Magnesium in PDB 8qoc: Crystal Structure of Staphylococcus Aureus Plp Synthase (PDX1)

The structure of Crystal Structure of Staphylococcus Aureus Plp Synthase (PDX1), PDB code: 8qoc was solved by N.Ullah, C.Wrenger, C.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.80 / 2.83
Space group	H 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.419, 192.419, 448.198, 90, 90, 120
R / Rfree (%)	20.2 / 26

The structure of Crystal Structure of Staphylococcus Aureus Plp Synthase (PDX1) also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Plp Synthase (PDX1) (pdb code 8qoc). 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 Staphylococcus Aureus Plp Synthase (PDX1), PDB code: 8qoc:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Staphylococcus Aureus Plp Synthase (PDX1)


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 Staphylococcus Aureus Plp Synthase (PDX1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:30.0 occ:1.00 O A:ALA269 3.5 64.8 1.0 NE2 A:GLN220 3.8 54.8 1.0 OE1 A:GLN220 4.3 58.4 1.0 C A:ALA269 4.4 69.4 1.0 OE1 A:GLU271 4.5 70.2 1.0 CB A:ALA269 4.5 60.7 1.0 CA A:ALA269 4.5 64.9 1.0 CD A:GLN220 4.5 56.6 1.0 CB A:THR218 4.6 58.2 1.0 CG A:GLU271 4.6 84.3 1.0 CD A:PRO219 4.7 60.9 1.0 CG2 A:THR218 4.7 52.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Staphylococcus Aureus Plp Synthase (PDX1)


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 Staphylococcus Aureus Plp Synthase (PDX1) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg305 b:30.0 occ:1.00 OE1 E:GLU271 3.8 30.0 1.0 CB E:THR218 4.1 60.1 1.0 CG2 E:THR218 4.1 53.8 1.0 CG E:GLU271 4.3 30.0 1.0 CD E:PRO219 4.4 59.3 1.0 OE1 E:GLN220 4.4 55.4 1.0 NE2 E:GLN220 4.4 51.0 1.0 CD E:GLU271 4.6 30.0 1.0 CB E:ALA269 4.6 60.6 1.0 CA E:THR218 4.8 56.1 1.0 CA E:ALA269 4.8 66.0 1.0 N E:GLY273 4.9 85.2 1.0 CD E:GLN220 4.9 55.8 1.0 CA E:GLY273 4.9 78.1 1.0 CZ E:PHE248 5.0 79.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Staphylococcus Aureus Plp Synthase (PDX1)


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 Staphylococcus Aureus Plp Synthase (PDX1) within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg303 b:30.0 occ:1.00 OD1 G:ASP25 3.0 81.1 1.0 NZ G:LYS82 3.3 59.9 1.0 OD2 G:ASP25 3.6 76.2 1.0 O4 G:PO4302 3.6 75.0 1.0 CG G:ASP25 3.7 77.1 1.0 CE G:LYS82 3.7 63.5 1.0 CG G:PRO50 4.6 83.2 1.0 CB G:PHE234 4.7 56.4 1.0 CD1 G:PHE234 4.7 45.1 1.0 CG G:PHE234 5.0 53.5 1.0 CB G:ALA213 5.0 52.8 1.0

A.L.C.Barra, N.Ullah, H.Brognaro, R.F.Gutierrez, C.Wrenger, C.Betzel, A.S.Nascimento. Structure and Dynamics of the Staphylococcal Pyridoxal 5-Phosphate Synthase Complex Reveal Transient Interactions at the Enzyme Interface. J.Biol.Chem. V. 300 07404 2024.
ISSN: ESSN 1083-351X
PubMed: 38782204
DOI: 10.1016/J.JBC.2024.107404