Zinc in PDB 8tr5: Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State

The structure of Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State (pdb code 8tr5). 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 the Apo Closed State, PDB code: 8tr5:
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 the Apo Closed State


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 the Apo Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:72.5 occ:1.00 SG A:CYS506 2.3 62.5 1.0 SG A:CYS499 2.3 60.8 1.0 SG A:CYS572 2.3 58.3 1.0 SG A:CYS479 2.3 64.4 1.0 HB3 A:CYS499 2.9 60.8 1.0 HB3 A:CYS572 3.1 58.3 1.0 CB A:CYS572 3.1 58.3 1.0 HB2 A:CYS572 3.1 58.3 1.0 HB2 A:CYS506 3.1 62.5 1.0 CB A:CYS499 3.2 60.8 1.0 HB2 A:CYS479 3.2 64.4 1.0 CB A:CYS479 3.2 64.4 1.0 CB A:CYS506 3.2 62.5 1.0 HA A:CYS506 3.2 62.5 1.0 HB3 A:CYS479 3.3 64.4 1.0 H A:CYS499 3.3 60.8 1.0 HB2 A:ASN481 3.6 63.3 1.0 H A:ILE507 3.6 60.1 1.0 ZN A:ZN703 3.7 76.5 1.0 CA A:CYS506 3.7 62.5 1.0 HB2 A:CYS499 3.8 60.8 1.0 HG22 A:ILE507 4.0 60.1 1.0 N A:CYS499 4.1 60.8 1.0 HB3 A:CYS506 4.1 62.5 1.0 SG A:CYS482 4.2 61.2 1.0 CA A:CYS499 4.2 60.8 1.0 N A:ILE507 4.3 60.1 1.0 HG23 A:THR508 4.4 59.9 1.0 H A:ASN481 4.4 63.3 1.0 H A:THR508 4.4 59.9 1.0 SG A:CYS498 4.4 59.1 1.0 CB A:ASN481 4.5 63.3 1.0 C A:CYS506 4.5 62.5 1.0 CA A:CYS572 4.6 58.3 1.0 H A:CYS572 4.6 58.3 1.0 CA A:CYS479 4.7 64.4 1.0 HB3 A:ASN481 4.7 63.3 1.0 HG2 A:ARG500 4.7 61.0 1.0 HG1 A:THR508 4.8 59.9 1.0 HA A:CYS499 4.9 60.8 1.0 H A:CYS573 4.9 57.5 1.0 N A:CYS506 4.9 62.5 1.0 HB2 A:PRO570 4.9 57.2 1.0 CG2 A:ILE507 5.0 60.1 1.0 H A:ARG500 5.0 61.0 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State


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 the Apo Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:76.5 occ:1.00 SG A:CYS479 2.3 64.4 1.0 SG A:CYS498 2.3 59.1 1.0 SG A:CYS482 2.3 61.2 1.0 SG A:CYS477 2.3 63.1 1.0 HB2 A:CYS482 2.9 61.2 1.0 H A:CYS479 2.9 64.4 1.0 H A:CYS482 3.1 61.2 1.0 CB A:CYS482 3.2 61.2 1.0 HB3 A:CYS479 3.3 64.4 1.0 CB A:CYS479 3.3 64.4 1.0 HA A:CYS477 3.4 63.1 1.0 CB A:CYS477 3.4 63.1 1.0 HB2 A:CYS477 3.4 63.1 1.0 H A:GLN478 3.5 62.9 1.0 N A:CYS479 3.5 64.4 1.0 H A:GLY480 3.5 65.6 1.0 HA A:CYS498 3.6 59.1 1.0 CB A:CYS498 3.6 59.1 1.0 H A:CYS499 3.6 60.8 1.0 N A:CYS482 3.7 61.2 1.0 H A:ASN481 3.7 63.3 1.0 HB2 A:CYS498 3.7 59.1 1.0 ZN A:ZN702 3.7 72.5 1.0 HB3 A:CYS572 3.8 58.3 1.0 CA A:CYS477 3.8 63.1 1.0 CA A:CYS479 3.9 64.4 1.0 N A:GLN478 3.9 62.9 1.0 HB3 A:CYS482 3.9 61.2 1.0 N A:GLY480 4.0 65.6 1.0 CA A:CYS482 4.0 61.2 1.0 CA A:CYS498 4.1 59.1 1.0 HB2 A:CYS479 4.2 64.4 1.0 C A:CYS477 4.2 63.1 1.0 C A:CYS479 4.2 64.4 1.0 HB3 A:CYS477 4.3 63.1 1.0 SG A:CYS572 4.3 58.3 1.0 N A:ASN481 4.3 63.3 1.0 HB3 A:CYS498 4.4 59.1 1.0 N A:CYS499 4.4 60.8 1.0 HZ3 A:TRP476 4.4 61.2 1.0 HA A:CYS482 4.5 61.2 1.0 C A:GLN478 4.5 62.9 1.0 CB A:CYS572 4.5 58.3 1.0 SG A:CYS499 4.6 60.8 1.0 C A:ASN481 4.7 63.3 1.0 HB2 A:ASN481 4.7 63.3 1.0 H A:CYS572 4.7 58.3 1.0 HA A:CYS479 4.8 64.4 1.0 CA A:GLN478 4.8 62.9 1.0 C A:CYS498 4.9 59.1 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State


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 the Apo Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:72.5 occ:1.00 SG B:CYS506 2.3 62.5 1.0 SG B:CYS499 2.3 60.8 1.0 SG B:CYS572 2.3 58.3 1.0 SG B:CYS479 2.3 64.4 1.0 HB3 B:CYS499 2.9 60.8 1.0 HB3 B:CYS572 3.1 58.3 1.0 CB B:CYS572 3.1 58.3 1.0 HB2 B:CYS572 3.1 58.3 1.0 HB2 B:CYS506 3.1 62.5 1.0 CB B:CYS499 3.2 60.8 1.0 HB2 B:CYS479 3.2 64.4 1.0 CB B:CYS479 3.2 64.4 1.0 CB B:CYS506 3.2 62.5 1.0 HA B:CYS506 3.2 62.5 1.0 HB3 B:CYS479 3.3 64.4 1.0 H B:CYS499 3.3 60.8 1.0 HB2 B:ASN481 3.6 63.3 1.0 H B:ILE507 3.6 60.1 1.0 ZN B:ZN703 3.7 76.5 1.0 CA B:CYS506 3.7 62.5 1.0 HB2 B:CYS499 3.8 60.8 1.0 HG22 B:ILE507 4.0 60.1 1.0 N B:CYS499 4.1 60.8 1.0 HB3 B:CYS506 4.1 62.5 1.0 SG B:CYS482 4.2 61.2 1.0 CA B:CYS499 4.2 60.8 1.0 N B:ILE507 4.3 60.1 1.0 HG23 B:THR508 4.4 59.9 1.0 H B:ASN481 4.4 63.3 1.0 H B:THR508 4.4 59.9 1.0 SG B:CYS498 4.4 59.1 1.0 CB B:ASN481 4.5 63.3 1.0 C B:CYS506 4.5 62.5 1.0 CA B:CYS572 4.6 58.3 1.0 H B:CYS572 4.6 58.3 1.0 CA B:CYS479 4.7 64.4 1.0 HB3 B:ASN481 4.7 63.3 1.0 HG2 B:ARG500 4.7 61.0 1.0 HG1 B:THR508 4.8 59.9 1.0 HA B:CYS499 4.9 60.8 1.0 H B:CYS573 4.9 57.5 1.0 N B:CYS506 4.9 62.5 1.0 HB2 B:PRO570 4.9 57.2 1.0 CG2 B:ILE507 5.0 60.1 1.0 H B:ARG500 5.0 61.0 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State


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 the Apo Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:76.5 occ:1.00 SG B:CYS479 2.3 64.4 1.0 SG B:CYS482 2.3 61.2 1.0 SG B:CYS498 2.3 59.1 1.0 SG B:CYS477 2.3 63.1 1.0 HB2 B:CYS482 2.9 61.2 1.0 H B:CYS479 2.9 64.4 1.0 H B:CYS482 3.1 61.2 1.0 CB B:CYS482 3.2 61.2 1.0 HB3 B:CYS479 3.3 64.4 1.0 CB B:CYS479 3.3 64.4 1.0 HA B:CYS477 3.4 63.1 1.0 CB B:CYS477 3.4 63.1 1.0 HB2 B:CYS477 3.4 63.1 1.0 H B:GLN478 3.5 62.9 1.0 N B:CYS479 3.5 64.4 1.0 H B:GLY480 3.5 65.6 1.0 HA B:CYS498 3.6 59.1 1.0 CB B:CYS498 3.6 59.1 1.0 H B:CYS499 3.6 60.8 1.0 N B:CYS482 3.7 61.2 1.0 H B:ASN481 3.7 63.3 1.0 HB2 B:CYS498 3.7 59.1 1.0 ZN B:ZN702 3.7 72.5 1.0 HB3 B:CYS572 3.8 58.3 1.0 CA B:CYS477 3.8 63.1 1.0 CA B:CYS479 3.9 64.4 1.0 N B:GLN478 3.9 62.9 1.0 HB3 B:CYS482 3.9 61.2 1.0 N B:GLY480 4.0 65.6 1.0 CA B:CYS482 4.0 61.2 1.0 CA B:CYS498 4.1 59.1 1.0 HB2 B:CYS479 4.2 64.4 1.0 C B:CYS477 4.2 63.1 1.0 C B:CYS479 4.2 64.4 1.0 HB3 B:CYS477 4.3 63.1 1.0 SG B:CYS572 4.3 58.3 1.0 N B:ASN481 4.3 63.3 1.0 HB3 B:CYS498 4.4 59.1 1.0 N B:CYS499 4.4 60.8 1.0 HZ3 B:TRP476 4.4 61.2 1.0 HA B:CYS482 4.5 61.2 1.0 C B:GLN478 4.5 62.9 1.0 CB B:CYS572 4.5 58.3 1.0 SG B:CYS499 4.6 60.8 1.0 C B:ASN481 4.7 63.3 1.0 HB2 B:ASN481 4.7 63.3 1.0 H B:CYS572 4.7 58.3 1.0 HA B:CYS479 4.8 64.4 1.0 CA B:GLN478 4.8 62.9 1.0 C B:CYS498 4.9 59.1 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State


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 the Apo Closed State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:72.5 occ:1.00 SG C:CYS506 2.3 62.5 1.0 SG C:CYS499 2.3 60.8 1.0 SG C:CYS572 2.3 58.3 1.0 SG C:CYS479 2.3 64.4 1.0 HB3 C:CYS499 2.9 60.8 1.0 HB3 C:CYS572 3.1 58.3 1.0 CB C:CYS572 3.1 58.3 1.0 HB2 C:CYS572 3.1 58.3 1.0 HB2 C:CYS506 3.1 62.5 1.0 CB C:CYS499 3.2 60.8 1.0 HB2 C:CYS479 3.2 64.4 1.0 CB C:CYS479 3.2 64.4 1.0 CB C:CYS506 3.2 62.5 1.0 HA C:CYS506 3.2 62.5 1.0 HB3 C:CYS479 3.3 64.4 1.0 H C:CYS499 3.3 60.8 1.0 HB2 C:ASN481 3.6 63.3 1.0 H C:ILE507 3.6 60.1 1.0 ZN C:ZN703 3.7 76.5 1.0 CA C:CYS506 3.7 62.5 1.0 HB2 C:CYS499 3.8 60.8 1.0 HG22 C:ILE507 4.0 60.1 1.0 N C:CYS499 4.1 60.8 1.0 HB3 C:CYS506 4.1 62.5 1.0 SG C:CYS482 4.2 61.2 1.0 CA C:CYS499 4.2 60.8 1.0 N C:ILE507 4.3 60.1 1.0 HG23 C:THR508 4.4 59.9 1.0 H C:ASN481 4.4 63.3 1.0 H C:THR508 4.4 59.9 1.0 SG C:CYS498 4.4 59.1 1.0 CB C:ASN481 4.5 63.3 1.0 C C:CYS506 4.5 62.5 1.0 CA C:CYS572 4.6 58.3 1.0 H C:CYS572 4.6 58.3 1.0 CA C:CYS479 4.7 64.4 1.0 HB3 C:ASN481 4.7 63.3 1.0 HG2 C:ARG500 4.7 61.0 1.0 HG1 C:THR508 4.8 59.9 1.0 HA C:CYS499 4.9 60.8 1.0 H C:CYS573 4.9 57.5 1.0 N C:CYS506 4.9 62.5 1.0 HB2 C:PRO570 4.9 57.2 1.0 CG2 C:ILE507 5.0 60.1 1.0 H C:ARG500 5.0 61.0 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Rat P2X7 Receptor in the Apo Closed State


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 the Apo Closed State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:76.5 occ:1.00 SG C:CYS479 2.3 64.4 1.0 SG C:CYS498 2.3 59.1 1.0 SG C:CYS482 2.3 61.2 1.0 SG C:CYS477 2.3 63.1 1.0 HB2 C:CYS482 2.9 61.2 1.0 H C:CYS479 2.9 64.4 1.0 H C:CYS482 3.1 61.2 1.0 CB C:CYS482 3.2 61.2 1.0 HB3 C:CYS479 3.3 64.4 1.0 CB C:CYS479 3.3 64.4 1.0 HA C:CYS477 3.4 63.1 1.0 CB C:CYS477 3.4 63.1 1.0 HB2 C:CYS477 3.4 63.1 1.0 H C:GLN478 3.5 62.9 1.0 N C:CYS479 3.5 64.4 1.0 H C:GLY480 3.5 65.6 1.0 HA C:CYS498 3.6 59.1 1.0 CB C:CYS498 3.6 59.1 1.0 H C:CYS499 3.6 60.8 1.0 N C:CYS482 3.7 61.2 1.0 H C:ASN481 3.7 63.3 1.0 HB2 C:CYS498 3.7 59.1 1.0 ZN C:ZN702 3.7 72.5 1.0 HB3 C:CYS572 3.8 58.3 1.0 CA C:CYS477 3.8 63.1 1.0 CA C:CYS479 3.9 64.4 1.0 N C:GLN478 3.9 62.9 1.0 HB3 C:CYS482 3.9 61.2 1.0 N C:GLY480 4.0 65.6 1.0 CA C:CYS482 4.0 61.2 1.0 CA C:CYS498 4.1 59.1 1.0 HB2 C:CYS479 4.2 64.4 1.0 C C:CYS477 4.2 63.1 1.0 C C:CYS479 4.2 64.4 1.0 HB3 C:CYS477 4.3 63.1 1.0 SG C:CYS572 4.3 58.3 1.0 N C:ASN481 4.3 63.3 1.0 HB3 C:CYS498 4.4 59.1 1.0 N C:CYS499 4.4 60.8 1.0 HZ3 C:TRP476 4.4 61.2 1.0 HA C:CYS482 4.5 61.2 1.0 C C:GLN478 4.5 62.9 1.0 CB C:CYS572 4.5 58.3 1.0 SG C:CYS499 4.6 60.8 1.0 C C:ASN481 4.7 63.3 1.0 HB2 C:ASN481 4.7 63.3 1.0 H C:CYS572 4.7 58.3 1.0 HA C:CYS479 4.8 64.4 1.0 CA C:GLN478 4.8 62.9 1.0 C C:CYS498 4.9 59.1 1.0

A.C.Oken, N.E.Lisi, I.Krishnamurthy, A.E.Mccarthy, M.H.Godsey, A.Glasfeld, S.E.Mansoor. High-Affinity Agonism at the P2X7 Receptor Is Mediated By Three Residues Outside the Orthosteric Pocket Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-50771-6