Magnesium in PDB 8e1u: Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate

The structure of Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate, PDB code: 8e1u was solved by M.J.Mcleod, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.77 / 2.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	134.131, 146.952, 151.094, 82.7, 84, 70.8
R / Rfree (%)	18.1 / 22.3

The binding sites of Magnesium atom in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate (pdb code 8e1u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate, PDB code: 8e1u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:31.0 occ:1.00 O A:HOH1436 1.9 35.4 1.0 O A:HOH1343 2.0 38.5 1.0 OD1 A:ASP642 2.0 38.6 1.0 O A:HOH1409 2.1 35.3 1.0 NE2 A:HIS345 2.1 38.9 1.0 NZ A:LYS325 2.2 37.3 1.0 CG A:ASP642 2.9 37.4 1.0 CE1 A:HIS345 3.0 38.5 1.0 OD2 A:ASP642 3.1 37.1 1.0 CD2 A:HIS345 3.1 38.0 1.0 CE A:LYS325 3.2 38.4 1.0 NZ A:LYS476 4.1 42.7 1.0 ND1 A:HIS345 4.1 37.4 1.0 CG A:HIS345 4.2 37.4 1.0 CB A:ASP642 4.3 34.9 1.0 CE A:LYS476 4.6 41.9 1.0 CD A:LYS325 4.6 36.7 1.0 CE2 A:PHE863 4.7 40.0 1.0 CZ A:PHE863 4.8 42.2 1.0 O A:HOH1484 4.9 35.5 1.0 CA A:ASP642 4.9 37.3 1.0

Magnesium binding site 2 out of 8 in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1201 b:33.5 occ:1.00 OD1 B:ASP642 2.0 40.3 1.0 O B:HOH1397 2.0 38.0 1.0 O B:HOH1359 2.1 39.1 1.0 NZ B:LYS325 2.1 38.8 1.0 O B:HOH1357 2.1 35.2 1.0 NE2 B:HIS345 2.1 42.2 1.0 CG B:ASP642 2.9 40.6 1.0 CE1 B:HIS345 3.0 41.0 1.0 OD2 B:ASP642 3.1 37.0 1.0 CE B:LYS325 3.2 40.4 1.0 CD2 B:HIS345 3.2 40.9 1.0 NZ B:LYS476 4.0 46.0 1.0 ND1 B:HIS345 4.2 39.8 1.0 CB B:ASP642 4.3 41.7 1.0 CG B:HIS345 4.3 39.6 1.0 CD B:LYS325 4.5 40.6 1.0 CE B:LYS476 4.6 46.6 1.0 CZ B:PHE863 4.8 48.2 1.0 CE2 B:PHE863 4.9 44.3 1.0 CA B:ASP642 5.0 43.8 1.0

Magnesium binding site 3 out of 8 in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1201 b:42.9 occ:1.00 O C:HOH1362 1.8 38.7 1.0 NZ C:LYS325 2.1 38.4 1.0 NE2 C:HIS345 2.1 40.0 1.0 O C:HOH1398 2.2 45.0 1.0 OD1 C:ASP642 2.2 37.9 1.0 O C:HOH1422 2.3 35.4 1.0 CE1 C:HIS345 3.0 36.8 1.0 CG C:ASP642 3.1 39.7 1.0 CE C:LYS325 3.2 40.0 1.0 CD2 C:HIS345 3.2 39.3 1.0 OD2 C:ASP642 3.3 40.0 1.0 ND1 C:HIS345 4.1 36.3 1.0 NZ C:LYS476 4.2 43.0 1.0 CG C:HIS345 4.3 38.6 1.0 CD C:LYS325 4.5 39.4 1.0 CE C:LYS476 4.5 38.9 1.0 CB C:ASP642 4.6 35.6 1.0 CE2 C:PHE863 4.6 40.8 1.0 CZ C:PHE863 4.6 39.1 1.0

Magnesium binding site 4 out of 8 in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1201 b:33.4 occ:1.00 O D:HOH1387 1.9 34.4 1.0 O D:HOH1330 1.9 31.1 1.0 NZ D:LYS325 2.0 36.9 1.0 NE2 D:HIS345 2.0 35.3 1.0 OD1 D:ASP642 2.1 37.0 1.0 O D:HOH1438 2.7 38.5 1.0 CE1 D:HIS345 2.8 38.2 1.0 CG D:ASP642 2.9 35.1 1.0 CD2 D:HIS345 3.1 35.0 1.0 OD2 D:ASP642 3.1 37.5 1.0 CE D:LYS325 3.2 34.1 1.0 ND1 D:HIS345 4.0 35.8 1.0 CG D:HIS345 4.1 37.0 1.0 NZ D:LYS476 4.3 44.5 1.0 CB D:ASP642 4.4 33.8 1.0 CE D:LYS476 4.4 37.4 1.0 CD D:LYS325 4.5 34.1 1.0 CZ D:PHE863 4.5 38.3 1.0 CE2 D:PHE863 4.5 38.4 1.0 NZ D:LYS324 5.0 32.5 1.0

Magnesium binding site 5 out of 8 in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1201 b:29.6 occ:1.00 O E:HOH1373 2.0 37.9 1.0 NE2 E:HIS345 2.1 37.8 1.0 NZ E:LYS325 2.1 41.4 1.0 OD1 E:ASP642 2.1 44.9 1.0 O E:HOH1423 2.1 41.6 1.0 O E:HOH1409 2.3 37.4 1.0 CG E:ASP642 2.9 44.5 1.0 CE1 E:HIS345 2.9 38.3 1.0 OD2 E:ASP642 3.0 44.6 1.0 CD2 E:HIS345 3.1 39.1 1.0 CE E:LYS325 3.2 43.4 1.0 NZ E:LYS476 4.1 44.2 1.0 ND1 E:HIS345 4.1 36.4 1.0 CG E:HIS345 4.2 39.3 1.0 CB E:ASP642 4.4 41.4 1.0 CE E:LYS476 4.4 43.8 1.0 CD E:LYS325 4.5 40.2 1.0 CZ E:PHE863 4.8 46.6 1.0 CE2 E:PHE863 4.9 40.4 1.0 O E:HOH1438 4.9 36.8 1.0

Magnesium binding site 6 out of 8 in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1201 b:32.4 occ:1.00 O F:HOH1330 1.9 40.0 1.0 O F:HOH1433 2.0 44.0 1.0 NZ F:LYS325 2.0 42.8 1.0 NE2 F:HIS345 2.1 42.6 1.0 OD1 F:ASP642 2.2 41.8 1.0 O F:HOH1434 2.3 39.3 1.0 CE1 F:HIS345 2.9 39.5 1.0 CG F:ASP642 3.0 40.4 1.0 CE F:LYS325 3.1 42.1 1.0 OD2 F:ASP642 3.2 40.3 1.0 CD2 F:HIS345 3.2 39.9 1.0 ND1 F:HIS345 4.1 36.5 1.0 NZ F:LYS476 4.2 43.5 1.0 CG F:HIS345 4.3 38.1 1.0 CD F:LYS325 4.4 40.5 1.0 CB F:ASP642 4.4 37.7 1.0 CE F:LYS476 4.7 44.7 1.0 CZ F:PHE863 4.7 50.1 1.0 CE2 F:PHE863 4.7 46.0 1.0 NZ F:LYS324 4.8 41.8 1.0

Magnesium binding site 7 out of 8 in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1201 b:31.7 occ:1.00 OD1 G:ASP642 1.9 40.1 1.0 O G:HOH1377 1.9 37.1 1.0 NZ G:LYS325 2.1 37.5 1.0 NE2 G:HIS345 2.1 40.7 1.0 O G:HOH1395 2.1 39.7 1.0 O G:HOH1425 2.6 38.8 1.0 CG G:ASP642 2.8 42.0 1.0 CE1 G:HIS345 3.0 39.0 1.0 CE G:LYS325 3.1 40.3 1.0 OD2 G:ASP642 3.1 41.7 1.0 CD2 G:HIS345 3.1 40.4 1.0 ND1 G:HIS345 4.1 38.6 1.0 CE G:LYS476 4.1 43.4 1.0 CB G:ASP642 4.2 40.4 1.0 NZ G:LYS476 4.2 48.0 1.0 CG G:HIS345 4.2 39.5 1.0 CD G:LYS325 4.5 39.1 1.0 CE2 G:PHE863 4.6 44.8 1.0 CZ G:PHE863 4.8 47.0 1.0 CA G:ASP642 4.9 38.8 1.0 O G:ASP642 4.9 42.9 1.0

Magnesium binding site 8 out of 8 in the Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Propionibacterium Freudenreichii Ppi-Dependent Pepck in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg1201 b:32.6 occ:1.00 O H:HOH1403 1.9 41.5 1.0 O H:HOH1331 2.0 31.6 1.0 NZ H:LYS325 2.0 36.0 1.0 NE2 H:HIS345 2.1 39.2 1.0 OD1 H:ASP642 2.1 37.2 1.0 O H:HOH1436 2.5 34.6 1.0 CE1 H:HIS345 2.9 37.5 1.0 CG H:ASP642 3.0 38.2 1.0 OD2 H:ASP642 3.1 36.5 1.0 CE H:LYS325 3.1 39.8 1.0 CD2 H:HIS345 3.2 40.3 1.0 NZ H:LYS476 4.0 41.0 1.0 ND1 H:HIS345 4.1 38.6 1.0 CG H:HIS345 4.2 41.3 1.0 CB H:ASP642 4.4 36.5 1.0 CD H:LYS325 4.4 38.2 1.0 NZ H:LYS324 4.5 39.1 1.0 CE H:LYS476 4.6 39.3 1.0 CE2 H:PHE863 4.7 40.5 1.0 CZ H:PHE863 4.8 40.8 1.0

M.J.Mcleod, T.Holyoak. Biochemical, Structural, and Kinetic Characterization of Pp I -Dependent Phosphoenolpyruvate Carboxykinase From Propionibacterium Freudenreichii. Proteins 2023.
ISSN: ESSN 1097-0134
PubMed: 37226637
DOI: 10.1002/PROT.26513