Sodium in PDB 7x23: Cryo-Em Structure of Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf State

All present enzymatic activity of Cryo-Em Structure of Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf State:
7.2.2.13; 7.2.2.19;

The binding sites of Sodium atom in the Cryo-Em Structure of Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf State (pdb code 7x23). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cryo-Em Structure of Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf State, PDB code: 7x23:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cryo-Em Structure of Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf 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 Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:16.9 occ:1.00 O A:VAL344 2.6 12.8 1.0 O A:HOH1204 2.6 13.3 1.0 OD1 A:ASP823 2.6 8.6 1.0 O A:ALA342 3.0 8.4 1.0 OD2 A:ASP823 3.0 8.6 1.0 CG A:ASP823 3.1 8.6 1.0 O A:VAL341 3.2 10.2 1.0 OE1 A:GLU346 3.7 18.7 1.0 C A:ALA342 3.7 8.4 1.0 C A:VAL344 3.8 12.8 1.0 N A:GLU346 4.0 18.7 1.0 CA A:ALA342 4.1 8.4 1.0 C A:VAL341 4.2 10.2 1.0 CD A:GLU346 4.3 18.7 1.0 NA A:NA1103 4.3 11.6 1.0 CA A:PRO345 4.4 13.2 1.0 O A:HOH1201 4.4 11.0 1.0 CB A:ASP823 4.5 8.6 1.0 CB A:GLU346 4.5 18.7 1.0 N A:VAL344 4.5 12.8 1.0 CB A:ASP827 4.6 9.1 1.0 N A:PRO345 4.6 13.2 1.0 C A:ASN343 4.6 8.7 1.0 N A:ASN343 4.7 8.7 1.0 N A:ALA342 4.7 8.4 1.0 C A:PRO345 4.7 13.2 1.0 CA A:VAL344 4.8 12.8 1.0 CA A:GLU346 4.8 18.7 1.0 O A:ASN343 4.9 8.7 1.0 CG A:GLU346 4.9 18.7 1.0 OD2 A:ASP827 4.9 9.1 1.0 CG2 A:VAL344 4.9 12.8 1.0 OE2 A:GLU346 5.0 18.7 1.0

Sodium binding site 2 out of 3 in the Cryo-Em Structure of Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf 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 Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:11.6 occ:1.00 OD1 A:ASN795 2.3 3.3 1.0 O A:ALA342 2.5 8.4 1.0 O A:HOH1201 2.6 11.0 1.0 OG A:SER794 2.9 3.2 1.0 O A:HOH1204 3.3 13.3 1.0 OE1 A:GLU798 3.3 3.7 1.0 CG A:ASN795 3.4 3.3 1.0 C A:ALA342 3.6 8.4 1.0 N A:ASN795 3.6 3.3 1.0 C A:SER794 3.7 3.2 1.0 CA A:ASN795 3.8 3.3 1.0 OD2 A:ASP827 3.8 9.1 1.0 O A:SER794 4.0 3.2 1.0 CB A:SER794 4.0 3.2 1.0 O A:HOH1202 4.1 11.3 1.0 CD A:GLU798 4.1 3.7 1.0 OE2 A:GLU798 4.2 3.7 1.0 O A:THR791 4.2 2.4 1.0 CB A:ASN795 4.2 3.3 1.0 CA A:ASN343 4.3 8.7 1.0 NA A:NA1102 4.3 16.9 1.0 CA A:SER794 4.4 3.2 1.0 N A:ASN343 4.4 8.7 1.0 ND2 A:ASN795 4.4 3.3 1.0 O A:ASN343 4.5 8.7 1.0 CA A:ALA342 4.5 8.4 1.0 C A:ASN343 4.6 8.7 1.0 N A:SER794 4.7 3.2 1.0 CB A:ALA342 4.7 8.4 1.0 CG A:ASP827 4.9 9.1 1.0

Sodium binding site 3 out of 3 in the Cryo-Em Structure of Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf 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 Non Gastric H,K-Atpase ALPHA2 Spwc Mutant in 3NA+E1-Amppcpf State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1104 b:8.2 occ:1.00 OG1 A:THR793 2.2 3.8 1.0 OE1 A:GLN942 2.5 5.8 1.0 NE2 A:GLN942 2.5 5.8 1.0 CD A:GLN942 2.8 5.8 1.0 O A:TYR790 2.8 6.1 1.0 OD1 A:ASP827 3.3 9.1 1.0 N A:SER794 3.4 3.2 1.0 CB A:SER794 3.5 3.2 1.0 OD2 A:ASP945 3.5 15.4 1.0 CB A:THR793 3.6 3.8 1.0 OG A:SER794 3.7 3.2 1.0 CA A:SER794 4.0 3.2 1.0 C A:TYR790 4.0 6.1 1.0 CZ A:TYR790 4.0 6.1 1.0 CE2 A:TYR790 4.1 6.1 1.0 CE1 A:TYR790 4.2 6.1 1.0 C A:THR793 4.2 3.8 1.0 CG A:ASP827 4.2 9.1 1.0 CA A:THR793 4.2 3.8 1.0 O A:THR791 4.2 2.4 1.0 N A:THR793 4.3 3.8 1.0 CG A:GLN942 4.3 5.8 1.0 CD2 A:TYR790 4.4 6.1 1.0 CD1 A:TYR790 4.4 6.1 1.0 OD2 A:ASP827 4.4 9.1 1.0 CG A:TYR790 4.5 6.1 1.0 OH A:TYR790 4.5 6.1 1.0 O A:HOH1201 4.6 11.0 1.0 C A:THR791 4.6 2.4 1.0 CG2 A:THR793 4.6 3.8 1.0 CG A:ASP945 4.6 15.4 1.0 CA A:THR791 4.7 2.4 1.0 N A:THR791 4.8 2.4 1.0 OE1 A:GLN873 4.9 4.2 1.0 NE2 A:GLN873 4.9 4.2 1.0 CA A:TYR790 4.9 6.1 1.0

V.C.Young, H.Nakanishi, D.J.Meyer, T.Nishizawa, A.Oshima, P.Artigas, K.Abe. Structure and Function of H + /K + Pump Mutants Reveal Na + /K + Pump Mechanisms. Nat Commun V. 13 5270 2022.
ISSN: ESSN 2041-1723
PubMed: 36085139
DOI: 10.1038/S41467-022-32793-0