Fluorine in PDB 5ylv: Crystal Structure of the Gastric Proton Pump Complexed with SCH28080

All present enzymatic activity of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080:
3.6.3.10;

The structure of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080, PDB code: 5ylv was solved by K.Abe, K.Irie, H.Nakanishi, Y.Fujiyoshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.30 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.050, 105.050, 368.540, 90.00, 90.00, 120.00
R / Rfree (%)	24 / 29.2

The structure of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 also contains other interesting chemical elements:

Rubidium	(Rb)	3 atoms
Magnesium	(Mg)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 (pdb code 5ylv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080, PDB code: 5ylv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:46.7 occ:1.00 F1 A:BFD385 0.0 46.7 1.0 MG A:MG1102 1.3 39.0 1.0 BE A:BFD385 1.8 44.3 1.0 OD2 A:BFD385 2.1 48.9 1.0 O A:THR387 2.7 47.4 1.0 OD1 A:BFD385 2.8 45.9 1.0 CG A:BFD385 2.9 46.9 1.0 F3 A:BFD385 3.0 49.4 1.0 F2 A:BFD385 3.0 48.8 1.0 OD1 A:ASP726 3.1 48.4 1.0 CB A:THR387 3.6 48.9 1.0 C A:THR387 3.7 43.8 1.0 O A:SER225 3.9 46.4 1.0 CA A:THR387 3.9 41.2 1.0 N A:THR387 3.9 37.6 1.0 CG A:ASP726 4.0 43.6 1.0 OD2 A:ASP726 4.1 43.4 1.0 OD1 A:ASN729 4.2 44.9 1.0 ND2 A:ASN729 4.2 40.8 1.0 CB A:BFD385 4.3 45.9 1.0 OD2 A:ASP730 4.4 47.5 1.0 OG1 A:THR387 4.4 47.4 1.0 CA A:GLY229 4.6 47.0 1.0 CG2 A:THR387 4.6 45.4 1.0 N A:LYS386 4.6 45.0 1.0 C A:LYS386 4.6 44.4 1.0 CG A:ASN729 4.6 39.1 1.0 NZ A:LYS707 4.7 44.9 1.0 O A:GLY229 4.8 50.3 1.0 N A:GLY727 4.8 38.3 1.0 OG1 A:THR389 4.9 34.7 1.0 N A:GLY388 4.9 38.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:48.8 occ:1.00 F2 A:BFD385 0.0 48.8 1.0 BE A:BFD385 1.7 44.3 1.0 OG1 A:THR626 2.6 46.8 1.0 N A:THR387 2.7 37.6 1.0 F3 A:BFD385 2.7 49.4 1.0 OD1 A:BFD385 2.8 45.9 1.0 N A:LYS386 3.0 45.0 1.0 F1 A:BFD385 3.0 46.7 1.0 OG1 A:THR387 3.2 47.4 1.0 CB A:THR626 3.4 48.7 1.0 CB A:LYS386 3.4 41.0 1.0 CA A:LYS386 3.4 42.3 1.0 CB A:THR387 3.4 48.9 1.0 C A:LYS386 3.4 44.4 1.0 CG A:BFD385 3.6 46.9 1.0 CA A:THR387 3.6 41.2 1.0 OD2 A:BFD385 3.8 48.9 1.0 CA A:THR626 3.9 49.5 1.0 C A:BFD385 4.1 47.5 1.0 O A:GLY229 4.2 50.3 1.0 CA A:GLY229 4.2 47.0 1.0 O A:THR387 4.3 47.4 1.0 N A:GLY627 4.3 50.2 1.0 MG A:MG1102 4.3 39.0 1.0 C A:THR387 4.4 43.8 1.0 CG A:LYS386 4.4 35.1 1.0 CA A:BFD385 4.5 38.2 1.0 O A:LYS386 4.5 41.9 1.0 NZ A:LYS707 4.6 44.9 1.0 C A:THR626 4.6 55.5 1.0 CB A:BFD385 4.6 45.9 1.0 CE A:LYS386 4.7 47.7 1.0 C A:GLY229 4.7 51.7 1.0 O A:VAL625 4.7 52.8 1.0 CG2 A:THR626 4.8 49.7 1.0 CD A:LYS386 4.9 46.2 1.0 CG2 A:THR387 4.9 45.4 1.0 N A:ASP628 4.9 54.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the Gastric Proton Pump Complexed with SCH28080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Gastric Proton Pump Complexed with SCH28080 within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:49.4 occ:1.00 F3 A:BFD385 0.0 49.4 1.0 BE A:BFD385 1.7 44.3 1.0 ND2 A:ASN729 2.6 40.8 1.0 NZ A:LYS707 2.7 44.9 1.0 F2 A:BFD385 2.7 48.8 1.0 OD1 A:BFD385 2.7 45.9 1.0 F1 A:BFD385 3.0 46.7 1.0 CA A:GLY229 3.4 47.0 1.0 N A:GLY627 3.4 50.2 1.0 CG A:ASN729 3.6 39.1 1.0 CE A:LYS707 3.8 50.5 1.0 OG1 A:THR626 3.9 46.8 1.0 CG A:BFD385 3.9 46.9 1.0 CA A:THR626 4.0 49.5 1.0 OD1 A:ASN729 4.0 44.9 1.0 MG A:MG1102 4.0 39.0 1.0 N A:GLY229 4.1 44.9 1.0 OD2 A:BFD385 4.1 48.9 1.0 C A:THR626 4.2 55.5 1.0 CA A:GLY627 4.3 48.3 1.0 O A:THR228 4.5 50.1 1.0 CB A:THR626 4.5 48.7 1.0 OD1 A:ASP730 4.5 50.3 1.0 C A:GLY229 4.6 51.7 1.0 C A:THR228 4.6 43.9 1.0 O A:VAL625 4.8 52.8 1.0 O A:GLY229 4.8 50.3 1.0 CB A:ASN729 4.9 35.5 1.0 N A:LYS386 4.9 45.0 1.0

K.Abe, K.Irie, H.Nakanishi, H.Suzuki, Y.Fujiyoshi. Crystal Structures of the Gastric Proton Pump Nature V. 556 214 2018.
ISSN: ESSN 1476-4687
PubMed: 29618813
DOI: 10.1038/S41586-018-0003-8