Sodium in PDB 7e21: Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State with Atp-Gamma-S

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

The structure of Cryo Em Structure of A Na+-Bound Na+,K+-Atpase in the E1 State with Atp-Gamma-S 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 with Atp-Gamma-S (pdb code 7e21). 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 with Atp-Gamma-S, PDB code: 7e21:
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 with Atp-Gamma-S


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 with Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:30.0 occ:1.00 O A:ALA330 2.3 45.4 1.0 OD1 A:ASN783 2.4 41.0 1.0 O A:HOH1202 2.5 30.0 1.0 OE1 A:GLU786 2.6 43.8 1.0 CG A:ASN783 3.4 41.0 1.0 C A:ALA330 3.4 45.4 1.0 O A:SER782 3.5 42.2 1.0 OD2 A:ASP811 3.6 50.4 1.0 CD A:GLU786 3.6 43.8 1.0 C A:SER782 3.9 42.2 1.0 CA A:ASN783 4.0 41.0 1.0 CA A:ASN331 4.0 45.1 1.0 OE2 A:GLU786 4.0 43.8 1.0 N A:ASN783 4.1 41.0 1.0 N A:ASN331 4.1 45.1 1.0 ND2 A:ASN783 4.2 41.0 1.0 CB A:ASN783 4.2 41.0 1.0 OG A:SER782 4.3 42.2 1.0 OD2 A:ASP815 4.4 53.0 1.0 CA A:ALA330 4.4 45.4 1.0 CB A:ALA330 4.5 45.4 1.0 CB A:SER782 4.6 42.2 1.0 OD1 A:ASN331 4.6 45.1 1.0 C A:ASN331 4.7 45.1 1.0 CA A:SER782 4.8 42.2 1.0 CG A:ASP811 4.8 50.4 1.0 O A:THR779 4.9 43.0 1.0 CG A:GLU786 4.9 43.8 1.0 CG A:ASN331 4.9 45.1 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 with Atp-Gamma-S


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 with Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:52.9 occ:1.00 O A:VAL329 2.6 44.7 1.0 OD1 A:ASP811 3.3 50.4 1.0 O A:VAL332 3.3 46.0 1.0 C A:VAL329 3.7 44.7 1.0 O A:HOH1203 3.7 30.0 1.0 O A:HOH1205 3.8 54.5 1.0 O A:HOH1204 3.8 30.0 1.0 CG1 A:VAL329 4.0 44.7 1.0 CG A:ASP811 4.1 50.4 1.0 OD2 A:ASP811 4.3 50.4 1.0 CA A:ALA330 4.3 45.4 1.0 N A:ALA330 4.5 45.4 1.0 C A:VAL332 4.5 46.0 1.0 CA A:VAL329 4.6 44.7 1.0 C A:ALA330 4.7 45.4 1.0 O A:ALA330 4.8 45.4 1.0 CB A:VAL329 4.9 44.7 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 with Atp-Gamma-S


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 with Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:45.8 occ:1.00 O A:TYR778 2.5 42.0 1.0 NE2 A:GLN930 2.6 38.7 1.0 OG1 A:THR781 2.8 41.0 1.0 OE1 A:GLN930 2.9 38.7 1.0 OG A:SER782 3.0 42.2 1.0 CD A:GLN930 3.2 38.7 1.0 OD2 A:ASP933 3.7 42.9 1.0 N A:SER782 3.7 42.2 1.0 CB A:SER782 3.7 42.2 1.0 C A:TYR778 3.7 42.0 1.0 CE1 A:TYR778 4.0 42.0 1.0 CZ A:TYR778 4.0 42.0 1.0 OD1 A:ASP815 4.0 53.0 1.0 CB A:THR781 4.0 41.0 1.0 N A:THR781 4.1 41.0 1.0 CD1 A:TYR778 4.1 42.0 1.0 C A:THR781 4.2 41.0 1.0 CE2 A:TYR778 4.2 42.0 1.0 CA A:SER782 4.2 42.2 1.0 O A:THR779 4.3 43.0 1.0 C A:THR779 4.3 43.0 1.0 CA A:THR781 4.3 41.0 1.0 CA A:THR779 4.3 43.0 1.0 CG A:TYR778 4.3 42.0 1.0 CD2 A:TYR778 4.4 42.0 1.0 N A:THR779 4.5 43.0 1.0 OH A:TYR778 4.5 42.0 1.0 CG A:GLN930 4.6 38.7 1.0 CA A:TYR778 4.7 42.0 1.0 O A:THR814 4.8 49.8 1.0 CG A:ASP815 4.9 53.0 1.0 CG A:ASP933 4.9 42.9 1.0 N A:LEU780 4.9 40.2 1.0 OD2 A:ASP815 5.0 53.0 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 with Atp-Gamma-S


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 with Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1104 b:70.3 occ:1.00 OD2 A:ASP747 2.6 65.1 1.0 O A:ALA728 3.2 67.7 1.0 OD1 A:ASP747 3.4 65.1 1.0 CG A:ASP747 3.4 65.1 1.0 O A:LEU725 3.7 69.6 1.0 O A:ASP729 4.1 65.9 1.0 CA A:LYS726 4.3 71.9 1.0 C A:ALA728 4.4 67.7 1.0 C A:ASP729 4.4 65.9 1.0 N A:GLY731 4.5 60.6 1.0 C A:LEU725 4.7 69.6 1.0 C A:LYS726 4.7 71.9 1.0 CB A:ASP747 4.8 65.1 1.0 CA A:ASP729 4.9 65.9 1.0 N A:LYS727 4.9 70.2 1.0 N A:ILE730 4.9 61.2 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