Potassium in PDB 6afs: Proton Pyrophosphatase - Two Phosphates-Bound

All present enzymatic activity of Proton Pyrophosphatase - Two Phosphates-Bound:
3.6.1.1;

The structure of Proton Pyrophosphatase - Two Phosphates-Bound, PDB code: 6afs was solved by J.-Y.Tsai, K.-M.Li, Y.-J.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.49 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	217.641, 88.433, 159.050, 90.00, 125.47, 90.00
R / Rfree (%)	20.8 / 24

The structure of Proton Pyrophosphatase - Two Phosphates-Bound also contains other interesting chemical elements:

Magnesium

(Mg)

10 atoms

The binding sites of Potassium atom in the Proton Pyrophosphatase - Two Phosphates-Bound (pdb code 6afs). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Proton Pyrophosphatase - Two Phosphates-Bound, PDB code: 6afs:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Proton Pyrophosphatase - Two Phosphates-Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Proton Pyrophosphatase - Two Phosphates-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:K1008 b:41.7 occ:1.00 O A:HOH1181 2.8 31.9 1.0 O A:HOH1264 2.8 34.2 1.0 O A:HOH1193 2.9 31.7 1.0 O A:HOH1215 3.1 35.7 1.0 O A:HOH1138 3.2 33.4 1.0 OD1 A:ASN534 3.3 34.9 1.0 O3 A:PO41001 3.4 36.1 1.0 O A:GLY533 3.5 35.5 1.0 C A:GLY533 3.8 34.6 1.0 N A:ASN534 4.0 33.5 1.0 CA A:ASN534 4.0 33.8 1.0 MG A:MG1007 4.0 37.1 1.0 O A:HOH1131 4.1 39.0 1.0 CB A:ALA537 4.1 30.3 1.0 CG A:ASN534 4.4 34.5 1.0 P A:PO41001 4.4 50.3 1.0 O A:HOH1152 4.4 26.2 1.0 C A:GLY503 4.5 34.2 1.0 O1 A:PO41001 4.5 36.0 1.0 OD2 A:ASP287 4.5 34.6 1.0 OD1 A:ASP530 4.6 37.8 1.0 O A:GLY503 4.6 31.1 1.0 O2 A:PO41001 4.6 32.0 1.0 CA A:GLY533 4.6 31.1 1.0 N A:PRO504 4.7 34.5 1.0 CA A:GLY503 4.7 30.0 1.0 CB A:ASN534 4.8 32.5 1.0 O A:ASP530 4.9 38.3 1.0 OD2 A:ASP507 4.9 34.8 1.0 CD A:PRO504 5.0 30.6 1.0

Potassium binding site 2 out of 2 in the Proton Pyrophosphatase - Two Phosphates-Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Proton Pyrophosphatase - Two Phosphates-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:K1008 b:57.6 occ:1.00 O B:HOH1205 2.7 44.0 1.0 O B:HOH1128 2.9 42.7 1.0 O B:HOH1202 2.9 42.2 1.0 O B:HOH1167 3.0 48.1 1.0 O3 B:PO41001 3.2 45.5 1.0 OD1 B:ASN534 3.2 44.2 1.0 MG B:MG1007 3.8 44.3 1.0 O B:GLY533 4.0 51.9 1.0 O1 B:PO41001 4.1 42.4 1.0 P B:PO41001 4.2 52.3 1.0 O B:HOH1158 4.2 49.7 1.0 CA B:ASN534 4.2 46.2 1.0 C B:GLY533 4.3 52.4 1.0 N B:ASN534 4.3 45.8 1.0 CG B:ASN534 4.4 48.8 1.0 CB B:ALA537 4.4 45.6 1.0 OD2 B:ASP287 4.4 49.4 1.0 O4 B:PO41001 4.6 41.5 1.0 C B:GLY503 4.7 45.8 1.0 OD1 B:ASP530 4.8 49.8 1.0 O B:GLY503 4.8 44.5 1.0 OD2 B:ASP507 4.9 44.6 1.0 N B:PRO504 4.9 48.2 1.0 CB B:ASN534 4.9 50.3 1.0 CA B:GLY503 5.0 43.5 1.0 O B:HOH1198 5.0 42.3 1.0

J.Y.Tsai, K.Z.Tang, K.M.Li, B.L.Hsu, Y.W.Chiang, A.Goldman, Y.J.Sun. Roles of the Hydrophobic Gate and Exit Channel in Vigna Radiata Pyrophosphatase Ion Translocation. J. Mol. Biol. V. 431 1619 2019.
ISSN: ESSN 1089-8638
PubMed: 30878480
DOI: 10.1016/J.JMB.2019.03.009