Magnesium in PDB 5oat: PINK1 Structure

The structure of PINK1 Structure, PDB code: 5oat was solved by A.Kumar, J.Tamjar, H.I.Woodroof, O.G.Raimi, A.Y.Waddell, M.Peggie, M.M.K.Muqit, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	178.84 / 2.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.915, 116.736, 179.344, 90.00, 94.29, 90.00
R / Rfree (%)	20.5 / 24.6

The binding sites of Magnesium atom in the PINK1 Structure (pdb code 5oat). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the PINK1 Structure, PDB code: 5oat:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the PINK1 Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PINK1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:73.7 occ:1.00 OD1 A:ASP359 3.2 73.8 1.0 OD2 A:ASP359 3.5 88.6 1.0 CG A:ASP359 3.8 80.5 1.0 OE2 A:GLU217 4.3 0.8 1.0 OD2 B:ASP229 4.4 0.4 1.0 CA A:GLY361 4.7 51.0 1.0

Magnesium binding site 2 out of 6 in the PINK1 Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PINK1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:68.7 occ:1.00 OD2 C:ASP229 2.9 90.7 1.0 OD1 B:ASP359 3.5 76.8 1.0 OE2 B:GLU217 3.8 85.3 1.0 OD2 B:ASP359 3.9 0.2 1.0 CG C:ASP229 3.9 0.2 1.0 CB C:ASP229 4.1 0.5 1.0 CG B:ASP359 4.1 89.6 1.0 CA B:GLY361 4.4 42.5 1.0 CD B:GLU217 4.8 87.5 1.0 C B:GLY361 4.9 44.7 1.0 N B:GLY361 5.0 39.9 1.0

Magnesium binding site 3 out of 6 in the PINK1 Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PINK1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:92.8 occ:1.00 OD2 C:ASP359 3.8 0.4 1.0 OD1 C:ASP359 3.9 79.8 1.0 CG C:ASP359 4.3 87.7 1.0 OE2 C:GLU217 4.5 92.0 1.0

Magnesium binding site 4 out of 6 in the PINK1 Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PINK1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:81.6 occ:1.00 OD2 E:ASP229 3.4 0.5 1.0 CG E:ASP229 4.4 0.2 1.0 CB E:ASP229 4.6 0.3 1.0

Magnesium binding site 5 out of 6 in the PINK1 Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of PINK1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:98.5 occ:1.00 OD1 E:ASP359 3.0 90.5 1.0 OD2 E:ASP359 3.4 99.1 1.0 CG E:ASP359 3.6 0.0 1.0 OE2 E:GLU217 3.8 95.9 1.0 CA E:GLY361 4.2 46.8 1.0 CD E:GLU217 4.6 0.6 1.0 N E:GLY361 4.7 45.1 1.0 C E:GLY361 4.7 44.8 1.0 SG E:CYS362 4.9 62.8 1.0

Magnesium binding site 6 out of 6 in the PINK1 Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of PINK1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:74.4 occ:1.00 OD2 F:ASP229 2.5 0.4 1.0 CG F:ASP229 3.5 0.4 1.0 OD1 D:ASP359 3.6 89.1 1.0 CB F:ASP229 3.7 0.3 1.0 OD2 D:ASP359 3.9 0.7 1.0 OE2 D:GLU217 4.1 85.0 1.0 CG D:ASP359 4.2 93.8 1.0 CA D:GLY361 4.4 43.8 1.0 OD1 F:ASP229 4.7 0.7 1.0 CD D:GLU217 4.9 93.5 1.0 C D:GLY361 5.0 46.6 1.0

A.Kumar, J.Tamjar, A.D.Waddell, H.I.Woodroof, O.G.Raimi, A.M.Shaw, M.Peggie, M.M.Muqit, D.M.Van Aalten. Structure of PINK1 and Mechanisms of Parkinson'S Disease Associated Mutations. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28980524
DOI: 10.7554/ELIFE.29985