Fluorine in PDB 7w49: Crystal Structure of the Gastric Proton Pump Complexed with Soraprazan

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

The structure of Crystal Structure of the Gastric Proton Pump Complexed with Soraprazan, PDB code: 7w49 was solved by K.Abe, S.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.53 / 3.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.533, 105.533, 370.889, 90, 90, 120
R / Rfree (%)	24.9 / 30.8

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

Magnesium	(Mg)	1 atom
Rubidium	(Rb)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Gastric Proton Pump Complexed with Soraprazan (pdb code 7w49). 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 Soraprazan, PDB code: 7w49:
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 Soraprazan


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 Soraprazan within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:80.2 occ:1.00 F1 A:BFD385 0.0 80.2 1.0 BE A:BFD385 1.8 59.1 1.0 MG A:MG1101 2.4 57.1 1.0 F3 A:BFD385 2.6 58.9 1.0 O A:SER225 2.8 77.7 1.0 OD1 A:BFD385 3.0 46.0 1.0 F2 A:BFD385 3.0 65.2 1.0 O A:THR228 3.2 74.3 1.0 CA A:GLY229 3.2 58.1 1.0 O A:THR387 3.4 55.0 1.0 CB A:THR387 3.4 59.1 1.0 ND2 A:ASN729 3.7 53.8 1.0 C A:SER225 3.9 73.1 1.0 C A:GLY229 3.9 68.7 1.0 C A:THR228 3.9 73.2 1.0 N A:GLY229 4.0 65.7 1.0 O A:GLY229 4.0 72.3 1.0 CA A:THR387 4.1 61.2 1.0 C A:THR387 4.1 66.2 1.0 CG A:BFD385 4.1 60.2 1.0 CG2 A:THR387 4.2 61.7 1.0 OG1 A:THR387 4.2 62.1 1.0 N A:THR387 4.2 60.1 1.0 OD2 A:BFD385 4.3 71.0 1.0 CA A:SER225 4.4 66.2 1.0 OD1 A:ASN729 4.6 66.5 1.0 CG A:ASN729 4.6 54.3 1.0 CB A:SER225 4.6 58.5 1.0 OD1 A:ASP726 4.7 66.0 1.0 OG1 A:THR626 4.8 78.4 1.0 N A:GLU230 4.9 55.9 1.0

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


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 Soraprazan within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:65.2 occ:1.00 F2 A:BFD385 0.0 65.2 1.0 BE A:BFD385 1.8 59.1 1.0 OG1 A:THR626 2.3 78.4 1.0 F3 A:BFD385 2.6 58.9 1.0 N A:THR387 2.8 60.1 1.0 N A:LYS386 2.9 62.6 1.0 OD1 A:BFD385 3.0 46.0 1.0 F1 A:BFD385 3.0 80.2 1.0 CB A:THR626 3.2 60.8 1.0 CG A:BFD385 3.4 60.2 1.0 CA A:LYS386 3.4 47.4 1.0 C A:LYS386 3.5 54.7 1.0 CB A:LYS386 3.5 59.3 1.0 OD2 A:BFD385 3.7 71.0 1.0 CA A:GLY229 3.7 58.1 1.0 CB A:THR387 3.7 59.1 1.0 CA A:THR387 3.7 61.2 1.0 OG1 A:THR387 3.8 62.1 1.0 CA A:THR626 3.9 58.4 1.0 C A:BFD385 3.9 69.0 1.0 O A:THR387 4.0 55.0 1.0 O A:GLY229 4.1 72.3 1.0 CA A:BFD385 4.3 60.7 1.0 N A:GLY627 4.3 69.1 1.0 CB A:BFD385 4.3 59.8 1.0 C A:THR387 4.4 66.2 1.0 C A:GLY229 4.4 68.7 1.0 CG2 A:THR626 4.5 51.4 1.0 C A:THR626 4.6 66.2 1.0 CD A:LYS386 4.7 73.6 1.0 MG A:MG1101 4.7 57.1 1.0 O A:LYS386 4.7 69.2 1.0 CG A:LYS386 4.7 74.6 1.0 NZ A:LYS707 4.8 65.9 1.0 O A:VAL625 4.9 66.4 1.0 N A:GLY229 4.9 65.7 1.0 CE A:LYS386 4.9 52.2 1.0 O A:BFD385 5.0 64.7 1.0

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


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 Soraprazan within 5.0Å range: probe atom residue distance (Å) B Occ A:F385 b:58.9 occ:1.00 F3 A:BFD385 0.0 58.9 1.0 BE A:BFD385 1.8 59.1 1.0 OD1 A:BFD385 2.6 46.0 1.0 F2 A:BFD385 2.6 65.2 1.0 F1 A:BFD385 2.6 80.2 1.0 ND2 A:ASN729 2.7 53.8 1.0 CA A:GLY229 3.2 58.1 1.0 NZ A:LYS707 3.2 65.9 1.0 N A:GLY229 3.6 65.7 1.0 OG1 A:THR626 3.6 78.4 1.0 N A:GLY627 3.6 69.1 1.0 CG A:ASN729 3.7 54.3 1.0 CG A:BFD385 3.8 60.2 1.0 MG A:MG1101 3.9 57.1 1.0 C A:THR228 4.0 73.2 1.0 O A:THR228 4.1 74.3 1.0 CA A:THR626 4.1 58.4 1.0 OD1 A:ASN729 4.1 66.5 1.0 CE A:LYS707 4.2 58.0 1.0 OD1 A:ASP730 4.3 70.2 1.0 CB A:THR626 4.4 60.8 1.0 C A:THR626 4.4 66.2 1.0 CA A:GLY627 4.5 56.9 1.0 C A:GLY229 4.5 68.7 1.0 CB A:BFD385 4.6 59.8 1.0 OD2 A:BFD385 4.6 71.0 1.0 O A:SER225 4.8 77.7 1.0 CB A:ASN729 4.9 55.3 1.0 N A:LYS386 4.9 62.6 1.0 O A:GLY229 4.9 72.3 1.0 O A:VAL625 5.0 66.4 1.0

K.Abe, S.Tanaka, M.Morita, T.Yamagishi. Crystal Structure of the Gastric Proton Pump with Pcab To Be Published.