Magnesium in PDB 9pgq: Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form)

The structure of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form), PDB code: 9pgq was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.97 / 1.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.461, 83.461, 166.173, 90, 90, 120
R / Rfree (%)	16.3 / 18.6

The binding sites of Magnesium atom in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form) (pdb code 9pgq). 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 Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form), PDB code: 9pgq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form)


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 Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:43.9 occ:1.00 O A:HOH504 2.0 31.3 1.0 O A:HOH644 2.0 33.6 1.0 O A:HOH527 2.1 39.3 1.0 O A:HOH743 2.3 46.1 1.0 O A:LEU86 3.9 28.9 1.0 OE2 A:GLU90 4.1 43.0 1.0 O A:ALA84 4.1 36.7 1.0 OE1 A:GLU90 4.2 31.9 1.0 O A:GLU85 4.3 32.9 1.0 C A:GLU85 4.5 33.0 1.0 O A:GLY115 4.6 33.4 1.0 C A:LEU86 4.6 29.3 1.0 CD A:GLU90 4.6 36.6 1.0 CA A:PRO87 4.8 29.5 1.0 CA A:GLU85 4.8 34.0 1.0 CA A:GLY115 4.9 33.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form)


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 Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:20.3 occ:1.00 O A:HOH532 2.0 23.5 1.0 OXT A:LYS336 2.1 21.3 1.0 O A:HOH533 2.1 20.2 1.0 C A:LYS336 3.1 20.6 1.0 O A:LYS336 3.5 23.2 1.0 OE2 A:GLU146 4.0 22.8 1.0 O A:HOH702 4.2 39.2 1.0 O A:HOH737 4.3 44.0 1.0 OE1 A:GLU146 4.3 22.6 1.0 CA A:LYS336 4.5 22.2 1.0 CD A:GLU146 4.6 21.2 1.0 CB A:ALA145 4.8 22.6 1.0 CB A:LYS336 4.9 27.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form)


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 Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:45.7 occ:1.00 O A:MET1 2.1 56.8 1.0 CA A:THR2 2.6 30.3 0.6 CA A:THR2 2.7 30.3 0.4 O A:HOH704 2.8 52.3 1.0 C A:MET1 2.9 49.3 1.0 C A:THR2 3.0 24.5 1.0 N A:THR2 3.1 32.0 1.0 N A:ILE3 3.4 22.9 1.0 O A:THR2 3.5 24.3 1.0 CB A:THR2 4.0 35.1 0.6 OD1 A:ASP29 4.1 38.6 1.0 OD2 A:ASP29 4.1 61.3 1.0 CG A:ASP29 4.1 43.6 1.0 CB A:THR2 4.1 34.9 0.4 OG1 A:THR2 4.3 31.9 0.6 CA A:MET1 4.3 45.1 1.0 CG1 A:ILE3 4.3 22.4 1.0 O A:ASP29 4.4 25.9 1.0 O A:HIS0 4.4 57.0 1.0 CA A:ILE3 4.5 19.0 1.0 CG2 A:THR2 4.6 31.5 0.4 OG1 A:THR2 4.7 34.2 0.4 CB A:MET1 4.8 52.0 1.0 CB A:ASP29 4.9 34.5 1.0

A.R.Ung, L.Liu, S.Lovell, K.P.Battaile. Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Apo, Trigonal Form) To Be Published.