE507 3.7 37.3 1.0 ZN B:ZN604 3.8 68.2 1.0 CA B:CYS506 3.8 41.3 1.0 HB2 B:CYS499 4.0 38.4 1.0 HG22 B:ILE507 4.0 37.3 1.0 HB3 B:CYS506 4.1 41.3 1.0 N B:CYS499 4.2 38.4 1.0 N B:ILE507 4.3 37.3 1.0 CA B:CYS499 4.4 38.4 1.0 SG B:CYS482 4.4 41.7 1.0 H B:THR508 4.4 38.4 1.0 HG23 B:THR508 4.5 38.4 1.0 H B:ASN481 4.5 43.4 1.0 SG B:CYS498 4.5 38.1 1.0 H B:CYS572 4.5 37.7 1.0 CA B:CYS479 4.6 43.9 1.0 CB B:ASN481 4.6 43.4 1.0 CA B:CYS572 4.6 37.7 1.0 C B:CYS506 4.6 41.3 1.0 OD1 B:ASN481 4.7 43.4 1.0 HG2 B:ARG500 4.7 40.3 1.0 HB2 B:PRO570 4.9 33.2 1.0 H B:CYS573 4.9 34.8 1.0 CG2 B:ILE507 5.0 37.3 1.0 HG21 B:THR508 5.0 38.4 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 GSK1482160


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 GSK1482160 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:68.2 occ:1.00 SG B:CYS482 2.3 41.7 1.0 SG B:CYS479 2.3 43.9 1.0 SG B:CYS477 2.3 42.4 1.0 SG B:CYS498 2.3 38.1 1.0 H B:CYS479 2.8 43.9 1.0 HB2 B:CYS482 3.0 41.7 1.0 H B:CYS482 3.1 41.7 1.0 HB3 B:CYS479 3.2 43.9 1.0 H B:GLN478 3.3 43.8 1.0 CB B:CYS479 3.3 43.9 1.0 CB B:CYS482 3.3 41.7 1.0 N B:CYS479 3.4 43.9 1.0 HA B:CYS477 3.5 42.4 1.0 CB B:CYS477 3.5 42.4 1.0 H B:ASN481 3.5 43.4 1.0 H B:GLY480 3.6 43.3 1.0 HB2 B:CYS477 3.6 42.4 1.0 CB B:CYS498 3.6 38.1 1.0 HB2 B:CYS498 3.6 38.1 1.0 HA B:CYS498 3.6 38.1 1.0 H B:CYS499 3.7 38.4 1.0 N B:CYS482 3.7 41.7 1.0 ZN B:ZN603 3.8 69.2 1.0 CA B:CYS479 3.8 43.9 1.0 N B:GLN478 3.8 43.8 1.0 HB3 B:CYS572 3.9 37.7 1.0 CA B:CYS477 3.9 42.4 1.0 N B:GLY480 4.0 43.3 1.0 HB3 B:CYS482 4.0 41.7 1.0 CA B:CYS482 4.1 41.7 1.0 HZ3 B:TRP476 4.1 41.0 1.0 HB2 B:CYS479 4.1 43.9 1.0 CA B:CYS498 4.2 38.1 1.0 SG B:CYS572 4.2 37.7 1.0 C B:CYS479 4.2 43.9 1.0 C B:CYS477 4.3 42.4 1.0 N B:ASN481 4.3 43.4 1.0 HB3 B:CYS477 4.3 42.4 1.0 HB3 B:CYS498 4.4 38.1 1.0 C B:GLN478 4.4 43.8 1.0 N B:CYS499 4.5 38.4 1.0 HA B:CYS482 4.5 41.7 1.0 CB B:CYS572 4.5 37.7 1.0 H B:CYS572 4.7 37.7 1.0 SG B:CYS499 4.7 38.4 1.0 C B:ASN481 4.7 43.4 1.0 HA B:CYS479 4.7 43.9 1.0 HB2 B:ASN481 4.7 43.4 1.0 CA B:GLN478 4.8 43.8 1.0 CZ3 B:TRP476 4.9 41.0 1.0 C B:CYS498 4.9 38.1 1.0 CA B:ASN481 5.0 43.4 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 GSK1482160


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 GSK1482160 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:69.2 occ:1.00 SG C:CYS572 2.3 37.7 1.0 SG C:CYS499 2.3 38.4 1.0 SG C:CYS506 2.3 41.3 1.0 SG C:CYS479 2.3 43.9 1.0 HB2 C:CYS479 3.0 43.9 1.0 CB C:CYS479 3.1 43.9 1.0 HB3 C:CYS499 3.1 38.4 1.0 HB3 C:CYS479 3.1 43.9 1.0 HB3 C:CYS572 3.1 37.7 1.0 CB C:CYS572 3.1 37.7 1.0 HB2 C:CYS572 3.1 37.7 1.0 HB2 C:CYS506 3.1 41.3 1.0 CB C:CYS506 3.3 41.3 1.0 HA C:CYS506 3.3 41.3 1.0 CB C:CYS499 3.3 38.4 1.0 H C:CYS499 3.4 38.4 1.0 HB2 C:ASN481 3.6 43.4 1.0 H C:ILE507 3.7 37.3 1.0 ZN C:ZN604 3.8 68.2 1.0 CA C:CYS506 3.8 41.3 1.0 HB2 C:CYS499 4.0 38.4 1.0 HG22 C:ILE507 4.0 37.3 1.0 HB3 C:CYS506 4.1 41.3 1.0 N C:CYS499 4.2 38.4 1.0 N C:ILE507 4.3 37.3 1.0 CA C:CYS499 4.4 38.4 1.0 SG C:CYS482 4.4 41.7 1.0 H C:THR508 4.4 38.4 1.0 HG23 C:THR508 4.5 38.4 1.0 H C:ASN481 4.5 43.4 1.0 SG C:CYS498 4.5 38.1 1.0 H C:CYS572 4.5 37.7 1.0 CA C:CYS479 4.6 43.9 1.0 CB C:ASN481 4.6 43.4 1.0 CA C:CYS572 4.6 37.7 1.0 C C:CYS506 4.6 41.3 1.0 OD1 C:ASN481 4.7 43.4 1.0 HG2 C:ARG500 4.7 40.3 1.0 HB2 C:PRO570 4.9 33.2 1.0 H C:CYS573 4.9 34.8 1.0 CG2 C:ILE507 5.0 37.3 1.0 HG21 C:THR508 5.0 38.4 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 GSK1482160


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 GSK1482160 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn604 b:68.2 occ:1.00 SG C:CYS482 2.3 41.7 1.0 SG C:CYS479 2.3 43.9 1.0 SG C:CYS498 2.3 38.1 1.0 SG C:CYS477 2.3 42.4 1.0 H C:CYS479 2.8 43.9 1.0 HB2 C:CYS482 3.0 41.7 1.0 H C:CYS482 3.1 41.7 1.0 HB3 C:CYS479 3.2 43.9 1.0 H C:GLN478 3.3 43.8 1.0 CB C:CYS479 3.3 43.9 1.0 CB C:CYS482 3.3 41.7 1.0 N C:CYS479 3.4 43.9 1.0 HA C:CYS477 3.5 42.4 1.0 CB C:CYS477 3.5 42.4 1.0 H C:ASN481 3.5 43.4 1.0 H C:GLY480 3.6 43.3 1.0 HB2 C:CYS477 3.6 42.4 1.0 CB C:CYS498 3.6 38.1 1.0 HB2 C:CYS498 3.6 38.1 1.0 HA C:CYS498 3.6 38.1 1.0 H C:CYS499 3.7 38.4 1.0 N C:CYS482 3.7 41.7 1.0 ZN C:ZN603 3.8 69.2 1.0 CA C:CYS479 3.8 43.9 1.0 N C:GLN478 3.8 43.8 1.0 HB3 C:CYS572 3.9 37.7 1.0 CA C:CYS477 3.9 42.4 1.0 N C:GLY480 4.0 43.3 1.0 HB3 C:CYS482 4.0 41.7 1.0 CA C:CYS482 4.1 41.7 1.0 HZ3 C:TRP476 4.1 41.0 1.0 HB2 C:CYS479 4.1 43.9 1.0 CA C:CYS498 4.1 38.1 1.0 SG C:CYS572 4.2 37.7 1.0 C C:CYS479 4.2 43.9 1.0 C C:CYS477 4.3 42.4 1.0 N C:ASN481 4.3 43.4 1.0 HB3 C:CYS477 4.3 42.4 1.0 HB3 C:CYS498 4.4 38.1 1.0 C C:GLN478 4.4 43.8 1.0 N C:CYS499 4.5 38.4 1.0 HA C:CYS482 4.5 41.7 1.0 CB C:CYS572 4.5 37.7 1.0 H C:CYS572 4.7 37.7 1.0 SG C:CYS499 4.7 38.4 1.0 C C:ASN481 4.7 43.4 1.0 HA C:CYS479 4.7 43.9 1.0 HB2 C:ASN481 4.7 43.4 1.0 CA C:GLN478 4.8 43.8 1.0 CZ3 C:TRP476 4.9 41.0 1.0 C C:CYS498 4.9 38.1 1.0 CA C:ASN481 5.0 43.4 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