Potassium in PDB 6pc3: Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp

The structure of Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp, PDB code: 6pc3 was solved by H.Song, C.Wang, G.X.Shaw, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.43 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.312, 90.856, 105.238, 90.00, 106.74, 90.00
R / Rfree (%)	17.9 / 22.5

The structure of Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Potassium atom in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp (pdb code 6pc3). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp, PDB code: 6pc3:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp within 5.0Å range: probe atom residue distance (Å) B Occ A:K505 b:32.7 occ:1.00 OE1 A:GLU143 2.6 34.5 1.0 O A:HOH603 2.7 31.1 1.0 O A:SER141 2.8 32.7 1.0 O A:ASP136 2.9 28.6 1.0 O1 A:PO4502 3.0 34.8 1.0 O A:HOH604 3.0 24.2 1.0 N A:GLY138 3.1 33.2 1.0 OD1 A:ASP136 3.1 35.1 1.0 O3 A:PO4502 3.3 36.9 1.0 P A:PO4502 3.5 37.5 1.0 OE2 A:GLU115 3.5 35.9 1.0 CA A:GLY138 3.5 30.4 1.0 O2 A:PO4502 3.5 32.4 1.0 CG A:ASP136 3.6 32.2 1.0 MG A:MG503 3.6 33.4 1.0 C A:SER141 3.7 40.7 1.0 C A:ASP136 3.7 34.7 1.0 CD A:GLU143 3.8 36.1 1.0 C A:ILE137 3.8 31.5 1.0 OG A:SER141 3.8 38.8 1.0 OD2 A:ASP136 4.0 33.9 1.0 OE2 A:GLU143 4.2 37.3 1.0 CA A:ILE137 4.2 34.9 1.0 N A:ILE137 4.3 30.4 1.0 CA A:THR142 4.3 36.5 1.0 N A:THR142 4.3 33.1 1.0 CB A:ASP136 4.4 32.0 1.0 CD A:GLU115 4.4 38.0 1.0 N A:GLU143 4.5 30.9 1.0 O A:ILE137 4.6 29.0 1.0 CA A:SER141 4.6 36.6 1.0 C A:GLY138 4.6 33.0 1.0 N A:SER141 4.7 32.0 1.0 CA A:ASP136 4.7 31.2 1.0 CB A:SER141 4.8 33.2 1.0 C A:THR142 4.9 38.4 1.0 O A:HOH662 4.9 31.8 1.0 O4 A:PO4502 4.9 33.7 1.0 CG A:GLU143 5.0 31.3 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp within 5.0Å range: probe atom residue distance (Å) B Occ B:K505 b:36.1 occ:1.00 OE1 B:GLU143 2.6 35.9 1.0 O B:HOH603 2.8 28.7 1.0 O B:ASP136 2.9 34.3 1.0 O B:SER141 2.9 35.8 1.0 O2 B:PO4502 3.0 30.5 1.0 N B:GLY138 3.2 29.9 1.0 OD1 B:ASP136 3.3 32.1 1.0 O B:HOH615 3.3 31.1 1.0 OE2 B:GLU115 3.3 40.5 1.0 O4 B:PO4502 3.4 41.3 1.0 CA B:GLY138 3.6 28.8 1.0 CG B:ASP136 3.6 34.2 1.0 P B:PO4502 3.6 37.6 1.0 C B:SER141 3.7 37.6 1.0 C B:ASP136 3.8 30.9 1.0 MG B:MG503 3.8 30.0 1.0 CD B:GLU143 3.8 41.4 1.0 OG B:SER141 3.9 37.2 1.0 O1 B:PO4502 3.9 30.0 1.0 OD2 B:ASP136 3.9 36.7 1.0 C B:ILE137 3.9 36.6 1.0 CD B:GLU115 4.2 35.2 1.0 CA B:THR142 4.2 31.9 1.0 OE2 B:GLU143 4.3 42.4 1.0 N B:THR142 4.3 37.9 1.0 CB B:ASP136 4.3 32.9 1.0 CA B:ILE137 4.4 28.7 1.0 N B:GLU143 4.4 32.5 1.0 N B:ILE137 4.4 31.9 1.0 O B:ILE137 4.6 31.8 1.0 CA B:SER141 4.6 36.6 1.0 CA B:ASP136 4.7 28.6 1.0 C B:GLY138 4.7 28.9 1.0 C B:THR142 4.7 33.9 1.0 N B:SER141 4.8 34.5 1.0 OE1 B:GLU115 4.8 32.8 1.0 CB B:SER141 4.8 39.1 1.0 CG B:GLU143 5.0 31.0 1.0

H.Song, M.N.Dharmasena, C.Wang, G.X.Shaw, S.Cherry, J.E.Tropea, D.J.Jin, X.Ji. Structure and Activity of Ppx/Gppa Homologs From Escherichia Coli and Helicobacter Pylori. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31679177
DOI: 10.1111/FEBS.15120