Magnesium in PDB 6uo6: Crystal Structure of the R422Q Missense Variant of Human PGM1

All present enzymatic activity of Crystal Structure of the R422Q Missense Variant of Human PGM1:
5.4.2.2;

The structure of Crystal Structure of the R422Q Missense Variant of Human PGM1, PDB code: 6uo6 was solved by L.J.Beamer, K.M.Stiers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.61 / 2.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	171.804, 171.804, 99.278, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.3

The binding sites of Magnesium atom in the Crystal Structure of the R422Q Missense Variant of Human PGM1 (pdb code 6uo6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the R422Q Missense Variant of Human PGM1, PDB code: 6uo6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the R422Q Missense Variant of Human PGM1


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 the R422Q Missense Variant of Human PGM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:46.0 occ:1.00 OG A:SER117 2.2 48.0 1.0 OD2 A:ASP288 2.2 32.1 1.0 OD1 A:ASP290 2.3 25.6 1.0 OD1 A:ASP292 2.4 42.8 1.0 O A:HOH777 2.4 29.9 1.0 O A:HOH986 2.4 59.0 1.0 CB A:SER117 2.8 37.4 1.0 CG A:ASP290 3.2 23.4 1.0 CG A:ASP288 3.3 29.1 1.0 CG A:ASP292 3.3 36.4 1.0 OD2 A:ASP290 3.4 25.4 1.0 CA A:SER117 3.6 37.2 1.0 OD2 A:ASP292 3.7 30.4 1.0 OD1 A:ASP288 3.9 27.2 1.0 C A:SER117 4.3 33.0 1.0 N A:HIS118 4.3 30.8 1.0 CD A:ARG293 4.4 50.4 1.0 CB A:ASP288 4.4 24.4 1.0 CB A:ASP290 4.6 16.9 1.0 N A:ASP292 4.6 23.3 1.0 CB A:ASP292 4.6 37.2 1.0 N A:ASP290 4.7 24.7 1.0 ND1 A:HIS118 4.7 49.5 1.0 N A:SER117 4.9 31.7 1.0 CA A:ASP292 5.0 30.8 1.0 N A:ARG293 5.0 23.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the R422Q Missense Variant of Human PGM1


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 the R422Q Missense Variant of Human PGM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:55.3 occ:1.00 OG B:SER117 2.0 70.6 1.0 OD1 B:ASP292 2.1 70.0 1.0 OD1 B:ASP290 2.4 48.8 1.0 OD2 B:ASP288 2.5 45.9 1.0 CB B:SER117 2.9 55.7 1.0 CG B:ASP292 3.0 51.4 1.0 CG B:ASP290 3.2 47.4 1.0 OD2 B:ASP290 3.3 51.1 1.0 OD2 B:ASP292 3.4 49.9 1.0 CG B:ASP288 3.6 45.5 1.0 CA B:SER117 3.8 50.0 1.0 OD1 B:ASP288 4.2 36.0 1.0 CB B:ASP292 4.3 45.6 1.0 CG B:ARG293 4.3 51.8 1.0 C B:SER117 4.4 54.0 1.0 N B:HIS118 4.5 52.3 1.0 N B:ASP292 4.6 39.5 1.0 CB B:ASP290 4.6 37.2 1.0 CB B:ASP288 4.8 44.7 1.0 ND1 B:HIS118 4.8 62.4 1.0 CA B:ASP292 4.8 38.3 1.0 N B:ASP290 4.9 38.4 1.0 N B:ARG293 4.9 39.0 1.0 CD B:ARG293 5.0 69.2 1.0 C B:ASP292 5.0 39.3 1.0

K.M.Stiers, R.P.Hansen, B.A.Daghlas, K.N.Mason, J.S.Zhu, D.L.Jakeman, L.J.Beamer. A Missense Variant Remote From the Active Site Impairs Stability of Human Phosphoglucomutase 1. J. Inherit. Metab. Dis. 2020.
ISSN: ISSN 1573-2665
PubMed: 32057119
DOI: 10.1002/JIMD.12222