Fluorine in PDB 8jmn: Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-21

The structure of Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-21 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-21 (pdb code 8jmn). 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-21, PDB code: 8jmn:
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-21


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-21 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 12.7 1.0 MG A:MG1102 2.3 21.5 1.0 O A:HOH1225 2.4 24.9 1.0 F3 A:BFD385 2.6 31.2 1.0 O A:HOH1205 3.0 25.4 1.0 OD1 A:BFD385 3.0 29.6 1.0 F2 A:BFD385 3.0 29.8 1.0 CA A:GLY229 3.2 26.9 1.0 O A:THR387 3.3 29.2 1.0 CB A:THR387 3.4 20.7 1.0 O A:SER225 3.5 36.8 1.0 OD2 A:BFD385 3.5 26.2 1.0 O A:THR228 3.6 44.1 1.0 ND2 A:ASN729 3.6 23.1 1.0 CG A:BFD385 3.7 19.4 1.0 CA A:THR387 4.0 17.9 1.0 N A:THR387 4.0 23.9 1.0 OG1 A:THR387 4.1 25.4 1.0 C A:THR387 4.1 20.3 1.0 C A:GLY229 4.1 28.3 1.0 O A:GLY229 4.1 30.1 1.0 N A:GLY229 4.1 30.6 1.0 OD1 A:ASN729 4.2 34.2 1.0 C A:THR228 4.2 33.7 1.0 CG2 A:THR387 4.3 20.0 1.0 CG A:ASN729 4.3 27.0 1.0 C A:SER225 4.7 35.1 1.0 OD1 A:ASP726 4.7 27.2 1.0 OG1 A:THR626 4.8 24.9 1.0 NZ A:LYS707 4.9 23.3 1.0 OD2 A:ASP730 4.9 29.6 1.0

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-21


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-21 within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:29.8 occ:1.00 F2 A:BFD385 0.0 29.8 1.0 BE A:BFD385 1.8 12.7 1.0 OG1 A:THR626 2.2 24.9 1.0 N A:THR387 2.6 23.9 1.0 F3 A:BFD385 2.6 31.2 1.0 OD1 A:BFD385 3.0 29.6 1.0 F1 A:BFD385 3.0 38.6 1.0 OG1 A:THR387 3.1 25.4 1.0 CB A:THR626 3.2 28.6 1.0 N A:LYS386 3.2 22.1 1.0 CB A:LYS386 3.3 14.4 1.0 CB A:THR387 3.3 20.7 1.0 C A:LYS386 3.4 20.3 1.0 CA A:LYS386 3.5 19.7 1.0 CA A:THR387 3.5 17.9 1.0 CA A:THR626 3.7 20.7 1.0 CG A:BFD385 3.8 19.4 1.0 O A:GLY229 3.9 30.1 1.0 OD2 A:BFD385 4.0 26.2 1.0 CA A:GLY229 4.1 26.9 1.0 N A:GLY627 4.1 17.9 1.0 O A:THR387 4.3 29.2 1.0 MG A:MG1102 4.3 21.5 1.0 C A:BFD385 4.3 16.2 1.0 NZ A:LYS386 4.4 27.1 1.0 CG A:LYS386 4.4 20.8 1.0 C A:THR387 4.4 20.3 1.0 CE A:LYS386 4.4 22.3 1.0 C A:THR626 4.4 22.7 1.0 C A:GLY229 4.5 28.3 1.0 CG2 A:THR626 4.5 9.0 1.0 O A:LYS386 4.6 23.8 1.0 N A:ASP628 4.7 27.3 1.0 O A:VAL625 4.7 29.4 1.0 CB A:ASP628 4.8 25.4 1.0 CA A:BFD385 4.8 21.7 1.0 CG2 A:THR387 4.8 20.0 1.0 CD A:LYS386 4.9 14.8 1.0 CB A:BFD385 4.9 13.7 1.0 N A:THR626 4.9 12.7 1.0 NZ A:LYS707 5.0 23.3 1.0

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-21


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-21 within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:31.2 occ:1.00 F3 A:BFD385 0.0 31.2 1.0 BE A:BFD385 1.8 12.7 1.0 OD1 A:BFD385 2.6 29.6 1.0 F2 A:BFD385 2.6 29.8 1.0 F1 A:BFD385 2.6 38.6 1.0 N A:GLY627 2.8 17.9 1.0 NZ A:LYS707 3.0 23.3 1.0 ND2 A:ASN729 3.1 23.1 1.0 CA A:GLY229 3.2 26.9 1.0 OG1 A:THR626 3.4 24.9 1.0 CA A:THR626 3.5 20.7 1.0 C A:THR626 3.6 22.7 1.0 CA A:GLY627 3.7 14.1 1.0 N A:GLY229 3.9 30.6 1.0 CG A:BFD385 4.0 19.4 1.0 CE A:LYS707 4.0 21.3 1.0 CB A:THR626 4.0 28.6 1.0 CG A:ASN729 4.2 27.0 1.0 O A:HOH1205 4.2 25.4 1.0 C A:GLY229 4.4 28.3 1.0 MG A:MG1102 4.4 21.5 1.0 O A:THR228 4.5 44.1 1.0 O A:VAL625 4.5 29.4 1.0 C A:THR228 4.5 33.7 1.0 O A:HOH1261 4.5 27.4 1.0 N A:ASP628 4.5 27.3 1.0 OD2 A:BFD385 4.5 26.2 1.0 C A:GLY627 4.5 28.6 1.0 O A:GLY229 4.5 30.1 1.0 OD1 A:ASN729 4.6 34.2 1.0 N A:THR626 4.7 12.7 1.0 OD1 A:ASP730 4.8 30.6 1.0 O A:THR626 4.8 27.2 1.0 O A:HOH1225 4.9 24.9 1.0 N A:LYS386 4.9 22.1 1.0 N A:THR387 4.9 23.9 1.0 OG1 A:THR387 5.0 25.4 1.0

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