Magnesium in PDB 5umb: Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound

The structure of Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound, PDB code: 5umb was solved by Y.Chen, T.Antoshchenko, J.C.Pizarro, J.H.Song, H.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.08 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.531, 112.264, 93.157, 90, 90.13, 90
R / Rfree (%)	22.7 / 26.5

The binding sites of Magnesium atom in the Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound (pdb code 5umb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound, PDB code: 5umb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound


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 Atpase Domain of Malaria GRP78 with Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:22.1 occ:1.00 O3B A:ADP503 2.2 13.9 1.0 O A:HOH641 2.3 11.0 1.0 O A:HOH610 2.7 18.8 1.0 O A:HOH635 3.3 9.1 1.0 O3 A:PO4502 3.3 18.3 1.0 OD2 A:ASP34 3.6 47.6 1.0 PB A:ADP503 3.7 17.3 1.0 O4 A:PO4502 3.7 15.2 1.0 P A:PO4502 3.9 20.2 1.0 O2 A:PO4502 3.9 24.2 1.0 O1A A:ADP503 4.1 18.9 1.0 OD1 A:ASP34 4.1 36.3 1.0 OD1 A:ASP221 4.3 34.2 1.0 CG A:ASP34 4.3 36.8 1.0 O3A A:ADP503 4.4 23.1 1.0 O1B A:ADP503 4.4 22.7 1.0 OE1 A:GLU199 4.5 33.2 1.0 OD2 A:ASP221 4.6 37.4 1.0 O2B A:ADP503 4.7 16.9 1.0 CD A:GLU199 4.8 38.2 1.0 PA A:ADP503 4.8 19.9 1.0 CG A:ASP221 4.9 31.4 1.0 CA A:GLY36 4.9 22.5 1.0 CG2 A:VAL391 4.9 21.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound


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 Atpase Domain of Malaria GRP78 with Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:21.1 occ:1.00 O3 B:PO4502 1.9 14.4 1.0 O2B B:ADP503 1.9 24.7 1.0 O B:HOH631 1.9 37.1 1.0 O B:HOH652 2.1 41.4 1.0 O B:HOH640 2.2 4.6 1.0 O B:HOH689 2.3 19.6 1.0 P B:PO4502 3.2 15.2 1.0 PB B:ADP503 3.3 29.3 1.0 O1 B:PO4502 3.4 22.8 1.0 O3B B:ADP503 3.8 31.9 1.0 O B:HOH654 3.9 11.8 1.0 OD1 B:ASP221 4.0 49.0 1.0 O2 B:PO4502 4.0 4.9 1.0 O3A B:ADP503 4.2 34.6 1.0 OE1 B:GLU199 4.2 13.9 1.0 O2A B:ADP503 4.3 34.5 1.0 O1B B:ADP503 4.3 28.8 1.0 O4 B:PO4502 4.4 10.8 1.0 O B:HOH603 4.5 14.2 1.0 OD1 B:ASP34 4.5 27.0 1.0 OD2 B:ASP221 4.5 58.4 1.0 OD2 B:ASP34 4.6 13.6 1.0 CG B:ASP221 4.7 46.8 1.0 CD B:GLU199 4.8 35.9 1.0 CA B:GLY36 4.9 13.3 1.0 O B:HOH611 4.9 44.7 1.0 PA B:ADP503 4.9 33.1 1.0 CG B:ASP34 5.0 21.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:26.5 occ:1.00 O3 C:PO4502 2.5 30.0 1.0 O C:HOH637 2.5 32.2 1.0 O C:HOH604 2.6 17.9 1.0 O3B C:ADP503 2.9 15.4 1.0 OD1 C:ASP221 3.6 50.1 1.0 P C:PO4502 3.6 29.4 1.0 OD2 C:ASP221 3.6 59.9 1.0 OE1 C:GLU199 3.7 7.9 1.0 O C:HOH618 3.7 26.2 1.0 O4 C:PO4502 3.9 29.1 1.0 O C:HOH608 3.9 17.6 1.0 CG C:ASP221 4.0 48.0 1.0 O2 C:PO4502 4.0 29.4 1.0 CD C:GLU199 4.2 27.3 1.0 O C:HOH615 4.2 22.4 1.0 OD1 C:ASP34 4.5 33.2 1.0 PB C:ADP503 4.5 20.5 1.0 O1A C:ADP503 4.5 27.7 1.0 OD2 C:ASP34 4.6 27.9 1.0 CG1 C:VAL359 4.7 27.0 1.0 CG2 C:VAL391 4.7 27.2 1.0 OE2 C:GLU199 4.7 30.3 1.0 CG C:GLU199 4.8 26.0 1.0 CG C:ASP34 4.9 30.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Atpase Domain of Malaria GRP78 with Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:3.9 occ:1.00 O2B D:ADP503 2.0 12.5 1.0 O3 D:PO4502 2.1 13.8 1.0 O D:HOH630 2.1 4.0 1.0 O D:HOH640 2.2 4.0 1.0 O D:HOH735 2.4 20.7 1.0 O D:HOH604 2.9 18.2 1.0 PB D:ADP503 2.9 13.8 1.0 O3B D:ADP503 3.1 12.7 1.0 P D:PO4502 3.5 13.1 1.0 O3A D:ADP503 3.8 21.4 1.0 O1 D:PO4502 3.8 21.1 1.0 O2A D:ADP503 3.9 10.7 1.0 O D:HOH617 4.0 14.8 1.0 OD1 D:ASP221 4.2 34.8 1.0 OD2 D:ASP34 4.2 21.3 1.0 O1B D:ADP503 4.3 12.5 1.0 OD1 D:ASP34 4.3 26.4 1.0 O4 D:PO4502 4.4 8.1 1.0 O2 D:PO4502 4.4 12.1 1.0 PA D:ADP503 4.5 16.1 1.0 O D:HOH702 4.7 28.9 1.0 CG D:ASP34 4.7 22.0 1.0 OE1 D:GLU199 4.7 33.0 1.0 OD2 D:ASP221 4.8 37.2 1.0 CA D:GLY36 4.8 13.5 1.0 CG D:ASP221 4.9 32.3 1.0

Y.Chen, C.Murillo-Solano, M.G.Kirkpatrick, T.Antoshchenko, H.W.Park, J.C.Pizarro. Repurposing Drugs to Target the Malaria Parasite Unfolding Protein Response. Sci Rep V. 8 10333 2018.
ISSN: ESSN 2045-2322
PubMed: 29985421
DOI: 10.1038/S41598-018-28608-2