Fluorine in PDB 7w4a: Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan

All present enzymatic activity of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan:
3.6.3.10;

The structure of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan (pdb code 7w4a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan, PDB code: 7w4a:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan


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 Complexed with Revaprazan within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:28.2 occ:1.00 F1 A:BFD385 0.0 28.2 1.0 BE A:BFD385 1.8 28.2 1.0 ND2 A:ASN729 2.4 32.4 1.0 F3 A:BFD385 2.6 28.2 1.0 NZ A:LYS707 2.7 31.1 1.0 OD1 A:BFD385 3.0 28.2 1.0 F2 A:BFD385 3.0 28.2 1.0 CA A:GLY229 3.2 41.5 1.0 N A:GLY627 3.4 37.2 1.0 CG A:ASN729 3.6 32.4 1.0 N A:GLY229 3.6 41.5 1.0 CE A:LYS707 3.6 31.1 1.0 OD1 A:ASN729 4.0 32.4 1.0 CA A:GLY627 4.1 37.2 1.0 C A:THR228 4.1 46.4 1.0 C A:THR626 4.1 32.4 1.0 CA A:THR626 4.2 32.4 1.0 CG A:BFD385 4.3 28.2 1.0 O A:THR228 4.3 46.4 1.0 OD1 A:ASP730 4.3 30.3 1.0 MG A:MG1103 4.4 26.5 1.0 OG1 A:THR626 4.5 32.4 1.0 C A:GLY229 4.6 41.5 1.0 OD2 A:BFD385 4.6 28.2 1.0 CB A:ASN729 4.7 32.4 1.0 CB A:THR626 4.9 32.4 1.0 O A:GLY229 5.0 41.5 1.0 CD A:LYS707 5.0 31.1 1.0

Fluorine binding site 2 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan


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 Complexed with Revaprazan within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:28.2 occ:1.00 F2 A:BFD385 0.0 28.2 1.0 BE A:BFD385 1.8 28.2 1.0 MG A:MG1103 2.0 26.5 1.0 F3 A:BFD385 2.6 28.2 1.0 OD2 A:BFD385 2.8 28.2 1.0 O A:THR387 2.8 31.4 1.0 OD1 A:BFD385 3.0 28.2 1.0 F1 A:BFD385 3.0 28.2 1.0 CB A:THR387 3.3 31.4 1.0 CG A:BFD385 3.3 28.2 1.0 CA A:GLY229 3.5 41.5 1.0 C A:THR387 3.7 31.4 1.0 N A:THR387 3.7 31.4 1.0 CA A:THR387 3.7 31.4 1.0 O A:SER225 4.0 48.7 1.0 OG1 A:THR387 4.0 31.4 1.0 ND2 A:ASN729 4.2 32.4 1.0 O A:GLY229 4.3 41.5 1.0 CG2 A:THR387 4.3 31.4 1.0 O A:THR228 4.3 46.4 1.0 C A:GLY229 4.3 41.5 1.0 OD2 A:ASP726 4.6 29.9 1.0 N A:GLY229 4.6 41.5 1.0 C A:LYS386 4.7 28.3 1.0 OD1 A:ASN729 4.7 32.4 1.0 N A:LYS386 4.8 28.3 1.0 OD2 A:ASP730 4.8 30.3 1.0 OD1 A:ASP726 4.8 29.9 1.0 CB A:BFD385 4.8 28.2 1.0 C A:THR228 4.9 46.4 1.0 NZ A:LYS707 4.9 31.1 1.0 CG A:ASN729 4.9 32.4 1.0 N A:GLY388 5.0 29.4 1.0

Fluorine binding site 3 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan


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 Complexed with Revaprazan within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:28.2 occ:1.00 F3 A:BFD385 0.0 28.2 1.0 BE A:BFD385 1.8 28.2 1.0 OG1 A:THR626 2.6 32.4 1.0 OD1 A:BFD385 2.6 28.2 1.0 F1 A:BFD385 2.6 28.2 1.0 F2 A:BFD385 2.6 28.2 1.0 CB A:THR626 3.2 32.4 1.0 CA A:THR626 3.3 32.4 1.0 N A:GLY627 3.5 37.2 1.0 N A:THR387 3.5 31.4 1.0 CA A:GLY229 3.6 41.5 1.0 CG A:BFD385 3.6 28.2 1.0 N A:LYS386 3.7 28.3 1.0 OG1 A:THR387 3.8 31.4 1.0 O A:GLY229 3.9 41.5 1.0 OD2 A:BFD385 3.9 28.2 1.0 C A:THR626 3.9 32.4 1.0 CB A:THR387 4.0 31.4 1.0 CB A:LYS386 4.1 28.3 1.0 O A:VAL625 4.1 27.3 1.0 NZ A:LYS707 4.1 31.1 1.0 CA A:LYS386 4.2 28.3 1.0 C A:GLY229 4.2 41.5 1.0 CA A:THR387 4.3 31.4 1.0 C A:LYS386 4.3 28.3 1.0 MG A:MG1103 4.3 26.5 1.0 N A:THR626 4.5 32.4 1.0 CA A:GLY627 4.6 37.2 1.0 O A:THR387 4.7 31.4 1.0 CG2 A:THR626 4.7 32.4 1.0 N A:GLY229 4.7 41.5 1.0 C A:VAL625 4.7 27.3 1.0 C A:BFD385 4.8 28.2 1.0 N A:ASP628 4.8 39.8 1.0 CB A:BFD385 4.9 28.2 1.0 ND2 A:ASN729 4.9 32.4 1.0 CA A:BFD385 4.9 28.2 1.0 C A:THR387 5.0 31.4 1.0

Fluorine binding site 4 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of the Gastric Proton Pump Complexed with Revaprazan within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:24.4 occ:1.00 F01 A:8CK1101 0.0 24.4 1.0 C18 A:8CK1101 1.3 24.4 1.0 C19 A:8CK1101 2.4 24.4 1.0 C17 A:8CK1101 2.4 24.4 1.0 CB A:MET334 3.1 29.5 1.0 C A:MET334 3.2 29.5 1.0 CB A:ALA123 3.2 37.5 1.0 N A:ALA335 3.3 25.1 1.0 O A:MET334 3.4 29.5 1.0 C20 A:8CK1101 3.6 24.4 1.0 C16 A:8CK1101 3.6 24.4 1.0 CA A:ALA335 3.7 25.1 1.0 CA A:MET334 3.8 29.5 1.0 OD1 A:ASN138 4.1 37.8 1.0 O A:ILE119 4.1 27.6 1.0 CG2 A:ILE119 4.1 27.6 1.0 C14 A:8CK1101 4.1 24.4 1.0 O A:VAL331 4.2 37.7 1.0 CG2 A:VAL338 4.2 22.1 1.0 CB A:ALA335 4.4 25.1 1.0 CA A:CYS120 4.4 31.5 1.0 CG A:MET334 4.4 29.5 1.0 C A:ILE119 4.6 27.6 1.0 N A:CYS120 4.7 31.5 1.0 CA A:ALA123 4.7 37.5 1.0 SD A:MET334 4.7 29.5 1.0 N A:MET334 4.8 29.5 1.0 CB A:VAL338 4.8 22.1 1.0 C A:ALA335 4.9 25.1 1.0 SG A:CYS120 4.9 31.5 1.0

S.Tanaka, M.Morita, T.Yamagishi, H.V.Madapally, K.Hayashida, H.Khandelia, C.Gerle, H.Shigematsu, A.Oshima, K.Abe. Structural Basis For Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump. J.Med.Chem. V. 65 7843 2022.
ISSN: ISSN 0022-2623
PubMed: 35604136
DOI: 10.1021/ACS.JMEDCHEM.2C00338