Magnesium 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:

Potassium	(K)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp, PDB code: 6pc3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg503 b:33.4 occ:1.00 O A:HOH662 2.0 31.8 1.0 O1 A:PO4502 2.0 34.8 1.0 O A:HOH681 2.1 32.3 1.0 O A:HOH603 2.2 31.1 1.0 O A:HOH650 2.2 28.1 1.0 O A:HOH604 2.3 24.2 1.0 P A:PO4502 3.4 37.5 1.0 OE2 A:GLU115 3.5 35.9 1.0 HS2P A:TS6509 3.6 44.7 1.0 K A:K505 3.6 32.7 1.0 O3 A:PO4502 4.0 36.9 1.0 OD1 A:ASP136 4.0 35.1 1.0 O4 A:PO4502 4.1 33.7 1.0 OD2 A:ASP136 4.2 33.9 1.0 OG1 A:THR83 4.3 32.2 1.0 O A:HOH731 4.3 37.3 1.0 O A:HOH694 4.3 31.1 1.0 OD2 A:ASP9 4.4 37.3 1.0 O A:HOH630 4.4 31.9 1.0 OD1 A:ASP9 4.4 41.3 1.0 CA A:GLY138 4.5 30.4 1.0 O2 A:PO4502 4.5 32.4 1.0 CG A:ASP136 4.5 32.2 1.0 CD A:GLU115 4.7 38.0 1.0 S2P A:TS6509 4.7 37.4 1.0 CA A:GLY11 4.8 27.7 1.0 CG2 A:VAL286 4.9 20.6 1.0 CG A:ASP9 4.9 43.2 1.0 CG2 A:THR83 4.9 28.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg504 b:43.9 occ:1.00 HOG2 A:GSP501 1.9 47.8 1.0 O A:VAL368 2.0 35.7 1.0 O2B A:GSP501 2.1 49.9 1.0 O1A A:GSP501 2.2 44.0 1.0 O B:HOH709 2.2 35.1 1.0 O2G A:GSP501 2.3 40.0 1.0 O A:HOH779 2.5 52.6 1.0 C A:VAL368 3.2 29.2 1.0 PB A:GSP501 3.3 47.9 1.0 PA A:GSP501 3.5 45.9 1.0 PG A:GSP501 3.5 45.2 1.0 H5'1 A:GSP501 3.7 52.8 1.0 O3A A:GSP501 3.8 59.5 1.0 O3G A:GSP501 3.9 42.4 1.0 O3B A:GSP501 3.9 48.2 1.0 CA A:TYR369 4.0 38.4 1.0 N A:TYR369 4.0 33.2 1.0 CA A:VAL368 4.2 28.7 1.0 O B:HOH702 4.3 31.2 1.0 OE2 B:GLU33 4.4 35.7 1.0 C5' A:GSP501 4.4 44.1 1.0 CB A:VAL368 4.4 32.2 1.0 CD1 A:TYR369 4.5 35.7 1.0 O2A A:GSP501 4.5 34.7 1.0 H5'2 A:GSP501 4.5 52.8 1.0 O1B A:GSP501 4.5 50.3 1.0 O5' A:GSP501 4.5 47.4 1.0 N A:LEU370 4.5 39.8 1.0 HOG3 A:GSP501 4.7 50.8 1.0 C A:TYR369 4.7 34.6 1.0 CB A:ALA371 4.8 32.9 1.0 N A:ALA371 4.8 34.9 1.0 CG2 A:VAL368 5.0 32.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:30.0 occ:1.00 O B:HOH636 2.0 20.8 1.0 O2 B:PO4502 2.1 30.5 1.0 O B:HOH652 2.1 33.1 1.0 O B:HOH603 2.2 28.7 1.0 O B:HOH744 2.3 28.8 1.0 O B:HOH615 2.4 31.1 1.0 P B:PO4502 3.5 37.6 1.0 OE2 B:GLU115 3.6 40.5 1.0 K B:K505 3.8 36.1 1.0 O B:HOH710 3.9 30.0 1.0 O3 B:PO4502 4.1 33.9 1.0 O4 B:PO4502 4.1 41.3 1.0 OG1 B:THR83 4.2 27.9 1.0 OD1 B:ASP136 4.2 32.1 1.0 OD1 B:ASP9 4.3 39.3 1.0 OD2 B:ASP9 4.4 38.5 1.0 O B:HOH682 4.4 30.7 1.0 OD2 B:ASP136 4.4 36.7 1.0 CA B:GLY138 4.5 28.8 1.0 O1 B:PO4502 4.5 30.0 1.0 S2P B:TS6507 4.5 30.5 1.0 O B:HOH697 4.5 33.9 1.0 CG B:ASP136 4.7 34.2 1.0 CA B:GLY11 4.7 29.7 1.0 CG B:ASP9 4.8 46.1 1.0 CD B:GLU115 4.8 35.2 1.0 CG2 B:VAL286 4.8 34.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:47.5 occ:1.00 O B:HOH753 2.1 46.1 1.0 O2G B:GSP501 2.2 43.9 1.0 O B:VAL368 2.2 35.7 1.0 HOG2 B:GSP501 2.2 52.5 1.0 O2B B:GSP501 2.2 47.6 1.0 O1A B:GSP501 2.2 43.2 1.0 O A:HOH689 2.3 39.5 1.0 PG B:GSP501 3.3 49.5 1.0 PB B:GSP501 3.3 43.7 1.0 C B:VAL368 3.4 35.2 1.0 PA B:GSP501 3.5 42.7 1.0 O3G B:GSP501 3.6 48.5 1.0 O3B B:GSP501 3.8 51.1 1.0 O3A B:GSP501 3.9 62.5 1.0 O A:HOH791 4.0 34.0 1.0 HOG3 B:GSP501 4.0 58.1 1.0 O A:HOH672 4.1 46.7 1.0 H5'1 B:GSP501 4.1 59.8 1.0 CA B:TYR369 4.2 32.9 1.0 N B:TYR369 4.2 34.3 1.0 CA B:VAL368 4.4 30.3 1.0 N B:LEU370 4.5 32.3 1.0 CB B:ALA371 4.5 32.4 1.0 O2A B:GSP501 4.5 48.5 1.0 CB B:VAL368 4.5 30.8 1.0 N B:ALA371 4.5 26.2 1.0 OE2 A:GLU33 4.6 41.6 1.0 O1B B:GSP501 4.6 65.3 1.0 O5' B:GSP501 4.6 46.4 1.0 C B:TYR369 4.7 35.7 1.0 C5' B:GSP501 4.8 49.9 1.0 S1G B:GSP501 5.0 50.9 1.0 H5'2 B:GSP501 5.0 59.8 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