Fluorine 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:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06, PDB code: 8ijw:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F385 b:38.6 occ:1.00 F1 A:BFD385 0.0 38.6 1.0 BE A:BFD385 1.8 19.4 1.0 MG A:MG1103 1.9 28.5 1.0 F3 A:BFD385 2.6 33.6 1.0 O A:HOH1210 2.7 28.4 1.0 O A:THR387 2.8 32.2 1.0 OD2 A:BFD385 2.9 35.3 1.0 O A:HOH1208 2.9 31.4 1.0 OD1 A:BFD385 3.0 29.6 1.0 F2 A:BFD385 3.0 42.8 1.0 CB A:THR387 3.3 24.2 1.0 CG A:BFD385 3.4 27.8 1.0 C A:THR387 3.7 22.1 1.0 CA A:GLY229 3.7 33.7 1.0 O A:SER225 3.7 43.3 1.0 N A:THR387 3.8 27.4 1.0 CA A:THR387 3.8 16.8 1.0 O A:THR228 3.9 46.1 1.0 ND2 A:ASN729 3.9 22.4 1.0 OD1 A:ASP726 4.1 30.7 1.0 OG1 A:THR387 4.2 32.5 1.0 OD1 A:ASN729 4.2 40.7 1.0 CG2 A:THR387 4.2 22.3 1.0 CG A:ASN729 4.5 28.5 1.0 C A:GLY229 4.6 36.7 1.0 O A:GLY229 4.6 40.9 1.0 N A:GLY229 4.6 37.1 1.0 C A:THR228 4.7 39.6 1.0 C A:LYS386 4.8 27.8 1.0 OG1 A:THR626 4.8 32.1 1.0 CB A:BFD385 4.8 20.6 1.0 NZ A:LYS707 4.9 35.0 1.0 OD2 A:ASP730 4.9 34.1 1.0 N A:LYS386 4.9 22.7 1.0 N A:GLY388 4.9 25.8 1.0 C A:SER225 5.0 37.7 1.0

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 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:F385 b:42.8 occ:1.00 F2 A:BFD385 0.0 42.8 1.0 BE A:BFD385 1.8 19.4 1.0 ND2 A:ASN729 2.6 22.4 1.0 F3 A:BFD385 2.6 33.6 1.0 N A:GLY627 2.6 27.7 1.0 OD1 A:BFD385 3.0 29.6 1.0 NZ A:LYS707 3.0 35.0 1.0 F1 A:BFD385 3.0 38.6 1.0 CA A:GLY229 3.1 33.7 1.0 CA A:GLY627 3.5 18.1 1.0 N A:GLY229 3.5 37.1 1.0 C A:THR626 3.6 27.2 1.0 OG1 A:THR626 3.6 32.1 1.0 CA A:THR626 3.6 27.5 1.0 CE A:LYS707 3.8 30.6 1.0 CG A:ASN729 3.8 28.5 1.0 C A:THR228 4.1 39.6 1.0 O A:THR228 4.1 46.1 1.0 O A:HOH1247 4.2 31.1 1.0 CB A:THR626 4.2 34.6 1.0 O A:HOH1208 4.3 31.4 1.0 CG A:BFD385 4.3 27.8 1.0 OD1 A:ASN729 4.4 40.7 1.0 C A:GLY627 4.4 25.6 1.0 C A:GLY229 4.4 36.7 1.0 N A:ASP628 4.5 36.3 1.0 OD2 A:BFD385 4.7 35.3 1.0 O A:THR626 4.7 29.8 1.0 MG A:MG1103 4.7 28.5 1.0 O A:VAL625 4.8 31.7 1.0 O A:GLY229 4.8 40.9 1.0 N A:THR626 4.8 20.5 1.0 CB A:ASN729 5.0 28.8 1.0

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-06


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 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:F385 b:33.6 occ:1.00 F3 A:BFD385 0.0 33.6 1.0 BE A:BFD385 1.8 19.4 1.0 OG1 A:THR626 2.3 32.1 1.0 OD1 A:BFD385 2.6 29.6 1.0 F1 A:BFD385 2.6 38.6 1.0 F2 A:BFD385 2.6 42.8 1.0 N A:THR387 2.8 27.4 1.0 CB A:THR626 3.3 34.6 1.0 OG1 A:THR387 3.3 32.5 1.0 CB A:THR387 3.4 24.2 1.0 N A:LYS386 3.4 22.7 1.0 CG A:BFD385 3.5 27.8 1.0 CA A:THR387 3.6 16.8 1.0 CA A:THR626 3.6 27.5 1.0 CA A:GLY229 3.7 33.7 1.0 OD2 A:BFD385 3.7 35.3 1.0 C A:LYS386 3.7 27.8 1.0 CB A:LYS386 3.8 16.5 1.0 CA A:LYS386 3.8 23.5 1.0 N A:GLY627 3.8 27.7 1.0 O A:GLY229 4.0 40.9 1.0 MG A:MG1103 4.1 28.5 1.0 O A:THR387 4.2 32.2 1.0 C A:THR626 4.3 27.2 1.0 C A:GLY229 4.3 36.7 1.0 C A:THR387 4.4 22.1 1.0 C A:BFD385 4.5 27.1 1.0 NZ A:LYS707 4.6 35.0 1.0 CG2 A:THR626 4.6 18.7 1.0 N A:ASP628 4.7 36.3 1.0 O A:VAL625 4.7 31.7 1.0 CG2 A:THR387 4.8 22.3 1.0 CB A:BFD385 4.8 20.6 1.0 CA A:BFD385 4.8 23.5 1.0 NZ A:LYS386 4.8 29.1 1.0 CG A:LYS386 4.8 21.8 1.0 O A:LYS386 4.9 29.4 1.0 N A:GLY229 4.9 37.1 1.0 N A:THR626 4.9 20.5 1.0 CA A:GLY627 4.9 18.1 1.0 O A:HOH1208 4.9 31.4 1.0 ND2 A:ASN729 4.9 22.4 1.0 CB A:ASP628 5.0 31.9 1.0 CE A:LYS386 5.0 27.9 1.0

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