Magnesium in PDB 2pnq: Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 (PDP1)

All present enzymatic activity of Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 (PDP1):
3.1.3.43;

The structure of Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 (PDP1), PDB code: 2pnq was solved by D.G.Vassylyev, J.Symersky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.318, 72.220, 96.094, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.6

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 (PDP1) (pdb code 2pnq). 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 Pyruvate Dehydrogenase Phosphatase 1 (PDP1), PDB code: 2pnq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 (PDP1)


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 Pyruvate Dehydrogenase Phosphatase 1 (PDP1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:30.6 occ:1.00 O A:HOH503 2.1 30.7 1.0 OD1 A:ASP73 2.1 31.6 1.0 O A:HOH505 2.2 29.1 1.0 O A:GLY74 2.2 29.7 1.0 O A:HOH506 2.2 31.8 1.0 CG A:ASP73 3.1 31.2 1.0 C A:GLY74 3.4 30.3 1.0 OD2 A:ASP73 3.5 31.3 1.0 MG A:MG502 3.7 30.8 1.0 O A:HOH511 3.8 30.6 1.0 N A:GLY74 3.9 29.2 1.0 OE1 A:GLU53 4.0 37.3 1.0 OD1 A:ASP54 4.1 27.3 1.0 C A:ASP73 4.1 29.4 1.0 O A:HOH504 4.2 30.1 1.0 CA A:GLY74 4.2 29.3 1.0 CB A:GLU53 4.3 31.7 1.0 N A:HIS75 4.3 28.8 1.0 OD1 A:ASP445 4.3 30.5 1.0 CB A:ASP73 4.4 29.0 1.0 O A:HOH507 4.4 31.4 1.0 CA A:HIS75 4.4 28.1 1.0 CB A:HIS75 4.4 26.1 1.0 CA A:ASP73 4.5 28.8 1.0 O A:ASP73 4.5 29.8 1.0 OD2 A:ASP446 4.5 37.5 1.0 CD A:GLU53 4.9 36.0 1.0 OD2 A:ASP445 5.0 33.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 (PDP1)


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 Pyruvate Dehydrogenase Phosphatase 1 (PDP1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.8 occ:1.00 OD1 A:ASP347 2.1 32.0 1.0 O A:HOH503 2.1 30.7 1.0 OD2 A:ASP445 2.1 33.1 1.0 OD2 A:ASP73 2.2 31.3 1.0 O A:HOH507 2.2 31.4 1.0 O A:HOH504 2.2 30.1 1.0 CG A:ASP347 2.9 31.9 1.0 CG A:ASP445 3.1 32.9 1.0 CG A:ASP73 3.1 31.2 1.0 OD2 A:ASP347 3.2 32.9 1.0 OD1 A:ASP445 3.4 30.5 1.0 OD1 A:ASP73 3.4 31.6 1.0 MG A:MG501 3.7 30.6 1.0 O A:HOH509 4.1 22.1 1.0 N A:GLY348 4.2 27.0 1.0 CB A:ASP347 4.3 28.7 1.0 OD1 A:ASP54 4.4 27.3 1.0 N A:ASP347 4.4 26.0 1.0 CB A:ASP73 4.4 29.0 1.0 O A:HOH524 4.4 21.3 1.0 CB A:ASP445 4.5 32.0 1.0 O A:ASP446 4.5 31.1 1.0 O A:HOH506 4.5 31.8 1.0 CB A:THR346 4.5 25.5 1.0 C A:ASP347 4.6 27.8 1.0 O A:HOH650 4.7 42.6 1.0 CA A:ASP347 4.7 26.5 1.0 OG1 A:THR346 4.8 24.5 1.0 CA A:GLY348 4.8 27.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 (PDP1)


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 Pyruvate Dehydrogenase Phosphatase 1 (PDP1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:21.8 occ:1.00 OD1 B:ASP73 2.1 20.9 1.0 O B:GLY74 2.1 23.4 1.0 O B:HOH505 2.1 19.9 1.0 O B:HOH507 2.1 20.4 1.0 O B:HOH508 2.1 20.7 1.0 CG B:ASP73 3.2 21.7 1.0 C B:GLY74 3.3 24.8 1.0 OD2 B:ASP73 3.6 21.1 1.0 MG B:MG504 3.8 20.6 1.0 N B:GLY74 3.8 22.1 1.0 OD1 B:ASP54 3.9 39.5 1.0 CB B:GLU53 4.0 40.2 1.0 OE1 B:GLU53 4.1 45.2 1.0 C B:ASP73 4.1 22.5 1.0 CA B:GLY74 4.1 23.7 1.0 N B:HIS75 4.2 27.2 1.0 CA B:HIS75 4.2 28.9 1.0 O B:HOH506 4.3 21.6 1.0 CB B:HIS75 4.3 29.2 1.0 CB B:ASP73 4.4 20.4 1.0 O B:HOH509 4.5 20.3 1.0 OD1 B:ASP445 4.5 24.4 1.0 O B:ASP73 4.5 20.8 1.0 CA B:ASP73 4.6 21.3 1.0 OD2 B:ASP446 4.9 24.9 1.0 CG B:GLU53 4.9 42.6 1.0 C B:GLU53 4.9 38.5 1.0 CD B:GLU53 5.0 43.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 (PDP1)


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 Pyruvate Dehydrogenase Phosphatase 1 (PDP1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:20.6 occ:1.00 OD2 B:ASP73 2.1 21.1 1.0 O B:HOH505 2.1 19.9 1.0 OD2 B:ASP445 2.1 24.0 1.0 OD1 B:ASP347 2.1 22.4 1.0 O B:HOH509 2.1 20.3 1.0 O B:HOH506 2.2 21.6 1.0 CG B:ASP445 3.0 25.9 1.0 CG B:ASP347 3.1 23.2 1.0 CG B:ASP73 3.2 21.7 1.0 OD1 B:ASP445 3.3 24.4 1.0 OD2 B:ASP347 3.4 21.4 1.0 OD1 B:ASP73 3.5 20.9 1.0 MG B:MG503 3.8 21.8 1.0 N B:GLY348 4.4 25.8 1.0 CB B:ASP445 4.4 25.0 1.0 OD1 B:ASP54 4.4 39.5 1.0 O B:HOH524 4.4 33.9 1.0 CB B:ASP73 4.5 20.4 1.0 CB B:ASP347 4.5 22.2 1.0 O B:HOH508 4.6 20.7 1.0 O B:ASP446 4.6 24.7 1.0 N B:ASP347 4.7 23.1 1.0 C B:ASP347 4.8 25.0 1.0 CB B:THR346 4.8 23.0 1.0 CA B:ASP347 4.9 23.3 1.0 CA B:GLY348 4.9 28.8 1.0

D.G.Vassylyev, J.Symersky. Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 and Its Functional Implications. J.Mol.Biol. V. 370 417 2007.
ISSN: ISSN 0022-2836
PubMed: 17532339
DOI: 10.1016/J.JMB.2007.05.002