Bromine in PDB 8u4d: TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure

The structure of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Bromine atom in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure (pdb code 8u4d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure, PDB code: 8u4d:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Br801 b:38.0 occ:1.00 BR10 A:VPN801 0.0 38.0 1.0 C09 A:VPN801 1.9 38.0 1.0 H091 A:VPN801 2.5 38.0 1.0 H082 A:VPN801 2.8 38.0 1.0 C08 A:VPN801 2.8 38.0 1.0 HD13 D:LEU669 2.8 26.9 1.0 C11 A:VPN801 2.8 38.0 1.0 H131 A:VPN801 2.9 38.0 1.0 H071 A:VPN801 2.9 38.0 1.0 BR12 A:VPN801 3.2 38.0 1.0 H041 A:VPN801 3.3 38.0 1.0 C13 A:VPN801 3.4 38.0 1.0 C07 A:VPN801 3.4 38.0 1.0 HD21 D:LEU669 3.6 26.9 1.0 CD1 D:LEU669 3.7 26.9 1.0 HB2 D:ALA665 3.7 24.9 1.0 H081 A:VPN801 3.8 38.0 1.0 H111 A:VPN801 3.8 38.0 1.0 H072 A:VPN801 3.9 38.0 1.0 HD12 D:LEU669 4.0 26.9 1.0 H142 A:VPN801 4.0 38.0 1.0 HG D:LEU669 4.1 26.9 1.0 C14 A:VPN801 4.2 38.0 1.0 H132 A:VPN801 4.2 38.0 1.0 CG D:LEU669 4.3 26.9 1.0 C04 A:VPN801 4.3 38.0 1.0 H141 A:VPN801 4.3 38.0 1.0 HD11 D:LEU669 4.4 26.9 1.0 CD2 D:LEU669 4.4 26.9 1.0 HZ D:PHE591 4.5 24.7 1.0 H021 A:VPN801 4.6 38.0 1.0 H042 A:VPN801 4.6 38.0 1.0 CB D:ALA665 4.6 24.9 1.0 C06 A:VPN801 4.7 38.0 1.0 H052 A:VPN801 4.7 38.0 1.0 HB1 D:ALA665 4.7 24.9 1.0 C05 A:VPN801 4.8 38.0 1.0 HD22 D:LEU669 4.9 26.9 1.0

Bromine binding site 2 out of 8 in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Br801 b:38.0 occ:1.00 BR12 A:VPN801 0.0 38.0 1.0 C11 A:VPN801 1.9 38.0 1.0 H111 A:VPN801 2.5 38.0 1.0 C09 A:VPN801 2.8 38.0 1.0 C13 A:VPN801 2.8 38.0 1.0 H132 A:VPN801 3.0 38.0 1.0 H082 A:VPN801 3.0 38.0 1.0 H131 A:VPN801 3.1 38.0 1.0 BR10 A:VPN801 3.2 38.0 1.0 C08 A:VPN801 3.3 38.0 1.0 H081 A:VPN801 3.5 38.0 1.0 HD22 A:LEU515 3.7 35.6 1.0 H091 A:VPN801 3.8 38.0 1.0 HD23 A:LEU515 3.9 35.6 1.0 CD2 A:LEU515 4.1 35.6 1.0 C14 A:VPN801 4.2 38.0 1.0 H563 A:VPN801 4.4 38.0 1.0 HD21 A:LEU515 4.4 35.6 1.0 H141 A:VPN801 4.4 38.0 1.0 HE3 A:MET547 4.5 32.3 1.0 H021 A:VPN801 4.8 38.0 1.0 C07 A:VPN801 4.8 38.0 1.0 H142 A:VPN801 4.8 38.0 1.0 H041 A:VPN801 4.8 38.0 1.0 HG2 A:MET547 4.9 32.3 1.0 H052 A:VPN801 4.9 38.0 1.0 H152 A:VPN801 5.0 38.0 1.0 H071 A:VPN801 5.0 38.0 1.0 C56 A:VPN801 5.0 38.0 1.0

Bromine binding site 3 out of 8 in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Br801 b:38.0 occ:1.00 BR10 D:VPN801 0.0 38.0 1.0 C09 D:VPN801 1.9 38.0 1.0 H091 D:VPN801 2.5 38.0 1.0 H082 D:VPN801 2.8 38.0 1.0 C08 D:VPN801 2.8 38.0 1.0 HD13 C:LEU669 2.8 26.9 1.0 C11 D:VPN801 2.8 38.0 1.0 H131 D:VPN801 2.9 38.0 1.0 H071 D:VPN801 2.9 38.0 1.0 BR12 D:VPN801 3.2 38.0 1.0 H041 D:VPN801 3.3 38.0 1.0 C13 D:VPN801 3.4 38.0 1.0 C07 D:VPN801 3.4 38.0 1.0 HD21 C:LEU669 3.6 26.9 1.0 CD1 C:LEU669 3.7 26.9 1.0 HB2 C:ALA665 3.7 24.9 1.0 H081 D:VPN801 3.8 38.0 1.0 H111 D:VPN801 3.8 38.0 1.0 H072 D:VPN801 3.9 38.0 1.0 HD12 C:LEU669 4.0 26.9 1.0 H142 D:VPN801 4.0 38.0 1.0 HG C:LEU669 4.1 26.9 1.0 C14 D:VPN801 4.2 38.0 1.0 H132 D:VPN801 4.2 38.0 1.0 CG C:LEU669 4.3 26.9 1.0 C04 D:VPN801 4.3 38.0 1.0 H141 D:VPN801 4.3 38.0 1.0 HD11 C:LEU669 4.4 26.9 1.0 CD2 C:LEU669 4.4 26.9 1.0 HZ C:PHE591 4.5 24.7 1.0 H021 D:VPN801 4.6 38.0 1.0 H042 D:VPN801 4.6 38.0 1.0 CB C:ALA665 4.6 24.9 1.0 C06 D:VPN801 4.7 38.0 1.0 H052 D:VPN801 4.7 38.0 1.0 HB1 C:ALA665 4.7 24.9 1.0 C05 D:VPN801 4.8 38.0 1.0 HD22 C:LEU669 4.9 26.9 1.0

Bromine binding site 4 out of 8 in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Br801 b:38.0 occ:1.00 BR12 D:VPN801 0.0 38.0 1.0 C11 D:VPN801 1.9 38.0 1.0 H111 D:VPN801 2.5 38.0 1.0 C09 D:VPN801 2.8 38.0 1.0 C13 D:VPN801 2.8 38.0 1.0 H132 D:VPN801 3.0 38.0 1.0 H082 D:VPN801 3.0 38.0 1.0 H131 D:VPN801 3.1 38.0 1.0 BR10 D:VPN801 3.2 38.0 1.0 C08 D:VPN801 3.3 38.0 1.0 H081 D:VPN801 3.5 38.0 1.0 HD22 D:LEU515 3.7 35.6 1.0 H091 D:VPN801 3.8 38.0 1.0 HD23 D:LEU515 3.9 35.6 1.0 CD2 D:LEU515 4.1 35.6 1.0 C14 D:VPN801 4.2 38.0 1.0 H563 D:VPN801 4.4 38.0 1.0 HD21 D:LEU515 4.4 35.6 1.0 H141 D:VPN801 4.4 38.0 1.0 HE3 D:MET547 4.5 32.3 1.0 H021 D:VPN801 4.8 38.0 1.0 C07 D:VPN801 4.8 38.0 1.0 H142 D:VPN801 4.8 38.0 1.0 H041 D:VPN801 4.8 38.0 1.0 HG2 D:MET547 4.9 32.3 1.0 H052 D:VPN801 4.9 38.0 1.0 H152 D:VPN801 5.0 38.0 1.0 H071 D:VPN801 5.0 38.0 1.0 C56 D:VPN801 5.0 38.0 1.0

Bromine binding site 5 out of 8 in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Br801 b:38.0 occ:1.00 BR10 B:VPN801 0.0 38.0 1.0 C09 B:VPN801 1.9 38.0 1.0 H091 B:VPN801 2.5 38.0 1.0 H082 B:VPN801 2.8 38.0 1.0 C08 B:VPN801 2.8 38.0 1.0 HD13 A:LEU669 2.8 26.9 1.0 C11 B:VPN801 2.8 38.0 1.0 H131 B:VPN801 2.9 38.0 1.0 H071 B:VPN801 2.9 38.0 1.0 BR12 B:VPN801 3.2 38.0 1.0 H041 B:VPN801 3.3 38.0 1.0 C13 B:VPN801 3.4 38.0 1.0 C07 B:VPN801 3.4 38.0 1.0 HD21 A:LEU669 3.6 26.9 1.0 CD1 A:LEU669 3.7 26.9 1.0 HB2 A:ALA665 3.7 24.9 1.0 H081 B:VPN801 3.8 38.0 1.0 H111 B:VPN801 3.8 38.0 1.0 H072 B:VPN801 3.9 38.0 1.0 HD12 A:LEU669 4.0 26.9 1.0 H142 B:VPN801 4.0 38.0 1.0 HG A:LEU669 4.1 26.9 1.0 C14 B:VPN801 4.2 38.0 1.0 H132 B:VPN801 4.2 38.0 1.0 CG A:LEU669 4.3 26.9 1.0 C04 B:VPN801 4.3 38.0 1.0 H141 B:VPN801 4.3 38.0 1.0 HD11 A:LEU669 4.4 26.9 1.0 CD2 A:LEU669 4.4 26.9 1.0 HZ A:PHE591 4.5 24.7 1.0 H021 B:VPN801 4.6 38.0 1.0 H042 B:VPN801 4.6 38.0 1.0 CB A:ALA665 4.6 24.9 1.0 C06 B:VPN801 4.7 38.0 1.0 H052 B:VPN801 4.7 38.0 1.0 HB1 A:ALA665 4.7 24.9 1.0 C05 B:VPN801 4.8 38.0 1.0 HD22 A:LEU669 4.9 26.9 1.0

Bromine binding site 6 out of 8 in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Br801 b:38.0 occ:1.00 BR12 B:VPN801 0.0 38.0 1.0 C11 B:VPN801 1.9 38.0 1.0 H111 B:VPN801 2.5 38.0 1.0 C09 B:VPN801 2.8 38.0 1.0 C13 B:VPN801 2.8 38.0 1.0 H132 B:VPN801 3.0 38.0 1.0 H082 B:VPN801 3.0 38.0 1.0 H131 B:VPN801 3.1 38.0 1.0 BR10 B:VPN801 3.2 38.0 1.0 C08 B:VPN801 3.3 38.0 1.0 H081 B:VPN801 3.5 38.0 1.0 HD22 B:LEU515 3.7 35.6 1.0 H091 B:VPN801 3.8 38.0 1.0 HD23 B:LEU515 3.9 35.6 1.0 CD2 B:LEU515 4.1 35.6 1.0 C14 B:VPN801 4.2 38.0 1.0 H563 B:VPN801 4.4 38.0 1.0 HD21 B:LEU515 4.4 35.6 1.0 H141 B:VPN801 4.4 38.0 1.0 HE3 B:MET547 4.5 32.3 1.0 H021 B:VPN801 4.8 38.0 1.0 C07 B:VPN801 4.8 38.0 1.0 H142 B:VPN801 4.8 38.0 1.0 H041 B:VPN801 4.8 38.0 1.0 HG2 B:MET547 4.9 32.3 1.0 H052 B:VPN801 4.9 38.0 1.0 H152 B:VPN801 5.0 38.0 1.0 H071 B:VPN801 5.0 38.0 1.0 C56 B:VPN801 5.0 38.0 1.0

Bromine binding site 7 out of 8 in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Br801 b:38.0 occ:1.00 BR10 C:VPN801 0.0 38.0 1.0 C09 C:VPN801 1.9 38.0 1.0 H091 C:VPN801 2.5 38.0 1.0 H082 C:VPN801 2.8 38.0 1.0 C08 C:VPN801 2.8 38.0 1.0 HD13 B:LEU669 2.8 26.9 1.0 C11 C:VPN801 2.8 38.0 1.0 H131 C:VPN801 2.9 38.0 1.0 H071 C:VPN801 2.9 38.0 1.0 BR12 C:VPN801 3.2 38.0 1.0 H041 C:VPN801 3.3 38.0 1.0 C13 C:VPN801 3.4 38.0 1.0 C07 C:VPN801 3.4 38.0 1.0 HD21 B:LEU669 3.6 26.9 1.0 CD1 B:LEU669 3.7 26.9 1.0 HB2 B:ALA665 3.7 24.9 1.0 H081 C:VPN801 3.8 38.0 1.0 H111 C:VPN801 3.8 38.0 1.0 H072 C:VPN801 3.9 38.0 1.0 HD12 B:LEU669 4.0 26.9 1.0 H142 C:VPN801 4.0 38.0 1.0 HG B:LEU669 4.1 26.9 1.0 C14 C:VPN801 4.2 38.0 1.0 H132 C:VPN801 4.2 38.0 1.0 CG B:LEU669 4.3 26.9 1.0 C04 C:VPN801 4.3 38.0 1.0 H141 C:VPN801 4.3 38.0 1.0 HD11 B:LEU669 4.4 26.9 1.0 CD2 B:LEU669 4.4 26.9 1.0 HZ B:PHE591 4.5 24.7 1.0 H021 C:VPN801 4.6 38.0 1.0 H042 C:VPN801 4.6 38.0 1.0 CB B:ALA665 4.6 24.9 1.0 C06 C:VPN801 4.7 38.0 1.0 H052 C:VPN801 4.7 38.0 1.0 HB1 B:ALA665 4.7 24.9 1.0 C05 C:VPN801 4.8 38.0 1.0 HD22 B:LEU669 4.9 26.9 1.0

Bromine binding site 8 out of 8 in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Br801 b:38.0 occ:1.00 BR12 C:VPN801 0.0 38.0 1.0 C11 C:VPN801 1.9 38.0 1.0 H111 C:VPN801 2.5 38.0 1.0 C09 C:VPN801 2.8 38.0 1.0 C13 C:VPN801 2.8 38.0 1.0 H132 C:VPN801 3.0 38.0 1.0 H082 C:VPN801 3.0 38.0 1.0 H131 C:VPN801 3.1 38.0 1.0 BR10 C:VPN801 3.2 38.0 1.0 C08 C:VPN801 3.3 38.0 1.0 H081 C:VPN801 3.5 38.0 1.0 HD22 C:LEU515 3.7 35.6 1.0 H091 C:VPN801 3.8 38.0 1.0 HD23 C:LEU515 3.9 35.6 1.0 CD2 C:LEU515 4.1 35.6 1.0 C14 C:VPN801 4.2 38.0 1.0 H563 C:VPN801 4.4 38.0 1.0 HD21 C:LEU515 4.4 35.6 1.0 H141 C:VPN801 4.4 38.0 1.0 HE3 C:MET547 4.5 32.3 1.0 H021 C:VPN801 4.8 38.0 1.0 C07 C:VPN801 4.8 38.0 1.0 H142 C:VPN801 4.8 38.0 1.0 H041 C:VPN801 4.8 38.0 1.0 HG2 C:MET547 4.9 32.3 1.0 H052 C:VPN801 4.9 38.0 1.0 H152 C:VPN801 5.0 38.0 1.0 H071 C:VPN801 5.0 38.0 1.0 C56 C:VPN801 5.0 38.0 1.0

W.R.Arnold, M.Mancino, F.R.Moss Iii, A.Frost, D.Julius, Y.Cheng. Structural Basis of TRPV1 Modulation By Endogenous Bioactive Lipids Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01299-2