Sodium in PDB 7e1z: Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State

All present enzymatic activity of Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State:
7.2.2.13;

The structure of Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State (pdb code 7e1z). 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 A Na+-Bound Na+,K+-Atpase in the E1 State, PDB code: 7e1z:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State


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 A Na+-Bound Na+,K+-Atpase in the E1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:62.1 occ:1.00 OD2 A:ASP815 2.3 61.0 1.0 O A:THR779 2.9 53.0 1.0 OG A:SER782 3.1 52.6 1.0 CG A:ASP815 3.4 61.0 1.0 OD1 A:ASN783 3.5 52.5 1.0 OD1 A:ASP815 3.8 61.0 1.0 O A:ALA330 3.9 53.2 1.0 O A:SER782 4.0 52.6 1.0 C A:THR779 4.1 53.0 1.0 CG2 A:THR779 4.2 53.0 1.0 CB A:SER782 4.4 52.6 1.0 OD1 A:ASP811 4.5 54.4 1.0 C A:SER782 4.5 52.6 1.0 CG A:ASN783 4.6 52.5 1.0 CB A:ASP815 4.6 61.0 1.0 NA A:NA1103 4.8 54.6 1.0 CA A:SER782 4.8 52.6 1.0 CA A:THR779 4.9 53.0 1.0 N A:SER782 4.9 52.6 1.0 O A:HOH1204 5.0 68.5 1.0

Sodium binding site 2 out of 4 in the Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State


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 A Na+-Bound Na+,K+-Atpase in the E1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:61.3 occ:1.00 O A:VAL332 2.6 55.0 1.0 O A:HOH1203 2.6 66.0 1.0 O A:VAL329 2.8 52.9 1.0 C A:VAL332 3.9 55.0 1.0 OD1 A:ASP811 3.9 54.4 1.0 N A:GLU334 3.9 67.1 1.0 OD2 A:ASP811 3.9 54.4 1.0 C A:VAL329 4.0 52.9 1.0 O A:HOH1204 4.3 68.5 1.0 CG A:ASP811 4.3 54.4 1.0 CB A:GLU334 4.4 67.1 1.0 CA A:PRO333 4.5 59.4 1.0 CA A:ALA330 4.5 53.2 1.0 N A:PRO333 4.6 59.4 1.0 O A:ALA330 4.7 53.2 1.0 N A:ALA330 4.7 53.2 1.0 C A:ALA330 4.7 53.2 1.0 N A:VAL332 4.7 55.0 1.0 C A:PRO333 4.8 59.4 1.0 CA A:GLU334 4.8 67.1 1.0 CA A:VAL332 4.8 55.0 1.0 CG1 A:VAL329 4.9 52.9 1.0 CA A:VAL329 5.0 52.9 1.0

Sodium binding site 3 out of 4 in the Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State


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 A Na+-Bound Na+,K+-Atpase in the E1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:54.6 occ:1.00 OG A:SER782 2.2 52.6 1.0 OE1 A:GLN930 2.3 45.9 1.0 CB A:SER782 2.4 52.6 1.0 OD1 A:ASP815 2.9 61.0 1.0 CD A:GLN930 3.4 45.9 1.0 N A:SER782 3.4 52.6 1.0 CA A:SER782 3.5 52.6 1.0 OG1 A:THR814 3.8 55.5 1.0 OG1 A:THR781 3.9 51.1 1.0 O A:TYR778 4.0 50.8 1.0 CG A:ASP815 4.0 61.0 1.0 NE2 A:GLN930 4.1 45.9 1.0 O A:THR814 4.2 55.5 1.0 O A:THR779 4.3 53.0 1.0 C A:THR781 4.5 51.1 1.0 OD2 A:ASP815 4.5 61.0 1.0 CG A:GLN930 4.5 45.9 1.0 CZ A:TYR778 4.6 50.8 1.0 OH A:TYR778 4.7 50.8 1.0 C A:SER782 4.7 52.6 1.0 OD2 A:ASP933 4.7 49.5 1.0 NA A:NA1101 4.8 62.1 1.0 CB A:THR814 4.8 55.5 1.0 C A:THR814 4.8 55.5 1.0 CE1 A:TYR778 4.8 50.8 1.0 C A:THR779 4.9 53.0 1.0 N A:THR781 4.9 51.1 1.0 O A:SER782 4.9 52.6 1.0 CE2 A:TYR778 5.0 50.8 1.0

Sodium binding site 4 out of 4 in the Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State


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 A Na+-Bound Na+,K+-Atpase in the E1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1104 b:85.1 occ:1.00 OD1 A:ASP747 2.6 80.7 1.0 O A:ALA745 2.6 87.9 1.0 CG A:ASP747 3.6 80.7 1.0 C A:ALA745 3.7 87.9 1.0 CB A:LYS726 3.8 89.7 1.0 CA A:LYS726 3.9 89.7 1.0 CA A:ALA746 4.1 83.0 1.0 C A:ALA746 4.1 83.0 1.0 OD2 A:ASP747 4.2 80.7 1.0 N A:ASP747 4.2 80.7 1.0 O A:LEU725 4.3 86.1 1.0 N A:ALA746 4.4 83.0 1.0 N A:LYS726 4.4 89.7 1.0 C A:LEU725 4.6 86.1 1.0 O A:ALA746 4.6 83.0 1.0 CB A:ASP747 4.8 80.7 1.0 CA A:ALA745 4.8 87.9 1.0 CA A:ASP747 4.9 80.7 1.0

Y.Guo, Y.Zhang, R.Yan, B.Huang, F.Ye, L.Wu, X.Chi, Y.Shi, Q.Zhou. Cryo-Em Structures of Recombinant Human Sodium-Potassium Pump Determined in Three Different States. Nat Commun V. 13 3957 2022.
ISSN: ESSN 2041-1723
PubMed: 35803952
DOI: 10.1038/S41467-022-31602-Y