Magnesium in PDB 5vbi: Crystal Structure of the R515W Missense Variant of Human PGM1

All present enzymatic activity of Crystal Structure of the R515W Missense Variant of Human PGM1:
5.4.2.2;

The structure of Crystal Structure of the R515W Missense Variant of Human PGM1, PDB code: 5vbi was solved by K.M.Stiers, L.J.Beamer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.50 / 1.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	172.330, 172.330, 99.370, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.1

The binding sites of Magnesium atom in the Crystal Structure of the R515W Missense Variant of Human PGM1 (pdb code 5vbi). 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 R515W Missense Variant of Human PGM1, PDB code: 5vbi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the R515W 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 R515W Missense Variant of Human PGM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:12.3 occ:0.70 O A:HOH899 2.0 16.8 0.6 OD1 A:ASP292 2.0 17.1 1.0 OD1 A:ASP288 2.0 17.0 1.0 OG A:SEP117 2.0 20.6 0.4 OG A:SEP117 2.1 19.8 0.6 OD2 A:ASP290 2.2 18.9 1.0 O A:HOH762 2.2 20.0 1.0 O1P A:SEP117 2.3 32.5 0.4 P A:SEP117 2.7 24.7 0.4 CG A:ASP292 3.0 20.0 1.0 CG A:ASP288 3.1 18.9 1.0 CG A:ASP290 3.1 19.3 1.0 CB A:SEP117 3.2 21.1 0.6 CB A:SEP117 3.3 20.6 0.4 OD1 A:ASP290 3.4 18.0 1.0 OD2 A:ASP292 3.4 20.5 1.0 OD2 A:ASP288 3.6 16.0 1.0 O3P A:SEP117 3.8 36.9 0.4 O A:HOH704 3.8 24.9 0.6 O2P A:SEP117 3.8 15.0 0.4 CA A:SEP117 3.9 19.5 0.4 CA A:SEP117 4.0 19.2 0.6 O A:HOH831 4.2 49.1 1.0 NE A:ARG293 4.3 28.7 1.0 CB A:ASP292 4.3 18.6 1.0 O A:HOH724 4.3 36.6 1.0 N A:ASP292 4.3 15.3 1.0 CB A:ASP288 4.4 13.2 1.0 CG A:ARG293 4.4 25.4 1.0 CB A:ASP290 4.5 14.2 1.0 C A:SEP117 4.6 20.1 0.4 C A:SEP117 4.6 20.4 0.6 N A:HIS118 4.7 18.2 1.0 N A:ASP290 4.7 14.4 1.0 CA A:ASP292 4.7 15.6 1.0 N A:ARG293 4.7 13.2 1.0 CD A:ARG293 4.8 29.6 1.0 C A:ASP292 4.8 16.9 1.0 N A:GLY291 4.9 14.9 1.0 CA A:ASP290 4.9 15.5 1.0 CB A:ARG293 5.0 22.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the R515W 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 R515W Missense Variant of Human PGM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:13.3 occ:0.59 OD1 B:ASP292 2.0 29.4 1.0 O B:HOH761 2.0 24.5 1.0 OD2 B:ASP288 2.0 23.7 1.0 OG B:SEP117 2.0 31.9 0.3 O1P B:SEP117 2.1 41.1 0.3 OG B:SEP117 2.1 30.9 0.7 O B:HOH873 2.1 26.8 0.7 OD1 B:ASP290 2.2 25.4 1.0 P B:SEP117 2.5 44.9 0.3 CG B:ASP292 3.0 29.9 1.0 CG B:ASP290 3.1 30.3 1.0 CB B:SEP117 3.1 29.3 0.3 CG B:ASP288 3.1 24.2 1.0 CB B:SEP117 3.2 28.5 0.7 OD2 B:ASP290 3.3 26.7 1.0 OD2 B:ASP292 3.4 29.7 1.0 OD1 B:ASP288 3.6 22.5 1.0 O3P B:SEP117 3.7 54.8 0.3 O B:HOH702 3.7 34.2 0.7 O2P B:SEP117 3.7 51.8 0.3 CA B:SEP117 3.9 28.5 0.3 CA B:SEP117 3.9 28.2 0.7 O B:HOH1037 4.1 37.7 0.7 CG B:ARG293 4.2 27.3 1.0 N B:ASP292 4.3 23.6 1.0 CB B:ASP292 4.3 22.7 1.0 CB B:ASP288 4.4 25.1 1.0 C B:SEP117 4.5 32.2 0.7 C B:SEP117 4.5 31.4 0.3 N B:HIS118 4.5 26.4 1.0 CB B:ASP290 4.5 24.3 1.0 CA B:ASP292 4.7 24.5 1.0 N B:ARG293 4.7 21.8 1.0 N B:ASP290 4.8 21.4 1.0 C B:ASP292 4.8 24.2 1.0 NE B:ARG293 4.9 44.6 1.0 CD B:ARG293 4.9 42.0 1.0 N B:GLY291 5.0 19.1 1.0

K.M.Stiers, L.J.Beamer. A Hotspot For Disease-Associated Variants of Human PGM1 Is Associated with Impaired Ligand Binding and Loop Dynamics. Structure V. 26 1337 2018.
ISSN: ISSN 1878-4186
PubMed: 30122451
DOI: 10.1016/J.STR.2018.07.005