Magnesium in PDB 8ijw: Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06

The structure of Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06 (pdb code 8ijw). 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 Gastric Proton Pump with Bound Dq-06, PDB code: 8ijw:

Magnesium binding site 1 out of 1 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06


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 Gastric Proton Pump with Bound Dq-06 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:28.5 occ:1.00 F1 A:BFD385 1.9 38.6 1.0 O A:THR387 2.0 32.2 1.0 OD2 A:BFD385 2.1 35.3 1.0 O A:HOH1210 2.2 28.4 1.0 OD1 A:ASP726 2.2 30.7 1.0 O A:HOH1208 2.4 31.4 1.0 CG A:BFD385 3.1 27.8 1.0 BE A:BFD385 3.2 19.4 1.0 C A:THR387 3.2 22.1 1.0 CG A:ASP726 3.2 27.8 1.0 OD1 A:BFD385 3.6 29.6 1.0 OD2 A:ASP726 3.6 40.3 1.0 N A:GLY727 4.0 26.3 1.0 CA A:THR387 4.1 16.8 1.0 F3 A:BFD385 4.1 33.6 1.0 OD2 A:ASP730 4.2 34.1 1.0 CB A:THR387 4.2 24.2 1.0 OG1 A:THR389 4.2 31.2 1.0 O A:SER225 4.2 43.3 1.0 N A:THR387 4.2 27.4 1.0 N A:GLY388 4.2 25.8 1.0 CB A:BFD385 4.4 20.6 1.0 OD1 A:ASN729 4.4 40.7 1.0 CA A:GLY388 4.4 18.6 1.0 N A:ASP726 4.4 30.4 1.0 CA A:GLY727 4.5 27.4 1.0 CB A:ASP726 4.5 25.7 1.0 N A:THR389 4.6 27.6 1.0 F2 A:BFD385 4.7 42.8 1.0 CG2 A:THR387 4.8 22.3 1.0 C A:GLY388 4.8 24.0 1.0 C A:ASP726 4.8 24.4 1.0 CA A:ASP726 4.8 25.6 1.0 C A:LYS386 4.9 27.8 1.0

K.Abe, S.Yokoshima, A.Yoshimori. Deep Learning Driven De Novo Drug Design Based on Gastric Proton Pump Structures To Be Published.