Magnesium in PDB 5f2r: Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Amp-Pcp

The structure of Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Amp-Pcp, PDB code: 5f2r 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)	44.00 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.958, 74.549, 88.414, 90.00, 98.15, 90.00
R / Rfree (%)	19.9 / 23.4

The binding sites of Magnesium atom in the Crystal Structure of Human GRP78 (70KDA Heat Shock Protein 5 / Bip) Atpase Domain in Complex with Amp-Pcp (pdb code 5f2r). 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 Amp-Pcp, PDB code: 5f2r:
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 Amp-Pcp


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 Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:23.1 occ:1.00 O A:HOH625 1.9 20.2 1.0 O A:HOH618 2.0 17.6 1.0 O1G A:ACP501 2.1 20.3 1.0 O A:HOH642 2.1 21.2 1.0 O1B A:ACP501 2.1 19.5 1.0 O A:HOH663 2.2 19.6 1.0 PG A:ACP501 3.2 24.9 1.0 PB A:ACP501 3.4 19.9 1.0 O2G A:ACP501 3.5 20.7 1.0 C3B A:ACP501 3.6 23.7 1.0 O A:HOH602 3.8 13.5 1.0 O1A A:ACP501 3.8 24.4 1.0 OD2 A:ASP224 3.8 24.6 1.0 O A:HOH601 3.9 15.3 1.0 OD1 A:ASP224 4.0 21.3 1.0 OE1 A:GLU201 4.1 18.9 1.0 OD2 A:ASP34 4.2 16.6 1.0 O3A A:ACP501 4.2 20.5 1.0 CG A:ASP224 4.4 21.3 1.0 O A:HOH709 4.4 24.3 1.0 OD1 A:ASP34 4.4 16.3 1.0 O2B A:ACP501 4.5 21.2 1.0 PA A:ACP501 4.6 19.3 1.0 O3G A:ACP501 4.6 23.0 1.0 CD A:GLU201 4.6 20.8 1.0 CG A:ASP34 4.7 17.2 1.0 CG2 A:VAL394 4.9 14.7 1.0 CG1 A:VAL362 4.9 22.9 1.0 O A:HOH670 4.9 21.3 1.0 O2A A:ACP501 5.0 26.6 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 Amp-Pcp


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 Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:28.8 occ:1.00 O B:HOH625 1.9 22.5 1.0 O B:HOH616 2.0 30.4 1.0 O2G B:ACP501 2.1 26.2 1.0 O2B B:ACP501 2.1 27.4 1.0 O B:HOH604 2.2 22.6 1.0 O B:HOH607 2.3 21.4 1.0 PG B:ACP501 3.3 25.9 1.0 PB B:ACP501 3.4 26.5 1.0 C3B B:ACP501 3.6 24.0 1.0 O1G B:ACP501 3.7 27.9 1.0 O B:HOH602 3.8 24.4 1.0 OD2 B:ASP224 3.9 28.9 1.0 O B:HOH603 3.9 23.3 1.0 O2A B:ACP501 3.9 24.5 1.0 OE1 B:GLU201 4.0 27.0 1.0 OD1 B:ASP224 4.1 28.2 1.0 OD2 B:ASP34 4.2 22.2 1.0 O3A B:ACP501 4.3 25.3 1.0 OD1 B:ASP34 4.4 24.9 1.0 O1B B:ACP501 4.4 21.3 1.0 CG B:ASP224 4.4 26.6 1.0 O B:HOH648 4.5 23.4 1.0 O3G B:ACP501 4.6 24.1 1.0 CD B:GLU201 4.6 26.9 1.0 PA B:ACP501 4.6 24.9 1.0 CG B:ASP34 4.7 22.6 1.0 O B:HOH620 4.9 22.5 1.0 CG1 B:VAL362 5.0 28.0 1.0 CG2 B:VAL394 5.0 27.2 1.0 OE2 B:GLU201 5.0 24.9 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