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

The structure of Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp with Ouabain 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 with Ouabain (pdb code 7wyz). 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 with Ouabain, PDB code: 7wyz:
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 with Ouabain


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 with Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:46.8 occ:1.00 OD2 A:ASP747 2.4 45.7 1.0 O A:LYS726 3.3 46.7 1.0 O A:ALA728 3.5 43.0 1.0 CG A:ASP747 3.6 45.7 1.0 O A:LEU725 3.7 45.0 1.0 C A:LYS726 4.1 46.7 1.0 CA A:LYS726 4.3 46.7 1.0 OD1 A:ASP747 4.4 45.7 1.0 O A:ASP729 4.5 42.9 1.0 CB A:ASP747 4.6 45.7 1.0 O A:VAL279 4.6 69.8 1.0 C A:LEU725 4.7 45.0 1.0 N A:GLY731 4.7 41.7 1.0 C A:ALA728 4.8 43.0 1.0 C A:ASP729 4.8 42.9 1.0 CA A:ILE730 4.9 40.3 1.0 CD A:LYS726 4.9 46.7 1.0 O A:ALA745 4.9 49.1 1.0 N A:ILE730 5.0 40.3 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 with Ouabain


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 with Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:32.5 occ:1.00 OE1 A:GLU786 2.9 31.7 1.0 O A:ALA330 3.0 34.4 1.0 OD2 A:ASP811 3.3 38.6 1.0 OD1 A:ASN783 3.5 29.9 1.0 CG A:ASP811 4.0 38.6 1.0 OD1 A:ASP811 4.0 38.6 1.0 OE2 A:GLU334 4.1 43.2 1.0 C A:ALA330 4.1 34.4 1.0 CD A:GLU786 4.2 31.7 1.0 O A:VAL332 4.3 39.5 1.0 CG2 A:ILE807 4.4 33.7 1.0 CG A:ASN783 4.4 29.9 1.0 CB A:GLU786 4.5 31.7 1.0 O23 A:OBN1104 4.7 35.7 1.0 CA A:ALA330 4.7 34.4 1.0 N A:VAL332 4.8 39.5 1.0 CG A:GLU786 5.0 31.7 1.0 OE2 A:GLU786 5.0 31.7 1.0 C A:VAL332 5.0 39.5 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 with Ouabain


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 with Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1102 b:46.7 occ:1.00 OD2 C:ASP747 2.4 46.5 1.0 O C:LYS726 3.3 46.8 1.0 O C:ALA728 3.5 43.5 1.0 CG C:ASP747 3.6 46.5 1.0 O C:LEU725 3.7 45.0 1.0 C C:LYS726 4.1 46.8 1.0 CA C:LYS726 4.3 46.8 1.0 OD1 C:ASP747 4.4 46.5 1.0 O C:ASP729 4.5 43.0 1.0 CB C:ASP747 4.6 46.5 1.0 O C:VAL279 4.6 70.2 1.0 C C:LEU725 4.7 45.0 1.0 N C:GLY731 4.7 42.2 1.0 C C:ALA728 4.8 43.5 1.0 C C:ASP729 4.8 43.0 1.0 CA C:ILE730 4.9 40.7 1.0 CD C:LYS726 4.9 46.8 1.0 O C:ALA745 4.9 49.8 1.0 N C:ILE730 5.0 40.7 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 with Ouabain


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 with Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1103 b:30.9 occ:1.00 OE1 C:GLU786 2.9 30.7 1.0 O C:ALA330 3.0 34.8 1.0 OD2 C:ASP811 3.3 37.9 1.0 OD1 C:ASN783 3.5 29.2 1.0 CG C:ASP811 4.0 37.9 1.0 OD1 C:ASP811 4.0 37.9 1.0 OE2 C:GLU334 4.1 42.2 1.0 C C:ALA330 4.1 34.8 1.0 CD C:GLU786 4.2 30.7 1.0 O C:VAL332 4.3 39.3 1.0 CG2 C:ILE807 4.4 33.0 1.0 CG C:ASN783 4.4 29.2 1.0 CB C:GLU786 4.5 30.7 1.0 O23 C:OBN1104 4.7 35.0 1.0 CA C:ALA330 4.7 34.8 1.0 N C:VAL332 4.8 39.3 1.0 CG C:GLU786 5.0 30.7 1.0 OE2 C:GLU786 5.0 30.7 1.0 C C:VAL332 5.0 39.3 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