Magnesium in PDB 5evz: Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Inorganic Phosphate

The structure of Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Inorganic Phosphate, PDB code: 5evz was solved by S.J.Hughes, T.Antoshchenko, J.H.Song, J.Pizarro, H.W.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.31 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.550, 74.802, 89.220, 90.00, 98.60, 90.00
R / Rfree (%)	16.5 / 20.5

The binding sites of Magnesium atom in the Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Inorganic Phosphate (pdb code 5evz). 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 Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Inorganic Phosphate, PDB code: 5evz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Inorganic Phosphate


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 Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Inorganic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:16.7 occ:1.00 O1B A:ADP503 2.0 15.5 1.0 O3 A:PO4502 2.0 17.7 1.0 O A:HOH653 2.0 18.8 1.0 O A:HOH692 2.1 15.8 1.0 O A:HOH622 2.1 15.9 1.0 O A:HOH673 2.2 19.6 1.0 PB A:ADP503 3.2 16.9 1.0 P A:PO4502 3.3 17.9 1.0 O A:HOH602 3.3 8.7 1.0 O A:HOH603 3.4 15.0 1.0 O3B A:ADP503 3.6 18.2 1.0 O2 A:PO4502 3.6 16.7 1.0 O1A A:ADP503 3.8 18.1 1.0 O1 A:PO4502 4.1 17.1 1.0 OD1 A:ASP224 4.1 19.7 1.0 OD2 A:ASP224 4.2 21.4 1.0 OE1 A:GLU201 4.2 19.7 1.0 O3A A:ADP503 4.3 17.4 1.0 O2B A:ADP503 4.4 15.3 1.0 O A:HOH813 4.4 20.6 1.0 O4 A:PO4502 4.4 20.5 1.0 OD2 A:ASP34 4.4 18.9 1.0 CG A:ASP224 4.6 22.3 1.0 OD1 A:ASP34 4.6 16.8 1.0 PA A:ADP503 4.6 17.7 1.0 O A:HOH781 4.9 19.4 1.0 CG A:ASP34 5.0 16.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Inorganic Phosphate


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 Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Adp and Inorganic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:19.7 occ:1.00 O4 B:PO4501 2.0 17.1 1.0 O3B B:ADP503 2.0 18.5 1.0 O B:HOH654 2.1 16.8 1.0 O B:HOH622 2.1 17.3 1.0 O B:HOH614 2.1 18.4 1.0 O B:HOH669 2.2 18.7 1.0 PB B:ADP503 3.3 19.0 1.0 P B:PO4501 3.3 18.2 1.0 O B:HOH601 3.3 18.1 1.0 O B:HOH603 3.3 10.4 1.0 O2 B:PO4501 3.6 18.4 1.0 O2B B:ADP503 3.6 18.9 1.0 O2A B:ADP503 3.9 18.2 1.0 O3 B:PO4501 4.1 19.9 1.0 OD2 B:ASP224 4.1 24.4 1.0 OD1 B:ASP224 4.1 22.1 1.0 OE1 B:GLU201 4.2 21.6 1.0 O1B B:ADP503 4.3 19.1 1.0 O3A B:ADP503 4.3 19.3 1.0 OD2 B:ASP34 4.4 20.2 1.0 O B:HOH742 4.4 24.3 1.0 O1 B:PO4501 4.5 18.8 1.0 CG B:ASP224 4.6 24.5 1.0 OD1 B:ASP34 4.6 19.0 1.0 PA B:ADP503 4.7 19.4 1.0 CG B:ASP34 4.9 18.9 1.0 O B:HOH696 5.0 22.2 1.0 CD B:GLU201 5.0 21.2 1.0

S.J.Hughes, T.Antoshchenko, Y.Chen, H.Lu, J.C.Pizarro, H.W.Park. Probing the Atp Site of GRP78 with Nucleotide Triphosphate Analogs. Plos One V. 11 54862 2016.
ISSN: ESSN 1932-6203
PubMed: 27144892
DOI: 10.1371/JOURNAL.PONE.0154862