Sodium in PDB 8ghf: Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles

The structure of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Calcium	(Ca)	8 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles (pdb code 8ghf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles, PDB code: 8ghf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


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 HSLO1 in Plasma Membrane Vesicles within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1529 b:10.8 occ:1.00 O A:ASN509 2.4 40.2 1.0 O A:VAL532 2.5 46.2 1.0 O A:SER512 2.6 35.8 1.0 O A:ASN534 2.9 43.5 1.0 OE2 A:GLU535 3.5 40.6 1.0 CG A:GLU535 3.6 33.0 1.0 C A:ASN509 3.7 42.9 1.0 C A:VAL532 3.8 38.3 1.0 C A:SER512 3.8 35.2 1.0 C A:ASN534 3.9 38.5 1.0 CD A:GLU535 3.9 39.5 1.0 OG A:SER512 4.0 43.9 1.0 CG A:ARG514 4.0 25.2 1.0 N A:ARG514 4.2 26.9 1.0 CB A:ARG514 4.3 31.1 1.0 C A:SER533 4.3 31.7 1.0 N A:ASN534 4.3 35.4 1.0 CA A:LEU510 4.5 26.1 1.0 N A:LEU510 4.5 33.8 1.0 N A:SER512 4.6 33.1 1.0 O A:SER533 4.6 37.1 1.0 CA A:SER533 4.6 32.1 1.0 C A:LEU510 4.6 26.4 1.0 CA A:ASN509 4.6 37.0 1.0 N A:GLU535 4.6 37.4 1.0 CG1 A:VAL532 4.6 31.8 1.0 N A:SER533 4.6 36.7 1.0 CA A:SER512 4.6 28.7 1.0 CA A:GLU535 4.7 33.2 1.0 CA A:VAL532 4.7 27.6 1.0 CB A:GLU535 4.7 28.7 1.0 N A:MET513 4.7 38.1 1.0 CA A:ASN534 4.8 31.4 1.0 CA A:ARG514 4.8 30.6 1.0 CA A:MET513 4.8 31.2 1.0 CB A:SER512 4.9 35.5 1.0 O A:LEU510 4.9 33.5 1.0 N A:PHE511 4.9 25.3 1.0 C A:MET513 4.9 34.9 1.0 CB A:ASN509 4.9 32.4 1.0

Sodium binding site 2 out of 4 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


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 HSLO1 in Plasma Membrane Vesicles within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1528 b:11.3 occ:1.00 O B:ASN509 2.4 39.2 1.0 O B:VAL532 2.5 45.6 1.0 O B:SER512 2.6 36.2 1.0 O B:ASN534 2.9 43.8 1.0 OE2 B:GLU535 3.4 40.9 1.0 CG B:GLU535 3.6 33.5 1.0 C B:ASN509 3.7 42.1 1.0 C B:VAL532 3.8 38.3 1.0 C B:SER512 3.8 35.4 1.0 C B:ASN534 3.9 38.5 1.0 CD B:GLU535 3.9 39.9 1.0 OG B:SER512 4.0 44.0 1.0 CG B:ARG514 4.0 25.6 1.0 N B:ARG514 4.2 27.1 1.0 CB B:ARG514 4.3 31.2 1.0 C B:SER533 4.3 31.6 1.0 N B:ASN534 4.3 35.7 1.0 CA B:LEU510 4.5 26.1 1.0 N B:LEU510 4.5 33.7 1.0 O B:SER533 4.6 36.8 1.0 C B:LEU510 4.6 26.5 1.0 CA B:SER533 4.6 32.4 1.0 CA B:ASN509 4.6 36.0 1.0 N B:GLU535 4.6 37.9 1.0 CG1 B:VAL532 4.6 31.6 1.0 N B:SER512 4.6 35.4 1.0 N B:SER533 4.6 37.3 1.0 CA B:SER512 4.7 29.8 1.0 CA B:GLU535 4.7 33.9 1.0 CA B:VAL532 4.7 27.2 1.0 CB B:GLU535 4.7 29.1 1.0 N B:MET513 4.7 38.9 1.0 CA B:ASN534 4.8 31.5 1.0 CA B:ARG514 4.8 30.5 1.0 CA B:MET513 4.8 31.1 1.0 O B:LEU510 4.8 33.6 1.0 CB B:SER512 4.9 36.7 1.0 N B:PHE511 4.9 26.6 1.0 C B:MET513 4.9 34.5 1.0 CB B:ASN509 4.9 31.5 1.0

Sodium binding site 3 out of 4 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1532 b:11.7 occ:1.00 O C:ASN509 2.4 39.3 1.0 O C:VAL532 2.5 46.4 1.0 O C:SER512 2.6 36.1 1.0 O C:ASN534 2.9 43.8 1.0 OE2 C:GLU535 3.4 40.8 1.0 CG C:GLU535 3.6 33.3 1.0 C C:ASN509 3.7 42.3 1.0 C C:VAL532 3.8 38.4 1.0 C C:SER512 3.8 34.9 1.0 C C:ASN534 3.9 38.6 1.0 CD C:GLU535 3.9 39.6 1.0 OG C:SER512 4.0 43.7 1.0 CG C:ARG514 4.0 25.9 1.0 N C:ARG514 4.2 27.8 1.0 CB C:ARG514 4.3 30.7 1.0 C C:SER533 4.3 32.3 1.0 N C:ASN534 4.3 35.6 1.0 CA C:LEU510 4.5 26.1 1.0 N C:LEU510 4.5 34.2 1.0 O C:SER533 4.6 37.5 1.0 CA C:SER533 4.6 32.5 1.0 C C:LEU510 4.6 26.5 1.0 CA C:ASN509 4.6 36.3 1.0 CG1 C:VAL532 4.6 31.9 1.0 N C:GLU535 4.6 37.8 1.0 N C:SER533 4.6 37.4 1.0 N C:SER512 4.6 35.6 1.0 CA C:SER512 4.7 29.7 1.0 CA C:GLU535 4.7 33.5 1.0 CA C:VAL532 4.7 27.3 1.0 CB C:GLU535 4.7 29.1 1.0 N C:MET513 4.7 39.0 1.0 CA C:ASN534 4.8 31.5 1.0 CA C:ARG514 4.8 30.3 1.0 CA C:MET513 4.8 31.7 1.0 O C:LEU510 4.8 33.7 1.0 CB C:SER512 4.9 37.1 1.0 N C:PHE511 4.9 26.8 1.0 C C:MET513 4.9 35.1 1.0 CB C:ASN509 4.9 32.0 1.0

Sodium binding site 4 out of 4 in the Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Structure of HSLO1 in Plasma Membrane Vesicles within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1532 b:12.3 occ:1.00 O D:ASN509 2.4 39.3 1.0 O D:VAL532 2.5 45.9 1.0 O D:SER512 2.6 36.2 1.0 O D:ASN534 2.9 44.2 1.0 OE2 D:GLU535 3.4 40.9 1.0 CG D:GLU535 3.6 33.8 1.0 C D:ASN509 3.7 42.5 1.0 C D:VAL532 3.8 38.3 1.0 C D:SER512 3.8 35.2 1.0 C D:ASN534 3.9 39.1 1.0 CD D:GLU535 3.9 40.1 1.0 OG D:SER512 4.0 43.6 1.0 CG D:ARG514 4.0 26.1 1.0 N D:ARG514 4.2 27.9 1.0 CB D:ARG514 4.3 31.4 1.0 C D:SER533 4.3 32.6 1.0 N D:ASN534 4.3 36.2 1.0 CA D:LEU510 4.5 26.5 1.0 N D:LEU510 4.5 34.4 1.0 O D:SER533 4.6 37.6 1.0 C D:LEU510 4.6 26.8 1.0 CA D:SER533 4.6 33.1 1.0 CA D:ASN509 4.6 36.5 1.0 N D:GLU535 4.6 38.6 1.0 CG1 D:VAL532 4.6 31.6 1.0 N D:SER512 4.6 35.5 1.0 N D:SER533 4.6 37.7 1.0 CA D:SER512 4.7 29.9 1.0 CA D:GLU535 4.7 34.6 1.0 CA D:VAL532 4.7 27.5 1.0 CB D:GLU535 4.7 30.1 1.0 N D:MET513 4.7 39.5 1.0 CA D:ASN534 4.8 32.1 1.0 CA D:ARG514 4.8 31.0 1.0 CA D:MET513 4.8 32.1 1.0 O D:LEU510 4.8 34.2 1.0 CB D:SER512 4.9 36.8 1.0 N D:PHE511 4.9 26.7 1.0 C D:MET513 4.9 35.2 1.0 CB D:ASN509 4.9 32.0 1.0

X.Tao, C.Zhao, R.Mackinnon. Membrane Protein Isolation and Structure Determination in Cell-Derived Membrane Vesicles. Proc.Natl.Acad.Sci.Usa V. 120 25120 2023.
ISSN: ESSN 1091-6490
PubMed: 37098056
DOI: 10.1073/PNAS.2302325120