Sodium in PDB 7lpa: Cryo-Em Structure of Full-Length TRPV1 with Capsaicin at 4 Degrees Celsius

Sodium Binding Sites:

The binding sites of Sodium atom in the Cryo-Em Structure of Full-Length TRPV1 with Capsaicin at 4 Degrees Celsius (pdb code 7lpa). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryo-Em Structure of Full-Length TRPV1 with Capsaicin at 4 Degrees Celsius, PDB code: 7lpa:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7lpa

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Sodium binding site 1 out of 2 in the Cryo-Em Structure of Full-Length TRPV1 with Capsaicin at 4 Degrees Celsius


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of Full-Length TRPV1 with Capsaicin at 4 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:38.8
occ:1.00
O C:GLY643 2.6 16.2 1.0
O B:GLY643 2.6 16.2 1.0
O D:GLY643 2.6 16.2 1.0
O A:GLY643 2.6 16.2 1.0
C C:GLY643 3.8 16.2 1.0
C B:GLY643 3.8 16.2 1.0
C D:GLY643 3.8 16.2 1.0
C A:GLY643 3.8 16.2 1.0
SD A:MET644 4.0 17.0 1.0
SD C:MET644 4.0 17.0 1.0
SD D:MET644 4.0 17.0 1.0
SD B:MET644 4.0 17.0 1.0
CA B:GLY643 4.5 16.2 1.0
CA C:GLY643 4.5 16.2 1.0
CA D:GLY643 4.5 16.2 1.0
CA A:GLY643 4.6 16.2 1.0
CG A:MET644 4.7 17.0 1.0
CG C:MET644 4.7 17.0 1.0
CG D:MET644 4.8 17.0 1.0
CG B:MET644 4.8 17.0 1.0
NA A:NA910 4.8 38.8 1.0
N C:MET644 4.8 17.0 1.0
N B:MET644 4.8 17.0 1.0
N A:MET644 4.8 17.0 1.0
N D:MET644 4.8 17.0 1.0
CA C:MET644 4.9 17.0 1.0
CA A:MET644 4.9 17.0 1.0
CA B:MET644 4.9 17.0 1.0
CA D:MET644 4.9 17.0 1.0

Sodium binding site 2 out of 2 in 7lpa

Go back to Sodium Binding Sites List in 7lpa
Sodium binding site 2 out of 2 in the Cryo-Em Structure of Full-Length TRPV1 with Capsaicin at 4 Degrees Celsius


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of Full-Length TRPV1 with Capsaicin at 4 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:38.8
occ:1.00
CA A:GLY643 4.4 16.2 1.0
CA C:GLY643 4.4 16.2 1.0
CA B:GLY643 4.4 16.2 1.0
OH B:TYR671 4.4 27.0 1.0
CA D:GLY643 4.4 16.2 1.0
OH D:TYR671 4.4 27.0 1.0
OH C:TYR671 4.4 27.0 1.0
OH A:TYR671 4.4 27.0 1.0
NA A:NA909 4.8 38.8 1.0
O A:GLY643 5.0 16.2 1.0
O C:GLY643 5.0 16.2 1.0
O D:GLY643 5.0 16.2 1.0
O B:GLY643 5.0 16.2 1.0

Reference:

D.H.Kwon, F.Zhang, Y.Suo, J.Bouvette, M.J.Borgnia, S.Y.Lee. Heat-Dependent Opening of TRPV1 in the Presence of Capsaicin. Nat.Struct.Mol.Biol. V. 28 554 2021.
ISSN: ESSN 1545-9985
PubMed: 34239123
DOI: 10.1038/S41594-021-00616-3
Page generated: Sat Aug 21 17:23:27 2021

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