Magnesium in PDB 9pg6: Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound)

The structure of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound), PDB code: 9pg6 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)	49.03 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.826, 130.061, 140.967, 90, 90.86, 90
R / Rfree (%)	19.3 / 23

The binding sites of Magnesium atom in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound) (pdb code 9pg6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound), PDB code: 9pg6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound)


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 (Nad Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:57.5 occ:1.00 O A:HOH564 2.1 50.8 1.0 O A:HOH513 2.3 40.4 1.0 O A:ALA84 3.5 57.4 1.0 O A:LEU86 3.8 43.5 1.0 O A:GLY115 4.2 37.6 1.0 CA A:GLY115 4.3 38.8 1.0 O A:GLU85 4.3 50.8 1.0 C A:GLU85 4.4 48.6 1.0 CA A:GLU85 4.6 49.8 1.0 C A:GLY115 4.6 39.3 1.0 C A:LEU86 4.6 37.7 1.0 C A:ALA84 4.6 44.6 1.0 OE1 A:GLU90 4.6 69.2 1.0 O A:LYS114 4.8 62.4 1.0 OE2 A:GLU90 4.8 86.2 1.0 CA A:PRO87 4.9 38.7 1.0 N A:LEU86 4.9 43.3 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound)


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 (Nad Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:53.2 occ:1.00 O B:HOH540 2.1 43.9 1.0 OE2 B:GLU90 4.0 70.1 1.0 OE1 B:GLU90 4.2 54.3 1.0 CD B:GLU90 4.5 55.4 1.0 O B:ALA84 4.5 51.5 1.0 O B:LEU86 4.6 39.4 1.0 O B:GLY115 4.6 42.7 1.0 CA B:GLY115 4.9 51.2 1.0 O B:GLU85 5.0 47.4 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound)


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 (Nad Bound) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:30.9 occ:1.00 O D:HOH507 2.1 23.6 1.0 O D:HOH503 2.1 24.5 1.0 O D:HOH546 2.3 27.1 1.0 OE2 D:GLU90 3.8 46.2 1.0 O D:LEU86 3.9 39.7 1.0 O D:HOH522 4.1 31.9 1.0 O D:GLU85 4.2 31.7 1.0 O D:ALA84 4.3 33.7 1.0 O D:GLY115 4.5 31.7 1.0 C D:LEU86 4.5 29.1 1.0 CA D:PRO87 4.5 36.2 1.0 C D:GLU85 4.6 39.1 1.0 CD D:GLU90 4.7 50.5 1.0 N D:PRO87 4.9 35.1 1.0 CA D:GLY115 4.9 32.8 1.0 OE1 D:GLU90 4.9 56.1 1.0 CA D:GLU85 5.0 33.2 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound)


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 Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:53.6 occ:1.00 O F:HOH563 1.9 54.0 1.0 O F:HOH569 2.1 48.5 1.0 O F:HOH507 2.1 40.5 1.0 O F:HOH566 2.2 45.6 1.0 O F:HOH501 2.3 44.6 1.0 OE2 F:GLU90 4.0 74.8 1.0 O F:ALA84 4.2 46.5 1.0 O F:LEU86 4.3 44.3 1.0 O F:GLY115 4.5 39.8 1.0 O F:GLU85 4.7 43.8 1.0 CA F:GLY115 4.7 47.1 1.0 CD F:GLU90 4.8 75.3 1.0 C F:GLU85 4.9 51.4 1.0 C F:LEU86 5.0 44.2 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Bordetella Pertussis (Nad Bound) within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg402 b:31.7 occ:1.00 O H:HOH563 1.9 28.7 1.0 O H:HOH513 1.9 27.8 1.0 O H:HOH520 2.0 26.2 1.0 OE2 H:GLU90 3.8 58.4 1.0 O H:LEU86 3.8 30.1 1.0 O H:GLU85 4.2 43.3 1.0 O H:HOH501 4.3 24.4 1.0 O H:ALA84 4.3 36.3 1.0 O H:GLY115 4.4 32.3 1.0 C H:LEU86 4.4 32.2 1.0 CA H:PRO87 4.4 37.2 1.0 C H:GLU85 4.5 39.6 1.0 N H:PRO87 4.8 30.4 1.0 CD H:GLU90 4.8 59.2 1.0 CA H:GLY115 4.8 37.2 1.0 CA H:GLU85 4.9 33.4 1.0

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