Magnesium in PDB 5ex5: Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with 7-Deaza-Adp and Inorganic Phosphate

The structure of Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with 7-Deaza-Adp and Inorganic Phosphate, PDB code: 5ex5 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)	37.87 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.270, 74.709, 88.722, 90.00, 98.38, 90.00
R / Rfree (%)	17.1 / 21.2

The binding sites of Magnesium atom in the Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with 7-Deaza-Adp and Inorganic Phosphate (pdb code 5ex5). 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 7-Deaza-Adp and Inorganic Phosphate, PDB code: 5ex5:
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 7-Deaza-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 7-Deaza-Adp and Inorganic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:13.7 occ:1.00 O3B A:7DD503 2.0 10.9 1.0 O3 A:PO4502 2.0 13.1 1.0 O A:HOH620 2.1 13.6 1.0 O A:HOH693 2.1 17.2 1.0 O A:HOH643 2.1 12.8 1.0 O A:HOH612 2.2 13.3 1.0 PB A:7DD503 3.2 11.8 1.0 P A:PO4502 3.3 14.0 1.0 O A:HOH603 3.4 4.7 1.0 O2B A:7DD503 3.5 13.7 1.0 O2 A:PO4502 3.5 14.1 1.0 O A:HOH601 3.6 21.7 1.0 O2A A:7DD503 3.8 11.0 1.0 O1 A:PO4502 4.0 12.5 1.0 OD1 A:ASP224 4.1 16.0 1.0 OD2 A:ASP224 4.2 19.8 1.0 OE1 A:GLU201 4.2 16.3 1.0 O3A A:7DD503 4.3 12.7 1.0 O1B A:7DD503 4.3 10.8 1.0 OD2 A:ASP34 4.4 17.0 1.0 OD1 A:ASP34 4.4 11.6 1.0 O4 A:PO4502 4.5 16.2 1.0 CG A:ASP224 4.6 18.9 1.0 PA A:7DD503 4.6 10.8 1.0 CG A:ASP34 4.8 10.7 1.0 O A:HOH752 4.9 13.4 1.0 CD A:GLU201 4.9 14.9 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 7-Deaza-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 7-Deaza-Adp and Inorganic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:19.8 occ:1.00 O2B B:7DD503 2.0 16.0 1.0 O4 B:PO4502 2.0 15.4 1.0 O B:HOH624 2.0 20.3 1.0 O B:HOH622 2.2 15.8 1.0 O B:HOH608 2.2 19.6 1.0 O B:HOH691 2.2 21.2 1.0 PB B:7DD503 3.2 14.9 1.0 P B:PO4502 3.3 17.8 1.0 O B:HOH601 3.4 26.4 1.0 O B:HOH602 3.4 6.7 1.0 O2 B:PO4502 3.5 16.9 1.0 O1B B:7DD503 3.6 17.4 1.0 O1A B:7DD503 3.9 12.5 1.0 O3 B:PO4502 4.0 19.5 1.0 OD2 B:ASP224 4.1 25.1 1.0 OD1 B:ASP224 4.2 22.9 1.0 OE1 B:GLU201 4.2 16.1 1.0 O3B B:7DD503 4.3 11.8 1.0 O3A B:7DD503 4.3 16.0 1.0 OD2 B:ASP34 4.3 17.9 1.0 O1 B:PO4502 4.4 17.1 1.0 OD1 B:ASP34 4.5 18.1 1.0 O B:HOH730 4.5 26.5 1.0 CG B:ASP224 4.6 23.0 1.0 PA B:7DD503 4.7 15.0 1.0 CG B:ASP34 4.9 16.3 1.0 CD B:GLU201 5.0 17.6 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