Potassium in PDB 9oc4: High-Resolution Cryo-Em Structure of Kdpfabc in the E1P-Adp State in Lipid Nanodisc

All present enzymatic activity of High-Resolution Cryo-Em Structure of Kdpfabc in the E1P-Adp State in Lipid Nanodisc:
7.2.2.6;

The structure of High-Resolution Cryo-Em Structure of Kdpfabc in the E1P-Adp State in Lipid Nanodisc also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium atom in the High-Resolution Cryo-Em Structure of Kdpfabc in the E1P-Adp State in Lipid Nanodisc (pdb code 9oc4). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the High-Resolution Cryo-Em Structure of Kdpfabc in the E1P-Adp State in Lipid Nanodisc, PDB code: 9oc4:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the High-Resolution Cryo-Em Structure of Kdpfabc in the E1P-Adp State in Lipid Nanodisc


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of High-Resolution Cryo-Em Structure of Kdpfabc in the E1P-Adp State in Lipid Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ A:K601 b:17.9 occ:1.00 O A:SER343 2.6 28.1 1.0 O A:ASN112 2.7 3.6 1.0 O A:ASN231 2.7 11.4 1.0 O A:ASN467 2.8 17.9 1.0 O A:CYS344 2.8 22.0 1.0 O A:THR113 2.9 16.2 1.0 O A:THR230 3.0 9.2 1.0 O A:ASN466 3.3 16.1 1.0 O A:HOH713 3.4 7.1 1.0 C A:THR113 3.5 8.3 1.0 C A:ASN231 3.5 1.0 1.0 CA A:THR113 3.6 6.5 1.0 C A:CYS344 3.6 10.9 1.0 C A:ASN112 3.6 11.2 1.0 C A:ASN467 3.6 0.5 1.0 C A:SER343 3.8 5.2 1.0 CA A:ASN231 3.9 10.2 1.0 O A:HOH735 3.9 3.7 1.0 C A:THR230 4.0 14.8 1.0 N A:THR113 4.0 11.3 1.0 CA A:CYS344 4.0 14.6 1.0 CA A:ASN467 4.2 10.4 1.0 C A:ASN466 4.2 10.4 1.0 N A:CYS344 4.4 8.3 1.0 N A:ASN231 4.4 19.4 1.0 N A:ASN114 4.5 16.8 1.0 N A:GLY232 4.6 11.4 1.0 N A:GLY468 4.6 8.2 1.0 N A:ASN467 4.6 14.9 1.0 N A:GLY345 4.6 14.6 1.0 CB A:ASN114 4.8 1.4 1.0 OD1 A:ASN112 4.8 17.7 1.0 CA A:ASN112 4.9 16.3 1.0 CA A:GLY468 4.9 19.8 1.0 CA A:SER343 4.9 16.4 1.0 CG A:ASN112 4.9 14.4 1.0 CB A:THR113 5.0 12.1 1.0 CB A:SER343 5.0 15.2 1.0

Potassium binding site 2 out of 2 in the High-Resolution Cryo-Em Structure of Kdpfabc in the E1P-Adp State in Lipid Nanodisc


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of High-Resolution Cryo-Em Structure of Kdpfabc in the E1P-Adp State in Lipid Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ B:K704 b:40.7 occ:1.00 O B:ILE263 2.6 29.3 1.0 OD1 B:ASN624 2.6 30.5 1.0 O B:CYS261 2.8 22.4 1.0 OG1 B:THR265 2.9 26.1 1.0 O B:HOH817 3.0 19.9 1.0 O B:VAL260 3.0 26.4 1.0 O B:HOH810 3.2 32.5 1.0 C B:CYS261 3.2 19.2 1.0 CA B:CYS261 3.7 22.9 1.0 CG B:ASN624 3.7 25.9 1.0 N B:THR265 3.8 24.7 1.0 C B:ILE263 3.8 25.9 1.0 O B:HOH804 3.9 28.8 1.0 O B:HOH815 4.0 31.8 1.0 N B:LEU262 4.0 19.7 1.0 C B:VAL260 4.0 20.7 1.0 CB B:THR265 4.0 21.4 1.0 C B:LEU262 4.1 20.7 1.0 ND2 B:ASN624 4.1 27.9 1.0 N B:ILE263 4.2 19.4 1.0 O B:HOH806 4.3 23.1 1.0 CG2 B:THR265 4.3 21.4 1.0 N B:CYS261 4.3 18.7 1.0 O B:LEU262 4.4 26.5 1.0 CA B:LEU262 4.5 13.3 1.0 CA B:THR265 4.5 17.0 1.0 OD1 B:ASP583 4.5 30.2 1.0 NZ B:LYS586 4.6 29.8 1.0 CA B:PRO264 4.6 19.9 1.0 CA B:ILE263 4.6 23.6 1.0 N B:PRO264 4.7 25.1 1.0 O B:HOH802 4.7 34.8 1.0 C B:PRO264 4.7 18.4 1.0 CB B:CYS261 4.9 20.6 1.0 N B:THR266 4.9 17.0 1.0 CG1 B:ILE263 5.0 23.2 1.0

A.Hussein, X.Zhang, B.P.Pedersen, D.L.Stokes. Conduction Pathway For Potassium Through the E. Coli Pump Kdpfabc Biorxiv 2025.
ISSN: ISSN 2692-8205
DOI: 10.1101/2025.05.05.652293