Zinc in PDB 8trk: Cryo-Em Structure of the Rat P2X7 Receptor in Complex with the Allosteric Antagonist Methyl Blue

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


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 Methyl Blue within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:59.3 occ:1.00 SG A:CYS506 2.3 43.7 1.0 SG A:CYS499 2.3 35.8 1.0 SG A:CYS572 2.3 34.6 1.0 SG A:CYS479 2.3 44.9 1.0 HB3 A:CYS572 2.9 34.6 1.0 HB3 A:CYS479 3.0 44.9 1.0 CB A:CYS572 3.0 34.6 1.0 HB2 A:CYS479 3.0 44.9 1.0 HB2 A:CYS572 3.0 34.6 1.0 CB A:CYS479 3.0 44.9 1.0 HB3 A:CYS499 3.0 35.8 1.0 HB2 A:CYS506 3.2 43.7 1.0 CB A:CYS499 3.3 35.8 1.0 CB A:CYS506 3.3 43.7 1.0 HA A:CYS506 3.3 43.7 1.0 H A:CYS499 3.4 35.8 1.0 H A:ILE507 3.6 37.9 1.0 HB2 A:ASN481 3.7 44.8 1.0 ZN A:ZN703 3.8 55.7 1.0 CA A:CYS506 3.8 43.7 1.0 HG23 A:ILE507 3.9 37.9 1.0 HB2 A:CYS499 4.0 35.8 1.0 N A:CYS499 4.1 35.8 1.0 HB3 A:CYS506 4.2 43.7 1.0 HG1 A:THR508 4.2 37.3 1.0 N A:ILE507 4.3 37.9 1.0 SG A:CYS498 4.4 32.8 1.0 CA A:CYS499 4.4 35.8 1.0 SG A:CYS482 4.4 42.3 1.0 H A:THR508 4.4 37.3 1.0 HG22 A:THR508 4.4 37.3 1.0 CA A:CYS572 4.5 34.6 1.0 H A:CYS572 4.5 34.6 1.0 H A:ASN481 4.5 44.8 1.0 CA A:CYS479 4.5 44.9 1.0 C A:CYS506 4.6 43.7 1.0 HG A:CYS573 4.6 30.9 1.0 CB A:ASN481 4.7 44.8 1.0 HB2 A:PRO570 4.8 28.8 1.0 H A:CYS479 4.8 44.9 1.0 CG2 A:ILE507 4.8 37.9 1.0 H A:CYS573 4.9 30.9 1.0 HG2 A:ARG500 4.9 39.8 1.0 HA A:CYS498 4.9 32.8 1.0 HA A:CYS572 5.0 34.6 1.0 N A:CYS572 5.0 34.6 1.0 HA A:CYS499 5.0 35.8 1.0 OG1 A:THR508 5.0 37.3 1.0 HG22 A:ILE507 5.0 37.9 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 Methyl Blue


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 Methyl Blue within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:55.7 occ:1.00 SG A:CYS479 2.3 44.9 1.0 SG A:CYS482 2.3 42.3 1.0 SG A:CYS498 2.3 32.8 1.0 SG A:CYS477 2.3 43.0 1.0 H A:CYS479 2.7 44.9 1.0 HB2 A:CYS482 2.9 42.3 1.0 H A:CYS482 3.1 42.3 1.0 CB A:CYS482 3.2 42.3 1.0 HB3 A:CYS479 3.3 44.9 1.0 CB A:CYS479 3.3 44.9 1.0 HB2 A:CYS477 3.4 43.0 1.0 H A:ASN481 3.4 44.8 1.0 CB A:CYS477 3.4 43.0 1.0 H A:GLY480 3.4 45.0 1.0 N A:CYS479 3.5 44.9 1.0 HA A:CYS477 3.5 43.0 1.0 CB A:CYS498 3.6 32.8 1.0 HB2 A:CYS498 3.6 32.8 1.0 N A:CYS482 3.6 42.3 1.0 HA A:CYS498 3.6 32.8 1.0 H A:GLN478 3.7 45.0 1.0 HB3 A:CYS572 3.7 34.6 1.0 ZN A:ZN702 3.8 59.3 1.0 H A:CYS499 3.8 35.8 1.0 CA A:CYS479 3.8 44.9 1.0 CA A:CYS477 3.9 43.0 1.0 N A:GLY480 3.9 45.0 1.0 HB3 A:CYS482 4.0 42.3 1.0 CA A:CYS482 4.0 42.3 1.0 N A:GLN478 4.1 45.0 1.0 N A:ASN481 4.1 44.8 1.0 CA A:CYS498 4.2 32.8 1.0 HB2 A:CYS479 4.2 44.9 1.0 C A:CYS479 4.2 44.9 1.0 HB3 A:CYS477 4.2 43.0 1.0 HZ3 A:TRP476 4.3 39.1 1.0 C A:CYS477 4.3 43.0 1.0 HB3 A:CYS498 4.4 32.8 1.0 HA A:CYS482 4.4 42.3 1.0 SG A:CYS572 4.4 34.6 1.0 C A:ASN481 4.5 44.8 1.0 CB A:CYS572 4.5 34.6 1.0 N A:CYS499 4.6 35.8 1.0 HB2 A:ASN481 4.6 44.8 1.0 C A:GLN478 4.6 45.0 1.0 H A:CYS572 4.6 34.6 1.0 SG A:CYS499 4.7 35.8 1.0 HA A:CYS479 4.8 44.9 1.0 CA A:ASN481 4.8 44.8 1.0 CA A:GLY480 4.9 45.0 1.0 C A:GLY480 5.0 45.0 1.0 C A:CYS498 5.0 32.8 1.0 CA A:GLN478 5.0 45.0 1.0 CZ3 A:TRP476 5.0 39.1 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 Methyl Blue


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 Methyl Blue within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:59.3 occ:1.00 SG C:CYS506 2.3 43.7 1.0 SG C:CYS499 2.3 35.8 1.0 SG C:CYS572 2.3 34.6 1.0 SG C:CYS479 2.3 44.9 1.0 HB3 C:CYS572 2.9 34.6 1.0 HB3 C:CYS479 3.0 44.9 1.0 CB C:CYS572 3.0 34.6 1.0 HB2 C:CYS479 3.0 44.9 1.0 HB2 C:CYS572 3.0 34.6 1.0 CB C:CYS479 3.0 44.9 1.0 HB3 C:CYS499 3.0 35.8 1.0 HB2 C:CYS506 3.2 43.7 1.0 CB C:CYS499 3.3 35.8 1.0 CB C:CYS506 3.3 43.7 1.0 HA C:CYS506 3.3 43.7 1.0 H C:CYS499 3.4 35.8 1.0 H C:ILE507 3.6 37.9 1.0 HB2 C:ASN481 3.7 44.8 1.0 ZN C:ZN703 3.8 55.7 1.0 CA C:CYS506 3.8 43.7 1.0 HG23 C:ILE507 4.0 37.9 1.0 HB2 C:CYS499 4.0 35.8 1.0 N C:CYS499 4.1 35.8 1.0 HB3 C:CYS506 4.2 43.7 1.0 HG1 C:THR508 4.2 37.3 1.0 N C:ILE507 4.3 37.9 1.0 SG C:CYS498 4.4 32.8 1.0 CA C:CYS499 4.4 35.8 1.0 SG C:CYS482 4.4 42.3 1.0 H C:THR508 4.4 37.3 1.0 HG22 C:THR508 4.4 37.3 1.0 CA C:CYS572 4.5 34.6 1.0 H C:CYS572 4.5 34.6 1.0 H C:ASN481 4.5 44.8 1.0 CA C:CYS479 4.5 44.9 1.0 C C:CYS506 4.6 43.7 1.0 HG C:CYS573 4.6 30.9 1.0 CB C:ASN481 4.7 44.8 1.0 HB2 C:PRO570 4.8 28.8 1.0 H C:CYS479 4.8 44.9 1.0 CG2 C:ILE507 4.8 37.9 1.0 H C:CYS573 4.9 30.9 1.0 HG2 C:ARG500 4.9 39.8 1.0 HA C:CYS498 4.9 32.8 1.0 HA C:CYS572 5.0 34.6 1.0 N C:CYS572 5.0 34.6 1.0 HA C:CYS499 5.0 35.8 1.0 OG1 C:THR508 5.0 37.3 1.0 HG22 C:ILE507 5.0 37.9 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 Methyl Blue


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 Methyl Blue within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:55.7 occ:1.00 SG C:CYS479 2.3 44.9 1.0 SG C:CYS482 2.3 42.3 1.0 SG C:CYS498 2.3 32.8 1.0 SG C:CYS477 2.3 43.0 1.0 H C:CYS479 2.7 44.9 1.0 HB2 C:CYS482 2.9 42.3 1.0 H C:CYS482 3.1 42.3 1.0 CB C:CYS482 3.2 42.3 1.0 HB3 C:CYS479 3.3 44.9 1.0 CB C:CYS479 3.3 44.9 1.0 HB2 C:CYS477 3.4 43.0 1.0 H C:ASN481 3.4 44.8 1.0 CB C:CYS477 3.4 43.0 1.0 H C:GLY480 3.4 45.0 1.0 N C:CYS479 3.5 44.9 1.0 HA C:CYS477 3.5 43.0 1.0 CB C:CYS498 3.6 32.8 1.0 HB2 C:CYS498 3.6 32.8 1.0 N C:CYS482 3.6 42.3 1.0 HA C:CYS498 3.6 32.8 1.0 H C:GLN478 3.7 45.0 1.0 HB3 C:CYS572 3.7 34.6 1.0 ZN C:ZN702 3.8 59.3 1.0 H C:CYS499 3.8 35.8 1.0 CA C:CYS479 3.8 44.9 1.0 CA C:CYS477 3.9 43.0 1.0 N C:GLY480 3.9 45.0 1.0 HB3 C:CYS482 4.0 42.3 1.0 CA C:CYS482 4.0 42.3 1.0 N C:GLN478 4.1 45.0 1.0 N C:ASN481 4.1 44.8 1.0 CA C:CYS498 4.2 32.8 1.0 HB2 C:CYS479 4.2 44.9 1.0 C C:CYS479 4.2 44.9 1.0 HB3 C:CYS477 4.2 43.0 1.0 HZ3 C:TRP476 4.3 39.1 1.0 C C:CYS477 4.3 43.0 1.0 HB3 C:CYS498 4.4 32.8 1.0 HA C:CYS482 4.4 42.3 1.0 SG C:CYS572 4.4 34.6 1.0 C C:ASN481 4.5 44.8 1.0 CB C:CYS572 4.5 34.6 1.0 N C:CYS499 4.6 35.8 1.0 HB2 C:ASN481 4.6 44.8 1.0 C C:GLN478 4.6 45.0 1.0 H C:CYS572 4.6 34.6 1.0 SG C:CYS499 4.7 35.8 1.0 HA C:CYS479 4.8 44.9 1.0 CA C:ASN481 4.8 44.8 1.0 CA C:GLY480 4.9 45.0 1.0 C C:CYS498 5.0 32.8 1.0 C C:GLY480 5.0 45.0 1.0 CA C:GLN478 5.0 45.0 1.0 CZ3 C:TRP476 5.0 39.1 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 Methyl Blue


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 Methyl Blue within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:59.3 occ:1.00 SG B:CYS506 2.3 43.7 1.0 SG B:CYS499 2.3 35.8 1.0 SG B:CYS572 2.3 34.6 1.0 SG B:CYS479 2.3 44.9 1.0 HB3 B:CYS572 2.9 34.6 1.0 HB3 B:CYS479 3.0 44.9 1.0 CB B:CYS572 3.0 34.6 1.0 HB2 B:CYS479 3.0 44.9 1.0 HB2 B:CYS572 3.0 34.6 1.0 CB B:CYS479 3.0 44.9 1.0 HB3 B:CYS499 3.0 35.8 1.0 HB2 B:CYS506 3.2 43.7 1.0 CB B:CYS499 3.3 35.8 1.0 CB B:CYS506 3.3 43.7 1.0 HA B:CYS506 3.3 43.7 1.0 H B:CYS499 3.4 35.8 1.0 H B:ILE507 3.6 37.9 1.0 HB2 B:ASN481 3.7 44.8 1.0 ZN B:ZN703 3.8 55.7 1.0 CA B:CYS506 3.8 43.7 1.0 HG23 B:ILE507 4.0 37.9 1.0 HB2 B:CYS499 4.0 35.8 1.0 N B:CYS499 4.1 35.8 1.0 HB3 B:CYS506 4.2 43.7 1.0 HG1 B:THR508 4.2 37.3 1.0 N B:ILE507 4.3 37.9 1.0 SG B:CYS498 4.4 32.8 1.0 CA B:CYS499 4.4 35.8 1.0 SG B:CYS482 4.4 42.3 1.0 H B:THR508 4.4 37.3 1.0 HG22 B:THR508 4.4 37.3 1.0 CA B:CYS572 4.5 34.6 1.0 H B:CYS572 4.5 34.6 1.0 H B:ASN481 4.5 44.8 1.0 CA B:CYS479 4.5 44.9 1.0 C B:CYS506 4.6 43.7 1.0 HG B:CYS573 4.6 30.9 1.0 CB B:ASN481 4.7 44.8 1.0 HB2 B:PRO570 4.8 28.8 1.0 H B:CYS479 4.8 44.9 1.0 CG2 B:ILE507 4.8 37.9 1.0 H B:CYS573 4.9 30.9 1.0 HG2 B:ARG500 4.9 39.8 1.0 HA B:CYS498 4.9 32.8 1.0 HA B:CYS572 5.0 34.6 1.0 N B:CYS572 5.0 34.6 1.0 HA B:CYS499 5.0 35.8 1.0 OG1 B:THR508 5.0 37.3 1.0 HG22 B:ILE507 5.0 37.9 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 Methyl Blue


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 Methyl Blue within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:55.7 occ:1.00 SG B:CYS479 2.3 44.9 1.0 SG B:CYS482 2.3 42.3 1.0 SG B:CYS498 2.3 32.8 1.0 SG B:CYS477 2.3 43.0 1.0 H B:CYS479 2.7 44.9 1.0 HB2 B:CYS482 2.9 42.3 1.0 H B:CYS482 3.1 42.3 1.0 CB B:CYS482 3.2 42.3 1.0 HB3 B:CYS479 3.3 44.9 1.0 CB B:CYS479 3.3 44.9 1.0 HB2 B:CYS477 3.4 43.0 1.0 H B:ASN481 3.4 44.8 1.0 CB B:CYS477 3.4 43.0 1.0 H B:GLY480 3.4 45.0 1.0 N B:CYS479 3.5 44.9 1.0 HA B:CYS477 3.5 43.0 1.0 CB B:CYS498 3.6 32.8 1.0 HB2 B:CYS498 3.6 32.8 1.0 N B:CYS482 3.6 42.3 1.0 HA B:CYS498 3.6 32.8 1.0 H B:GLN478 3.7 45.0 1.0 HB3 B:CYS572 3.7 34.6 1.0 ZN B:ZN702 3.8 59.3 1.0 H B:CYS499 3.8 35.8 1.0 CA B:CYS479 3.8 44.9 1.0 CA B:CYS477 3.9 43.0 1.0 N B:GLY480 3.9 45.0 1.0 HB3 B:CYS482 4.0 42.3 1.0 CA B:CYS482 4.0 42.3 1.0 N B:GLN478 4.1 45.0 1.0 N B:ASN481 4.1 44.8 1.0 CA B:CYS498 4.2 32.8 1.0 HB2 B:CYS479 4.2 44.9 1.0 C B:CYS479 4.2 44.9 1.0 HB3 B:CYS477 4.2 43.0 1.0 HZ3 B:TRP476 4.3 39.1 1.0 C B:CYS477 4.3 43.0 1.0 HB3 B:CYS498 4.4 32.8 1.0 HA B:CYS482 4.4 42.3 1.0 SG B:CYS572 4.4 34.6 1.0 C B:ASN481 4.5 44.8 1.0 CB B:CYS572 4.5 34.6 1.0 N B:CYS499 4.6 35.8 1.0 HB2 B:ASN481 4.6 44.8 1.0 C B:GLN478 4.6 45.0 1.0 H B:CYS572 4.6 34.6 1.0 SG B:CYS499 4.7 35.8 1.0 HA B:CYS479 4.8 44.9 1.0 CA B:ASN481 4.8 44.8 1.0 CA B:GLY480 4.9 45.0 1.0 C B:GLY480 5.0 45.0 1.0 C B:CYS498 5.0 32.8 1.0 CA B:GLN478 5.0 45.0 1.0 CZ3 B:TRP476 5.0 39.1 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