Magnesium in PDB 5f0x: Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with 2'-Deoxy-Adp and Inorganic Phosphate

The structure of Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with 2'-Deoxy-Adp and Inorganic Phosphate, PDB code: 5f0x 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)	37.95 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.347, 74.448, 85.882, 90.00, 97.67, 90.00
R / Rfree (%)	17.4 / 20.4

The binding sites of Magnesium atom in the Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with 2'-Deoxy-Adp and Inorganic Phosphate (pdb code 5f0x). 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 2'-Deoxy-Adp and Inorganic Phosphate, PDB code: 5f0x:
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 2'-Deoxy-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 2'-Deoxy-Adp and Inorganic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:27.0 occ:1.00 O4 A:PO4502 2.0 24.5 1.0 O A:HOH615 2.0 26.9 1.0 O A:HOH605 2.2 19.3 1.0 O A:HOH662 2.2 29.7 1.0 O A:HOH665 2.4 18.2 1.0 P A:PO4502 3.2 28.9 1.0 O3 A:PO4502 3.4 19.1 1.0 O A:HOH620 3.7 23.6 1.0 OD1 A:ASP224 3.9 16.7 1.0 OD2 A:ASP224 4.0 21.4 1.0 O1 A:PO4502 4.0 24.0 1.0 OE1 A:GLU201 4.2 15.5 1.0 O A:HOH816 4.2 20.5 1.0 OD2 A:ASP34 4.3 15.8 1.0 OD1 A:ASP34 4.4 11.2 1.0 CG A:ASP224 4.4 19.1 1.0 O2 A:PO4502 4.4 25.4 1.0 CD A:GLU201 4.7 13.9 1.0 CG A:ASP34 4.8 11.5 1.0 CG1 A:VAL362 4.9 12.8 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 2'-Deoxy-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 2'-Deoxy-Adp and Inorganic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:12.9 occ:1.00 O3B B:DAT504 2.0 14.8 1.0 O B:HOH627 2.1 16.6 1.0 O B:HOH621 2.1 15.9 1.0 O4 B:PO4502 2.1 14.5 1.0 O B:HOH614 2.1 17.0 1.0 O B:HOH651 2.1 21.0 1.0 PB B:DAT504 3.3 16.2 1.0 P B:PO4502 3.3 16.6 1.0 O B:HOH603 3.4 7.4 1.0 O B:HOH601 3.4 9.4 0.8 O1 B:PO4502 3.6 13.6 1.0 O2B B:DAT504 3.6 20.8 1.0 O2A B:DAT504 3.8 14.7 1.0 O3 B:PO4502 4.1 17.5 1.0 OD2 B:ASP224 4.2 19.9 1.0 OD1 B:ASP224 4.2 16.3 1.0 O1B B:DAT504 4.3 16.8 1.0 O3A B:DAT504 4.3 16.2 1.0 OD2 B:ASP34 4.3 13.2 1.0 OE1 B:GLU201 4.4 13.4 1.0 O B:HOH849 4.5 19.2 1.0 O2 B:PO4502 4.5 18.3 1.0 OD1 B:ASP34 4.5 12.2 1.0 CG B:ASP224 4.6 18.7 1.0 PA B:DAT504 4.7 14.7 1.0 CG B:ASP34 4.9 12.2 1.0 O B:HOH746 4.9 15.5 1.0 O B:HOH749 5.0 15.2 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