Sodium in PDB 7wyu: Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp

The structure of Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp (pdb code 7wyu). 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 Na+,K+-Atpase in the E2P State Formed By Atp, PDB code: 7wyu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp


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 Na+,K+-Atpase in the E2P State Formed By Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:59.5 occ:1.00 O A:LYS726 3.2 49.9 1.0 OD2 A:ASP747 3.2 42.7 1.0 O A:VAL279 3.3 68.4 1.0 O A:ALA728 3.6 42.4 1.0 C A:VAL279 4.3 68.4 1.0 C A:LYS726 4.3 49.9 1.0 CG A:ASP747 4.4 42.7 1.0 CG1 A:VAL279 4.4 68.4 1.0 O A:ASP729 4.5 40.9 1.0 CA A:VAL279 4.7 68.4 1.0 O A:LEU725 4.7 44.9 1.0 CA A:LYS726 4.8 49.9 1.0 C A:ALA728 4.8 42.4 1.0 OD1 A:ASP747 4.9 42.7 1.0 C A:ASP729 4.9 40.9 1.0

Sodium binding site 2 out of 4 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp


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 Na+,K+-Atpase in the E2P State Formed By Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:36.9 occ:1.00 OD2 A:ASP811 3.1 39.2 1.0 OE1 A:GLU786 3.2 30.3 1.0 OD1 A:ASN783 3.3 28.4 1.0 OD1 A:ASP811 3.3 39.2 1.0 O A:VAL332 3.3 39.2 1.0 O A:ALA330 3.3 35.5 1.0 CG A:ASP811 3.4 39.2 1.0 CG A:ASN783 4.2 28.4 1.0 C A:VAL332 4.3 39.2 1.0 CD A:GLU786 4.5 30.3 1.0 C A:ALA330 4.5 35.5 1.0 OE2 A:GLU334 4.6 41.7 1.0 ND2 A:ASN783 4.7 28.4 1.0 CB A:ASP811 4.7 39.2 1.0 CG2 A:ILE807 4.8 34.8 1.0 CA A:PRO333 4.8 39.6 1.0 N A:VAL332 4.8 39.2 1.0 CD A:GLU334 4.9 41.7 1.0 OE1 A:GLU334 4.9 41.7 1.0

Sodium binding site 3 out of 4 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp


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 Na+,K+-Atpase in the E2P State Formed By Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1102 b:57.1 occ:1.00 O C:LYS726 3.2 48.9 1.0 OD2 C:ASP747 3.2 43.1 1.0 O C:VAL279 3.3 68.3 1.0 O C:ALA728 3.6 42.2 1.0 C C:VAL279 4.3 68.3 1.0 C C:LYS726 4.3 48.9 1.0 CG C:ASP747 4.4 43.1 1.0 CG1 C:VAL279 4.4 68.3 1.0 O C:ASP729 4.5 40.2 1.0 CA C:VAL279 4.7 68.3 1.0 O C:LEU725 4.7 44.5 1.0 CA C:LYS726 4.8 48.9 1.0 C C:ALA728 4.8 42.2 1.0 OD1 C:ASP747 4.9 43.1 1.0 C C:ASP729 4.9 40.2 1.0

Sodium binding site 4 out of 4 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp


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 Na+,K+-Atpase in the E2P State Formed By Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1103 b:35.3 occ:1.00 OD2 C:ASP811 3.1 39.5 1.0 OE1 C:GLU786 3.2 30.3 1.0 OD1 C:ASN783 3.3 28.0 1.0 OD1 C:ASP811 3.3 39.5 1.0 O C:VAL332 3.3 39.5 1.0 O C:ALA330 3.3 36.2 1.0 CG C:ASP811 3.4 39.5 1.0 CG C:ASN783 4.2 28.0 1.0 C C:VAL332 4.3 39.5 1.0 CD C:GLU786 4.5 30.3 1.0 C C:ALA330 4.5 36.2 1.0 OE2 C:GLU334 4.6 41.8 1.0 ND2 C:ASN783 4.7 28.0 1.0 CB C:ASP811 4.7 39.5 1.0 CG2 C:ILE807 4.8 34.6 1.0 CA C:PRO333 4.8 39.3 1.0 N C:VAL332 4.8 39.5 1.0 CD C:GLU334 4.9 41.8 1.0 OE1 C:GLU334 4.9 41.8 1.0

R.Kanai, F.Cornelius, B.Vilsen, C.Toyoshima. Cryoelectron Microscopy of Na + ,K + -Atpase in the Two E2P States with and Without Cardiotonic Steroids. Proc.Natl.Acad.Sci.Usa V. 119 26119 2022.
ISSN: ESSN 1091-6490
PubMed: 35380894
DOI: 10.1073/PNAS.2123226119