Bromine in PDB 8jv5: Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430

The binding sites of Bromine atom in the Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430 (pdb code 8jv5). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430, PDB code: 8jv5:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in the Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br501 b:134.0 occ:1.00 BR1 A:P73501 0.0 134.0 1.0 C06 A:P73501 1.9 97.4 1.0 C05 A:P73501 2.9 98.2 1.0 C08 A:P73501 2.9 93.0 1.0 N09 A:P73501 3.2 92.5 1.0 OH B:TYR302 3.3 74.7 1.0 CZ B:TYR302 3.3 73.9 1.0 CE1 B:TYR302 3.4 75.9 1.0 OD2 A:ASP91 3.4 65.5 1.0 NZ A:LYS301 3.5 76.2 1.0 CG A:ASP91 3.6 61.8 1.0 C10 A:P73501 3.6 93.0 1.0 O18 A:P73501 3.7 92.9 1.0 NH1 A:ARG85 3.7 78.5 1.0 OD1 A:ASP91 3.8 64.3 1.0 CE2 B:TYR302 4.1 75.3 1.0 CD1 B:TYR302 4.1 75.8 1.0 C19 A:P73501 4.2 96.1 1.0 C04 A:P73501 4.2 94.7 1.0 CB A:ASP91 4.3 56.7 1.0 N11 A:P73501 4.6 94.1 1.0 CE A:LYS301 4.6 74.3 1.0 CZ3 A:TRP87 4.7 66.0 1.0 C21 A:P73501 4.7 95.3 1.0 CA A:ASP91 4.8 54.1 1.0 CD2 B:TYR302 4.8 76.5 1.0 CG B:TYR302 4.8 75.1 1.0 CZ2 B:TRP167 4.8 84.3 1.0 CZ A:ARG85 5.0 84.2 1.0

Bromine binding site 2 out of 6 in the Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br501 b:137.5 occ:1.00 BR2 A:P73501 0.0 137.5 1.0 C19 A:P73501 1.9 96.1 1.0 C08 A:P73501 2.9 93.0 1.0 C21 A:P73501 2.9 95.3 1.0 N09 A:P73501 3.0 92.5 1.0 CZ A:PHE299 3.4 53.9 1.0 CG2 A:ILE315 3.6 56.7 1.0 CD2 A:LEU105 3.6 32.3 1.0 CE2 A:PHE299 3.6 52.5 1.0 C10 A:P73501 3.7 93.0 1.0 O18 A:P73501 4.0 92.9 1.0 C06 A:P73501 4.2 97.4 1.0 C04 A:P73501 4.2 94.7 1.0 SD A:MET108 4.2 62.5 1.0 CZ3 A:TRP87 4.2 66.0 1.0 CG1 A:ILE315 4.2 54.0 1.0 CB A:ILE315 4.3 51.4 1.0 CH2 A:TRP87 4.4 64.2 1.0 N11 A:P73501 4.6 94.1 1.0 CE1 A:PHE299 4.6 55.6 1.0 CD1 A:ILE315 4.7 55.7 1.0 C05 A:P73501 4.7 98.2 1.0 CG A:LEU105 4.9 33.0 1.0 O A:ASP91 4.9 67.0 1.0 CE A:MET108 5.0 55.0 1.0 CD2 A:PHE299 5.0 54.9 1.0 CD1 A:LEU105 5.0 37.8 1.0

Bromine binding site 3 out of 6 in the Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br501 b:134.3 occ:1.00 BR1 B:P73501 0.0 134.3 1.0 C06 B:P73501 1.9 96.9 1.0 C05 B:P73501 2.9 97.3 1.0 C08 B:P73501 2.9 92.6 1.0 N09 B:P73501 3.2 92.6 1.0 OH C:TYR302 3.3 74.7 1.0 CZ C:TYR302 3.3 73.5 1.0 CE1 C:TYR302 3.4 75.8 1.0 OD2 B:ASP91 3.4 61.9 1.0 NZ B:LYS301 3.5 75.7 1.0 CG B:ASP91 3.6 58.7 1.0 C10 B:P73501 3.6 93.1 1.0 O18 B:P73501 3.7 92.5 1.0 NH1 B:ARG85 3.7 76.2 1.0 OD1 B:ASP91 3.8 61.7 1.0 CE2 C:TYR302 4.1 76.0 1.0 CD1 C:TYR302 4.2 75.4 1.0 C19 B:P73501 4.2 95.3 1.0 C04 B:P73501 4.2 93.3 1.0 CB B:ASP91 4.3 53.7 1.0 N11 B:P73501 4.6 92.9 1.0 CE B:LYS301 4.6 74.9 1.0 CZ3 B:TRP87 4.7 63.2 1.0 C21 B:P73501 4.7 94.7 1.0 CA B:ASP91 4.8 50.1 1.0 CD2 C:TYR302 4.8 77.6 1.0 CG C:TYR302 4.8 75.6 1.0 CZ2 C:TRP167 4.8 83.3 1.0 CZ B:ARG85 4.9 81.6 1.0

Bromine binding site 4 out of 6 in the Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br501 b:135.1 occ:1.00 BR2 B:P73501 0.0 135.1 1.0 C19 B:P73501 1.9 95.3 1.0 C08 B:P73501 2.9 92.6 1.0 C21 B:P73501 2.9 94.7 1.0 N09 B:P73501 3.0 92.6 1.0 CZ B:PHE299 3.4 53.9 1.0 CG2 B:ILE315 3.6 58.4 1.0 CD2 B:LEU105 3.6 32.8 1.0 CE2 B:PHE299 3.6 52.2 1.0 C10 B:P73501 3.7 93.1 1.0 O18 B:P73501 4.0 92.5 1.0 C06 B:P73501 4.2 96.9 1.0 SD B:MET108 4.2 62.3 1.0 C04 B:P73501 4.2 93.3 1.0 CZ3 B:TRP87 4.2 63.2 1.0 CG1 B:ILE315 4.3 56.5 1.0 CB B:ILE315 4.3 53.5 1.0 CH2 B:TRP87 4.4 61.2 1.0 N11 B:P73501 4.6 92.9 1.0 CE1 B:PHE299 4.6 56.9 1.0 CD1 B:ILE315 4.7 57.6 1.0 C05 B:P73501 4.7 97.3 1.0 CG B:LEU105 4.9 35.1 1.0 O B:ASP91 4.9 65.2 1.0 CE B:MET108 4.9 56.3 1.0 CD1 B:LEU105 5.0 37.5 1.0 CD2 B:PHE299 5.0 55.5 1.0

Bromine binding site 5 out of 6 in the Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br501 b:133.3 occ:1.00 BR1 C:P73501 0.0 133.3 1.0 C06 C:P73501 1.9 97.6 1.0 C05 C:P73501 2.9 98.7 1.0 C08 C:P73501 2.9 93.2 1.0 N09 C:P73501 3.2 92.6 1.0 OH A:TYR302 3.3 73.2 1.0 CZ A:TYR302 3.4 72.1 1.0 CE1 A:TYR302 3.4 74.5 1.0 OD2 C:ASP91 3.4 63.5 1.0 NZ C:LYS301 3.5 74.8 1.0 CG C:ASP91 3.6 59.9 1.0 C10 C:P73501 3.6 93.6 1.0 NH1 C:ARG85 3.7 79.0 1.0 O18 C:P73501 3.7 94.0 1.0 OD1 C:ASP91 3.8 62.8 1.0 CE2 A:TYR302 4.2 74.3 1.0 CD1 A:TYR302 4.2 74.5 1.0 C19 C:P73501 4.2 96.1 1.0 C04 C:P73501 4.2 95.1 1.0 CB C:ASP91 4.3 55.9 1.0 N11 C:P73501 4.6 93.8 1.0 CE C:LYS301 4.6 73.9 1.0 CZ3 C:TRP87 4.7 66.5 1.0 C21 C:P73501 4.7 95.5 1.0 CA C:ASP91 4.8 51.8 1.0 CD2 A:TYR302 4.8 75.5 1.0 CZ2 A:TRP167 4.8 83.8 1.0 CG A:TYR302 4.8 73.8 1.0 CZ C:ARG85 4.9 85.5 1.0

Bromine binding site 6 out of 6 in the Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Cryo-Em Structure of the Zebrafish P2X4 Receptor in Complex with BX430 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br501 b:137.1 occ:1.00 BR2 C:P73501 0.0 137.1 1.0 C19 C:P73501 1.9 96.1 1.0 C08 C:P73501 2.9 93.2 1.0 C21 C:P73501 2.9 95.5 1.0 N09 C:P73501 3.0 92.6 1.0 CZ C:PHE299 3.3 55.3 1.0 CG2 C:ILE315 3.6 58.2 1.0 CE2 C:PHE299 3.6 53.9 1.0 CD2 C:LEU105 3.6 32.5 1.0 C10 C:P73501 3.7 93.6 1.0 O18 C:P73501 4.0 94.0 1.0 C06 C:P73501 4.2 97.6 1.0 SD C:MET108 4.2 64.5 1.0 C04 C:P73501 4.2 95.1 1.0 CG1 C:ILE315 4.2 56.4 1.0 CZ3 C:TRP87 4.2 66.5 1.0 CB C:ILE315 4.3 53.8 1.0 CH2 C:TRP87 4.4 64.0 1.0 N11 C:P73501 4.6 93.8 1.0 CE1 C:PHE299 4.6 56.9 1.0 CD1 C:ILE315 4.7 58.3 1.0 C05 C:P73501 4.7 98.7 1.0 CG C:LEU105 4.9 35.0 1.0 O C:ASP91 4.9 66.9 1.0 CE C:MET108 5.0 57.6 1.0 CD2 C:PHE299 5.0 56.2 1.0 CD1 C:LEU105 5.0 40.6 1.0

M.Hattori, C.Shen. Structural Insights Into the Allosteric Inhibition of P2X4 Receptors Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-42164-Y