Magnesium in PDB 6pc2: Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gnp

The structure of Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gnp, PDB code: 6pc2 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)	35.88 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.016, 94.475, 107.197, 90.00, 108.53, 90.00
R / Rfree (%)	25.4 / 31

The binding sites of Magnesium atom in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gnp (pdb code 6pc2). 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 Gnp, PDB code: 6pc2:
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 Gnp


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 Gnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:84.7 occ:1.00 O A:HOH603 2.2 97.2 1.0 O4 A:PO4502 2.6 0.1 1.0 OE2 A:GLU115 3.1 95.2 1.0 OD2 A:ASP136 3.1 86.4 1.0 O A:HOH601 3.5 1.0 1.0 CG2 A:VAL286 3.6 83.6 1.0 P A:PO4502 3.9 98.8 1.0 O1 A:PO4502 3.9 97.0 1.0 CG A:ASP136 4.0 86.8 1.0 OD1 A:ASP136 4.0 89.6 1.0 OD2 A:ASP9 4.2 0.9 1.0 CD A:GLU115 4.2 94.0 1.0 OG1 A:THR83 4.5 0.7 1.0 CB A:VAL286 4.7 80.8 1.0 OD1 A:ASP9 4.7 0.1 1.0 O2 A:PO4502 4.7 0.2 1.0 CG A:GLU115 4.8 87.6 1.0 NH1 A:ARG16 4.9 91.6 1.0 O3 A:PO4502 4.9 90.1 1.0 CG A:ASP9 4.9 1.0 1.0 CG2 A:THR83 4.9 92.0 1.0 CB A:THR83 4.9 0.3 1.0

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


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 Gnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:53.4 occ:1.00 O2B A:GNP505 2.0 70.6 1.0 O A:VAL368 2.0 62.0 1.0 O1G A:GNP505 2.6 74.3 1.0 O1A A:GNP505 2.9 79.5 1.0 C A:VAL368 3.1 59.3 1.0 PB A:GNP505 3.1 65.4 1.0 O2G A:GNP505 3.5 63.7 1.0 PG A:GNP505 3.6 67.8 1.0 PA A:GNP505 3.8 67.9 1.0 O3A A:GNP505 3.8 74.1 1.0 N3B A:GNP505 3.8 75.6 1.0 N A:TYR369 3.9 55.8 1.0 CA A:VAL368 4.0 68.4 1.0 CA A:TYR369 4.1 58.8 1.0 CB A:VAL368 4.1 48.5 1.0 O1B A:GNP505 4.3 73.4 1.0 O2A A:GNP505 4.5 60.8 1.0 N A:LEU370 4.6 48.3 1.0 CB A:ALA371 4.7 53.4 1.0 CG2 A:VAL368 4.7 44.5 1.0 C A:TYR369 4.8 63.5 1.0 N A:ALA371 4.8 48.1 1.0 O3G A:GNP505 4.9 55.2 1.0 CG B:GLU33 4.9 64.0 1.0

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


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 Gnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:64.0 occ:1.00 O B:HOH606 2.0 69.3 1.0 O B:VAL368 2.1 71.2 1.0 O2B B:GNP502 2.1 97.8 1.0 O1G B:GNP502 2.6 75.5 1.0 O1A B:GNP502 2.9 77.0 1.0 C B:VAL368 3.2 62.5 1.0 PB B:GNP502 3.2 94.8 1.0 O2G B:GNP502 3.5 74.8 1.0 PG B:GNP502 3.6 86.6 1.0 PA B:GNP502 3.9 69.5 1.0 O3A B:GNP502 3.9 77.8 1.0 N3B B:GNP502 3.9 86.4 1.0 CA B:VAL368 4.0 62.4 1.0 CB B:VAL368 4.0 63.2 1.0 N B:TYR369 4.2 68.2 1.0 O A:HOH605 4.3 59.9 1.0 CA B:TYR369 4.4 60.0 1.0 O1B B:GNP502 4.4 83.0 1.0 CB B:ALA371 4.5 54.7 1.0 O2A B:GNP502 4.6 74.8 1.0 CG2 B:VAL368 4.8 70.4 1.0 N B:ALA371 4.9 65.2 1.0 O3G B:GNP502 4.9 80.7 1.0 N B:LEU370 4.9 56.0 1.0

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


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 Gnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:69.0 occ:1.00 O B:HOH607 2.2 69.7 1.0 O4 B:PO4504 2.7 84.3 1.0 O B:HOH604 2.9 69.2 1.0 OE2 B:GLU115 3.1 88.1 1.0 OD2 B:ASP136 3.2 87.0 1.0 CG2 B:VAL286 3.6 68.5 1.0 O2 B:PO4504 3.9 0.3 1.0 P B:PO4504 3.9 94.6 1.0 CG B:ASP136 4.0 85.6 1.0 OD1 B:ASP136 4.0 85.5 1.0 OD2 B:ASP9 4.1 85.5 1.0 CD B:GLU115 4.3 87.4 1.0 OG1 B:THR83 4.6 87.3 1.0 CB B:VAL286 4.6 63.5 1.0 OD1 B:ASP9 4.6 81.2 1.0 CG B:GLU115 4.8 88.6 1.0 O1 B:PO4504 4.8 77.9 1.0 CG B:ASP9 4.8 84.6 1.0 NH1 B:ARG16 4.9 92.2 1.0 CG2 B:THR83 4.9 88.2 1.0 CB B:THR83 4.9 85.5 1.0 O3 B:PO4504 5.0 75.4 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