Sodium in PDB 8zpb: Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom

The structure of Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom (pdb code 8zpb). 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 Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom, PDB code: 8zpb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom


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 Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:34.3 occ:1.00 O A:ALA73 2.0 23.2 1.0 OG A:SER318 2.1 30.6 1.0 OD1 A:ASP75 2.1 27.8 1.0 OD1 A:ASN78 2.2 15.6 1.0 OD1 A:ASN350 2.4 18.6 1.0 O A:SER318 2.4 28.2 1.0 HG A:SER318 2.7 25.3 1.0 HA A:SER318 2.9 24.2 1.0 C A:SER318 3.0 22.5 1.0 H A:ASP75 3.0 24.3 1.0 CB A:SER318 3.1 21.2 1.0 CA A:SER318 3.1 22.9 1.0 CG A:ASN78 3.2 17.4 1.0 HD22 A:ASN78 3.2 24.9 1.0 HA A:VAL74 3.2 26.3 1.0 C A:ALA73 3.3 28.1 1.0 CG A:ASP75 3.3 26.9 1.0 HB3 A:ALA77 3.5 23.9 1.0 CG A:ASN350 3.5 31.4 1.0 ND2 A:ASN78 3.6 25.8 1.0 N A:ASP75 3.6 17.8 1.0 HB2 A:SER318 3.7 24.3 1.0 HB3 A:SER318 3.7 23.5 1.0 HD22 A:ASN350 3.7 26.1 1.0 H A:ASN78 3.9 25.5 1.0 CA A:VAL74 3.9 22.8 1.0 HB3 A:ASP75 4.0 24.2 1.0 N A:VAL74 4.0 24.6 1.0 N A:LEU319 4.0 22.6 1.0 ND2 A:ASN350 4.1 31.4 1.0 CB A:ASP75 4.1 25.5 1.0 HA A:ALA73 4.2 24.4 1.0 OD2 A:ASP75 4.2 23.7 1.0 O A:HOH830 4.2 26.3 1.0 C A:VAL74 4.2 21.3 1.0 HA A:LEU319 4.3 25.3 1.0 CA A:ALA73 4.4 22.2 1.0 N A:ASN78 4.4 28.0 1.0 CA A:ASP75 4.4 16.5 1.0 HD21 A:ASN78 4.4 25.8 1.0 CB A:ALA77 4.4 26.2 1.0 CB A:ASN78 4.5 27.2 1.0 N A:SER318 4.6 26.0 1.0 H A:LEU319 4.6 24.6 1.0 CA A:LEU319 4.7 25.6 1.0 CL A:CL704 4.7 29.4 1.0 HB2 A:ASN350 4.8 25.9 1.0 HB1 A:ALA73 4.8 25.1 1.0 O A:PHE72 4.8 25.5 1.0 CB A:ASN350 4.8 28.6 1.0 HB1 A:ALA77 4.8 24.5 1.0 HG22 A:VAL74 4.8 25.5 1.0 HB2 A:ASN78 4.8 25.1 1.0 H A:ALA77 4.8 25.0 1.0 HA A:ASN78 4.9 24.5 1.0 O A:ASP75 4.9 28.5 1.0 HB2 A:ALA77 4.9 24.8 1.0 H A:VAL74 4.9 25.1 1.0 HNAA A:LNR701 4.9 22.1 1.0 CA A:ASN78 4.9 23.2 1.0 HD21 A:ASN350 4.9 25.8 1.0 C A:ASP75 4.9 22.0 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom


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 Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:22.6 occ:1.00 HG A:SER419 2.0 25.8 1.0 O A:GLY71 2.1 28.2 1.0 OD1 A:ASP418 2.1 29.6 1.0 O A:LEU415 2.2 23.4 1.0 O A:VAL74 2.3 29.3 1.0 HA A:ASP75 2.4 23.6 1.0 OG A:SER419 2.4 28.8 1.0 H A:SER419 3.0 24.6 1.0 CG A:ASP418 3.2 37.3 1.0 HA A:LEU415 3.2 25.6 1.0 C A:LEU415 3.2 25.9 1.0 CA A:ASP75 3.2 16.5 1.0 C A:GLY71 3.3 23.0 1.0 C A:VAL74 3.3 21.3 1.0 O A:HOH835 3.4 27.2 1.0 N A:SER419 3.5 22.3 1.0 CB A:SER419 3.5 19.7 1.0 HB2 A:SER419 3.6 23.9 1.0 HB3 A:ASP75 3.6 24.2 1.0 O A:HOH801 3.6 32.8 1.0 N A:ASP75 3.7 17.8 1.0 CA A:LEU415 3.7 25.6 1.0 HB2 A:ASP75 3.8 24.4 1.0 CB A:ASP75 3.8 25.5 1.0 OD2 A:ASP418 3.8 38.3 1.0 HA2 A:GLY71 3.8 26.3 1.0 HA A:PHE72 3.8 23.9 1.0 CA A:SER419 4.0 19.7 1.0 HH A:TYR152 4.1 22.8 1.0 CA A:GLY71 4.1 24.2 1.0 HD23 A:LEU415 4.1 24.6 1.0 HA A:SER419 4.2 24.6 1.0 CB A:ASP418 4.2 26.7 1.0 O A:ALA414 4.2 21.1 1.0 HB2 A:ASP418 4.2 28.7 1.0 H A:ASP418 4.2 28.0 1.0 HB3 A:LEU415 4.3 25.8 1.0 HB3 A:SER419 4.3 23.0 1.0 C A:ASP418 4.3 22.9 1.0 N A:PHE72 4.3 18.6 1.0 C A:ASP75 4.4 22.0 1.0 O A:PHE72 4.4 25.5 1.0 N A:GLY416 4.4 28.6 1.0 CA A:PHE72 4.4 18.9 1.0 HA3 A:GLY71 4.4 25.2 1.0 HA2 A:GLY416 4.4 24.2 1.0 H A:LEU76 4.5 23.4 1.0 C A:PHE72 4.5 23.9 1.0 HD22 A:LEU415 4.5 25.6 1.0 CB A:LEU415 4.6 24.3 1.0 H A:ASP75 4.6 24.3 1.0 CA A:ASP418 4.6 26.1 1.0 N A:ASP418 4.6 27.8 1.0 CA A:VAL74 4.7 22.8 1.0 HG12 A:VAL74 4.7 26.3 1.0 OH A:TYR152 4.7 20.6 1.0 CA A:GLY416 4.8 24.8 1.0 N A:LEU76 4.8 22.5 1.0 CD2 A:LEU415 4.8 23.3 1.0 C A:GLY416 4.9 24.6 1.0 N A:VAL74 4.9 24.6 1.0 N A:LEU415 4.9 25.9 1.0 HB A:VAL74 4.9 26.0 1.0 H A:VAL74 4.9 25.1 1.0

A.Song, X.Wu. Mechanistic Insights of Substrate Transport and Inhibitor Binding Revealed By High-Resolution Structures of Human Norepinephrine Transporter Cell Res. 2024.
ISSN: ISSN 1001-0602
DOI: 10.1038/S41422-024-01024-0