Calcium in PDB 5jn5: Crystal Structure of the D263Y Missense Variant of Human PGM1

All present enzymatic activity of Crystal Structure of the D263Y Missense Variant of Human PGM1:
5.4.2.2;

The structure of Crystal Structure of the D263Y Missense Variant of Human PGM1, PDB code: 5jn5 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)	54.70 / 1.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	172.988, 172.988, 100.001, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.9

The binding sites of Calcium atom in the Crystal Structure of the D263Y Missense Variant of Human PGM1 (pdb code 5jn5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the D263Y Missense Variant of Human PGM1, PDB code: 5jn5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the D263Y Missense Variant of Human PGM1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the D263Y Missense Variant of Human PGM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:9.5 occ:1.00 OD1 A:ASP292 2.0 15.3 1.0 OD1 A:ASP290 2.1 14.4 1.0 OD2 A:ASP288 2.1 12.7 1.0 O1P A:SEP117 2.1 26.4 0.8 CG A:ASP292 3.0 18.5 1.0 CG A:ASP290 3.0 15.6 1.0 CG A:ASP288 3.0 12.8 1.0 OG A:SEP117 3.0 24.6 0.8 P A:SEP117 3.1 31.3 0.8 OD2 A:ASP290 3.2 20.2 1.0 OD1 A:ASP288 3.3 12.6 1.0 OD2 A:ASP292 3.4 16.8 1.0 CB A:SEP117 3.7 25.4 0.8 O3P A:SEP117 3.8 31.2 0.8 O A:HOH835 3.9 28.9 1.0 CA A:SEP117 4.1 18.1 0.8 N A:ASP292 4.2 11.1 1.0 CB A:ASP292 4.3 13.1 1.0 CB A:ASP288 4.3 9.8 1.0 CB A:ASP290 4.4 13.2 1.0 O2P A:SEP117 4.4 28.1 0.8 NE A:ARG293 4.5 22.1 1.0 CG A:ARG293 4.5 12.9 1.0 N A:ASP290 4.5 10.0 1.0 O A:HOH701 4.6 40.5 1.0 N A:ARG293 4.6 10.1 1.0 CA A:ASP292 4.6 12.0 1.0 O A:HOH1061 4.6 31.7 1.0 N A:HIS118 4.7 19.5 1.0 C A:SEP117 4.7 18.7 0.8 CD A:ARG293 4.7 17.9 1.0 C A:ASP292 4.7 13.3 1.0 N A:GLY291 4.8 11.8 1.0 CA A:ASP290 4.8 13.2 1.0 C A:ASP290 4.9 12.1 1.0 CB A:ARG293 4.9 10.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the D263Y Missense Variant of Human PGM1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the D263Y Missense Variant of Human PGM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:15.3 occ:1.00 OD2 B:ASP292 1.9 19.3 1.0 OD1 B:ASP288 2.0 20.4 1.0 OD1 B:ASP290 2.1 20.2 1.0 O3P B:SEP117 2.3 39.1 0.8 OG B:SEP117 2.6 36.1 0.8 CG B:ASP292 2.9 20.9 1.0 CG B:ASP288 3.0 24.9 1.0 P B:SEP117 3.0 38.3 0.8 CG B:ASP290 3.0 21.3 1.0 OD2 B:ASP288 3.3 18.1 1.0 OD2 B:ASP290 3.3 21.2 1.0 OD1 B:ASP292 3.3 20.9 1.0 CB B:SEP117 3.7 28.1 0.8 O B:HOH883 3.9 32.3 1.0 O1P B:SEP117 4.0 38.6 0.8 CA B:SEP117 4.0 22.7 0.8 N B:ASP292 4.1 15.0 1.0 CG B:ARG293 4.2 17.8 1.0 CB B:ASP292 4.2 16.1 1.0 O2P B:SEP117 4.3 38.7 0.8 CB B:ASP288 4.3 18.3 1.0 O B:HOH719 4.3 39.9 1.0 N B:HIS118 4.4 22.9 1.0 C B:SEP117 4.4 21.2 0.8 NE B:ARG293 4.5 29.6 1.0 CB B:ASP290 4.5 17.6 1.0 N B:ARG293 4.5 15.8 1.0 CA B:ASP292 4.5 16.4 1.0 N B:ASP290 4.6 17.9 1.0 C B:ASP292 4.6 19.7 1.0 CD B:ARG293 4.7 26.8 1.0 N B:GLY291 4.8 15.0 1.0 CA B:ASP290 4.9 16.6 1.0 C B:ASP290 4.9 16.6 1.0 CB B:ARG293 4.9 18.4 1.0

K.M.Stiers, A.C.Graham, B.N.Kain, L.J.Beamer. ASP263 Missense Variants Perturb the Active Site of Human Phosphoglucomutase 1. Febs J. V. 284 937 2017.
ISSN: ISSN 1742-4658
PubMed: 28117557
DOI: 10.1111/FEBS.14025