Cobalt in PDB 5vin: Crystal Structure of the R515Q Missense Variant of Human PGM1

All present enzymatic activity of Crystal Structure of the R515Q Missense Variant of Human PGM1:
5.4.2.2;

The structure of Crystal Structure of the R515Q Missense Variant of Human PGM1, PDB code: 5vin 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)	61.50 / 2.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	173.960, 173.960, 99.483, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 29.5

The binding sites of Cobalt atom in the Crystal Structure of the R515Q Missense Variant of Human PGM1 (pdb code 5vin). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of the R515Q Missense Variant of Human PGM1, PDB code: 5vin:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of the R515Q Missense Variant of Human PGM1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the R515Q Missense Variant of Human PGM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co614 b:55.2 occ:1.00 OG A:SER117 2.0 51.6 1.0 OD2 A:ASP292 2.0 73.1 1.0 OD2 A:ASP288 2.2 54.7 1.0 OD1 A:ASP290 2.4 52.5 1.0 CG A:ASP292 3.0 56.9 1.0 CB A:SER117 3.1 42.4 1.0 CG A:ASP290 3.2 46.7 1.0 OD2 A:ASP290 3.2 47.9 1.0 CG A:ASP288 3.4 55.7 1.0 OD1 A:ASP292 3.4 51.6 1.0 CA A:SER117 3.8 48.2 1.0 OD1 A:ASP288 3.9 57.4 1.0 CD A:ARG293 4.0 62.5 1.0 CB A:ASP292 4.3 44.2 1.0 N A:ASP292 4.4 52.9 1.0 C A:SER117 4.6 53.7 1.0 CB A:ASP288 4.6 50.3 1.0 CG A:ARG293 4.6 53.7 1.0 CB A:ASP290 4.6 47.1 1.0 CA A:ASP292 4.7 45.4 1.0 N A:HIS118 4.8 50.6 1.0 N A:ARG293 4.8 23.6 1.0 ND1 A:HIS118 4.9 92.3 1.0 C A:ASP292 4.9 35.4 1.0 N A:ASP290 5.0 53.6 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of the R515Q Missense Variant of Human PGM1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the R515Q Missense Variant of Human PGM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co607 b:79.5 occ:1.00 OG B:SER117 1.8 0.0 1.0 OD2 B:ASP292 2.0 0.4 1.0 OD1 B:ASP290 2.1 95.1 1.0 OD2 B:ASP288 2.5 87.7 1.0 CB B:SER117 2.9 92.3 1.0 CG B:ASP290 3.0 84.7 1.0 CG B:ASP288 3.1 77.4 1.0 CG B:ASP292 3.1 86.6 1.0 OD2 B:ASP290 3.2 90.4 1.0 OD1 B:ASP288 3.3 89.3 1.0 OD1 B:ASP292 3.5 94.5 1.0 CA B:SER117 3.5 85.0 1.0 C B:SER117 4.1 78.0 1.0 CB B:ASP288 4.2 64.6 1.0 N B:HIS118 4.2 68.0 1.0 ND1 B:HIS118 4.3 94.6 1.0 N B:ASP292 4.4 54.7 1.0 CB B:ASP292 4.4 67.3 1.0 CB B:ASP290 4.5 73.7 1.0 N B:ARG293 4.6 51.8 1.0 N B:ASP290 4.7 66.7 1.0 CA B:ASP292 4.7 54.9 1.0 C B:ASP292 4.8 49.5 1.0 N B:SER117 4.9 79.9 1.0 O B:SER117 4.9 75.6 1.0 CB B:ARG293 4.9 64.3 1.0 O B:HOH722 5.0 64.8 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