Fluorine in PDB 8ijx: Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-18

The structure of Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-18 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-18 (pdb code 8ijx). 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-18, PDB code: 8ijx:
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-18


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-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:41.5 occ:1.00 F1 A:BFD385 0.0 41.5 1.0 BE A:BFD385 1.8 20.3 1.0 MG A:MG1102 2.2 30.7 1.0 F3 A:BFD385 2.6 33.2 1.0 O A:HOH1225 3.0 28.2 1.0 OD1 A:BFD385 3.0 31.1 1.0 F2 A:BFD385 3.0 35.4 1.0 O A:HOH1203 3.2 29.2 1.0 O A:THR387 3.4 28.1 1.0 CA A:GLY229 3.4 34.6 1.0 OD2 A:BFD385 3.4 32.4 1.0 CB A:THR387 3.5 24.6 1.0 ND2 A:ASN729 3.5 25.3 1.0 O A:THR228 3.5 42.4 1.0 O A:SER225 3.6 36.0 1.0 CG A:BFD385 3.7 11.8 1.0 N A:THR387 4.1 20.5 1.0 OD1 A:ASN729 4.1 42.0 1.0 CA A:THR387 4.1 14.5 1.0 C A:THR387 4.1 20.4 1.0 C A:GLY229 4.2 32.9 1.0 CG A:ASN729 4.2 30.7 1.0 O A:GLY229 4.2 38.9 1.0 OG1 A:THR387 4.2 36.7 1.0 N A:GLY229 4.2 25.7 1.0 CG2 A:THR387 4.3 19.1 1.0 C A:THR228 4.3 39.1 1.0 OD1 A:ASP726 4.5 33.6 1.0 NZ A:LYS707 4.7 24.6 1.0 C A:SER225 4.8 28.1 1.0 OG1 A:THR626 5.0 32.0 1.0

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-18


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-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:35.4 occ:1.00 F2 A:BFD385 0.0 35.4 1.0 BE A:BFD385 1.8 20.3 1.0 OG1 A:THR626 2.3 32.0 1.0 F3 A:BFD385 2.6 33.2 1.0 N A:THR387 2.7 20.5 1.0 OD1 A:BFD385 3.0 31.1 1.0 F1 A:BFD385 3.0 41.5 1.0 CB A:THR626 3.2 28.7 1.0 OG1 A:THR387 3.2 36.7 1.0 CB A:THR387 3.3 24.6 1.0 N A:LYS386 3.3 19.9 1.0 CB A:LYS386 3.4 15.2 1.0 CA A:THR387 3.6 14.5 1.0 C A:LYS386 3.6 10.4 1.0 CA A:LYS386 3.6 22.6 1.0 CA A:THR626 3.7 19.4 1.0 O A:GLY229 3.8 38.9 1.0 CG A:BFD385 3.8 11.8 1.0 CA A:GLY229 3.9 34.6 1.0 OD2 A:BFD385 4.0 32.4 1.0 N A:GLY627 4.0 25.0 1.0 C A:GLY229 4.3 32.9 1.0 MG A:MG1102 4.3 30.7 1.0 CE A:LYS386 4.3 31.0 1.0 C A:THR626 4.4 20.5 1.0 O A:THR387 4.4 28.1 1.0 C A:BFD385 4.5 17.9 1.0 C A:THR387 4.5 20.4 1.0 CG A:LYS386 4.5 24.9 1.0 CG2 A:THR626 4.5 16.1 1.0 N A:ASP628 4.5 30.7 1.0 NZ A:LYS386 4.6 33.1 1.0 CB A:ASP628 4.7 21.0 1.0 O A:LYS386 4.7 27.9 1.0 CG2 A:THR387 4.8 19.1 1.0 O A:VAL625 4.8 37.2 1.0 CA A:BFD385 4.9 19.3 1.0 NZ A:LYS707 5.0 24.6 1.0 N A:THR626 5.0 13.1 1.0 CD A:LYS386 5.0 24.9 1.0 CB A:BFD385 5.0 12.0 1.0

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-18


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-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:33.2 occ:1.00 F3 A:BFD385 0.0 33.2 1.0 BE A:BFD385 1.8 20.3 1.0 OD1 A:BFD385 2.6 31.1 1.0 F2 A:BFD385 2.6 35.4 1.0 F1 A:BFD385 2.6 41.5 1.0 N A:GLY627 2.7 25.0 1.0 ND2 A:ASN729 3.0 25.3 1.0 NZ A:LYS707 3.0 24.6 1.0 CA A:GLY229 3.2 34.6 1.0 CA A:THR626 3.5 19.4 1.0 OG1 A:THR626 3.5 32.0 1.0 C A:THR626 3.6 20.5 1.0 CA A:GLY627 3.7 13.4 1.0 N A:GLY229 3.8 25.7 1.0 CE A:LYS707 3.9 30.6 1.0 CG A:BFD385 4.0 11.8 1.0 CB A:THR626 4.0 28.7 1.0 CG A:ASN729 4.2 30.7 1.0 O A:THR228 4.4 42.4 1.0 C A:GLY229 4.4 32.9 1.0 C A:THR228 4.4 39.1 1.0 MG A:MG1102 4.5 30.7 1.0 OD2 A:BFD385 4.5 32.4 1.0 O A:VAL625 4.5 37.2 1.0 N A:ASP628 4.5 30.7 1.0 C A:GLY627 4.5 24.8 1.0 O A:HOH1203 4.5 29.2 1.0 O A:HOH1249 4.6 34.5 1.0 O A:GLY229 4.6 38.9 1.0 OD1 A:ASN729 4.7 42.0 1.0 N A:THR626 4.7 13.1 1.0 O A:THR626 4.7 26.5 1.0 N A:LYS386 5.0 19.9 1.0 N A:THR387 5.0 20.5 1.0

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