Magnesium in PDB 6pc1: Crystal Structure of Helicobacter Pylori Ppx/Gppa (E143A) in Complex with Ppgpp

The structure of Crystal Structure of Helicobacter Pylori Ppx/Gppa (E143A) in Complex with Ppgpp, PDB code: 6pc1 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)	40.00 / 2.76
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	194.507, 194.507, 136.862, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.2

The binding sites of Magnesium atom in the Crystal Structure of Helicobacter Pylori Ppx/Gppa (E143A) in Complex with Ppgpp (pdb code 6pc1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Helicobacter Pylori Ppx/Gppa (E143A) in Complex with Ppgpp, PDB code: 6pc1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa (E143A) in Complex with Ppgpp


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 (E143A) in Complex with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:72.3 occ:1.00 O B:HOH670 2.0 36.8 1.0 O B:HOH628 2.0 73.4 1.0 O B:HOH658 2.1 65.8 1.0 O B:HOH671 2.1 56.4 1.0 O B:HOH625 2.2 67.7 1.0 O2 B:PO4503 2.4 55.0 1.0 O B:HOH689 3.0 46.4 1.0 P B:PO4503 3.7 61.0 1.0 O1B B:LMR504 3.8 53.9 1.0 C2 B:LMR504 3.9 54.6 1.0 O2 B:LMR504 4.0 59.3 1.0 O4 B:PO4503 4.1 60.6 1.0 O B:HOH611 4.2 42.4 1.0 C1 B:LMR504 4.2 47.8 1.0 OD2 B:ASP9 4.3 41.0 1.0 OE2 B:GLU115 4.4 54.6 1.0 O B:HOH677 4.4 44.9 1.0 O3 B:PO4503 4.5 47.7 1.0 OD1 B:ASP9 4.6 34.8 1.0 O1 B:PO4503 4.8 54.7 1.0 CA B:GLY11 4.8 29.1 1.0 OD1 B:ASP136 4.8 44.2 1.0 OG1 B:THR83 4.8 43.3 1.0 CG B:ASP9 4.8 30.3 1.0 O B:HOH612 4.8 52.1 1.0 CA B:GLY138 4.9 31.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa (E143A) in Complex with Ppgpp


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 (E143A) in Complex with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:50.5 occ:1.00 O C:HOH698 2.1 45.4 1.0 O C:HOH673 2.1 59.0 1.0 O C:HOH640 2.1 54.2 1.0 O C:HOH638 2.1 49.7 1.0 O C:HOH604 2.1 41.8 1.0 O2 C:PO4503 2.1 55.2 1.0 P C:PO4503 3.3 47.9 1.0 O4 C:PO4503 3.4 46.8 1.0 O C:HOH690 3.9 34.1 1.0 OE2 C:GLU115 4.0 53.5 1.0 O C:HOH643 4.0 37.5 1.0 C2 C:LMR504 4.0 59.0 1.0 O2 C:LMR504 4.1 69.5 1.0 O1A C:LMR504 4.1 70.5 1.0 O C:HOH641 4.3 44.2 1.0 CA C:GLY138 4.3 35.5 1.0 O1 C:PO4503 4.3 42.0 1.0 OD2 C:ASP9 4.4 42.2 1.0 O3 C:PO4503 4.4 47.0 1.0 O C:HOH672 4.5 41.7 1.0 OG1 C:THR83 4.5 41.0 1.0 OD1 C:ASP136 4.5 34.2 1.0 C1 C:LMR504 4.6 44.4 1.0 CA C:GLY11 4.7 41.8 1.0 OD1 C:ASP9 4.7 40.8 1.0 OD2 C:ASP136 4.8 36.3 1.0 CG2 C:THR83 4.8 37.2 1.0 CG C:ASP9 5.0 41.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa (E143A) in Complex with Ppgpp


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 (E143A) in Complex with Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg505 b:83.7 occ:1.00 O C:HOH695 2.1 52.4 1.0 O D:HOH735 2.1 41.3 1.0 O3B C:G4P502 2.3 65.1 1.0 O1A C:G4P502 3.3 57.8 1.0 PB C:G4P502 3.8 0.6 1.0 ND1 D:HIS372 4.3 37.1 1.0 PA C:G4P502 4.4 73.6 1.0 O2B C:G4P502 4.4 54.2 1.0 O D:VAL368 4.5 41.4 1.0 O3A C:G4P502 4.5 0.3 1.0 C5' C:G4P502 4.5 58.2 1.0 N D:LEU370 4.5 41.5 1.0 N D:ALA371 4.7 34.3 1.0 O5' C:G4P502 4.8 83.1 1.0 O1B C:G4P502 4.8 98.5 1.0 CA D:LEU370 4.9 37.1 1.0 CE1 D:HIS372 5.0 39.9 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