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Sodium in PDB 8t3l: TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers

Sodium Binding Sites:

The binding sites of Sodium atom in the TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers (pdb code 8t3l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers, PDB code: 8t3l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8t3l

Go back to Sodium Binding Sites List in 8t3l
Sodium binding site 1 out of 2 in the TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:25.9
occ:1.00
O A:GLY643 2.3 38.1 1.0
O C:GLY643 2.3 40.4 1.0
O D:GLY643 2.4 36.8 1.0
O B:GLY643 2.5 38.4 1.0
C A:GLY643 3.4 38.1 1.0
C C:GLY643 3.5 40.4 1.0
HG2 D:MET644 3.6 37.8 1.0
HG2 C:MET644 3.7 42.4 1.0
NA B:NA802 3.7 36.6 1.0
C D:GLY643 3.7 36.8 1.0
C B:GLY643 3.7 38.4 1.0
HA3 A:GLY643 3.7 38.1 1.0
HA D:MET644 3.8 37.8 1.0
HA3 C:GLY643 3.9 40.4 1.0
HA3 B:GLY643 3.9 38.4 1.0
HA C:MET644 4.0 42.4 1.0
HA A:MET644 4.0 38.1 1.0
SD D:MET644 4.1 37.8 1.0
CA A:GLY643 4.1 38.1 1.0
SD A:MET644 4.2 38.1 1.0
HA3 D:GLY643 4.2 36.8 1.0
HG2 B:MET644 4.2 41.7 1.0
HA B:MET644 4.2 41.7 1.0
CG D:MET644 4.3 37.8 1.0
HG2 A:MET644 4.3 38.1 1.0
CA C:GLY643 4.3 40.4 1.0
SD C:MET644 4.4 42.4 1.0
CA B:GLY643 4.4 38.4 1.0
HA2 A:GLY643 4.4 38.1 1.0
CG C:MET644 4.4 42.4 1.0
N C:MET644 4.5 42.4 1.0
N A:MET644 4.5 38.1 1.0
CA D:GLY643 4.5 36.8 1.0
N D:MET644 4.6 37.8 1.0
CA D:MET644 4.6 37.8 1.0
HA2 B:GLY643 4.6 38.4 1.0
CA C:MET644 4.7 42.4 1.0
CA A:MET644 4.7 38.1 1.0
N B:MET644 4.7 41.7 1.0
HA2 C:GLY643 4.8 40.4 1.0
CG A:MET644 4.8 38.1 1.0
O C:ILE642 4.8 41.5 1.0
HA2 D:GLY643 4.9 36.8 1.0
CA B:MET644 5.0 41.7 1.0

Sodium binding site 2 out of 2 in 8t3l

Go back to Sodium Binding Sites List in 8t3l
Sodium binding site 2 out of 2 in the TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:36.6
occ:1.00
HA3 C:GLY643 2.4 40.4 1.0
HA3 B:GLY643 2.6 38.4 1.0
HA2 B:GLY643 3.1 38.4 1.0
CA B:GLY643 3.3 38.4 1.0
CA C:GLY643 3.3 40.4 1.0
HA3 A:GLY643 3.5 38.1 1.0
O C:ILE642 3.6 41.5 1.0
NA A:NA802 3.7 25.9 1.0
O C:GLY643 3.7 40.4 1.0
HA3 D:GLY643 3.7 36.8 1.0
O B:GLY643 3.8 38.4 1.0
HA2 C:GLY643 3.9 40.4 1.0
C C:GLY643 3.9 40.4 1.0
C B:GLY643 4.0 38.4 1.0
N C:GLY643 4.0 40.4 1.0
C C:ILE642 4.1 41.5 1.0
HA2 A:GLY643 4.2 38.1 1.0
O D:GLY643 4.3 36.8 1.0
CA A:GLY643 4.3 38.1 1.0
HH A:TYR671 4.4 41.1 1.0
N B:GLY643 4.5 38.4 1.0
O A:GLY643 4.5 38.1 1.0
CA D:GLY643 4.6 36.8 1.0
H C:GLY643 4.7 40.4 1.0
H B:GLY643 4.8 38.4 1.0
OH A:TYR671 4.9 41.1 1.0
C A:GLY643 4.9 38.1 1.0
C D:GLY643 4.9 36.8 1.0
HA2 D:GLY643 4.9 36.8 1.0

Reference:

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
Page generated: Wed Oct 9 13:38:28 2024

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