Magnesium in PDB 7vpk: Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P State)

The structure of Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P State) also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P State) (pdb code 7vpk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P State), PDB code: 7vpk:

Magnesium binding site 1 out of 1 in the Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P State)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Human ATP13A2 (Spm-Bound E2P State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:63.2 occ:1.00 F2 A:BEF1202 1.8 58.8 1.0 O A:THR515 2.2 62.1 1.0 OD2 A:ASP878 2.4 58.1 1.0 OD2 A:ASP513 2.5 57.5 1.0 BE A:BEF1202 2.7 58.0 1.0 OD1 A:ASP878 2.7 58.1 1.0 CG A:ASP878 2.7 57.8 1.0 C A:THR515 3.4 62.5 1.0 CG A:ASP513 3.4 56.6 1.0 F1 A:BEF1202 3.8 58.2 1.0 OD1 A:ASP513 3.9 57.5 1.0 CB A:ASP878 3.9 57.0 1.0 CA A:THR515 3.9 61.6 1.0 CB A:THR515 3.9 61.6 1.0 F3 A:BEF1202 4.0 58.1 1.0 N A:THR515 4.0 60.9 1.0 O A:GLY347 4.1 111.8 1.0 CA A:GLY347 4.3 108.8 1.0 N A:GLY516 4.5 63.7 1.0 CB A:ASP513 4.5 55.5 1.0 C A:GLY347 4.7 111.8 1.0 CG2 A:THR515 4.7 61.9 1.0 C A:LYS514 4.9 60.1 1.0 OG1 A:THR515 5.0 61.4 1.0 CA A:GLY516 5.0 64.5 1.0

A.Tomita, T.Daiho, T.Kusakizako, K.Yamashita, S.Ogasawara, T.Murata, T.Nishizawa, O.Nureki. Cryo-Em Reveals Mechanistic Insights Into Lipid-Facilitated Polyamine Export By Human ATP13A2. Mol.Cell V. 81 4799 2021.
ISSN: ISSN 1097-2765
PubMed: 34798056
DOI: 10.1016/J.MOLCEL.2021.11.001