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Fluorine in PDB 5ylu: Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan

Enzymatic activity of Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan

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

Protein crystallography data

The structure of Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan, PDB code: 5ylu 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) 48.18 / 2.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.820, 104.820, 367.080, 90.00, 90.00, 120.00
R / Rfree (%) 23.7 / 28.8

Other elements in 5ylu:

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

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan (pdb code 5ylu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan, PDB code: 5ylu:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5ylu

Go back to Fluorine Binding Sites List in 5ylu
Fluorine binding site 1 out of 4 in the Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan


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 Vonoprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:28.7
occ:1.00
 F1 A:BFD385 0.0 28.7 1.0
BE A:BFD385 1.7 26.9 1.0
OG1 A:THR626 2.6 26.8 1.0
F3 A:BFD385 2.6 32.9 1.0
N A:LYS386 2.7 26.8 1.0
N A:THR387 2.8 26.3 1.0
OD1 A:BFD385 2.9 25.8 1.0
F2 A:BFD385 3.0 33.1 1.0
CB A:LYS386 3.0 20.7 1.0
CB A:THR626 3.1 24.2 1.0
CA A:LYS386 3.1 23.7 1.0
C A:LYS386 3.4 29.7 1.0
CA A:THR626 3.5 27.5 1.0
CG A:BFD385 3.6 25.1 1.0
OD2 A:BFD385 3.8 24.9 1.0
C A:BFD385 3.8 26.2 1.0
CA A:THR387 3.9 26.8 1.0
OG1 A:THR387 3.9 25.0 1.0
CB A:THR387 3.9 25.5 1.0
N A:GLY627 4.0 27.8 1.0
C A:THR626 4.2 28.5 1.0
CG A:LYS386 4.2 20.3 1.0
CA A:BFD385 4.3 23.4 1.0
O A:GLY229 4.3 30.7 1.0
MG A:MG1104 4.3 56.1 1.0
O A:THR387 4.4 30.6 1.0
NZ A:LYS707 4.5 27.1 1.0
CE A:LYS386 4.5 23.6 1.0
CG2 A:THR626 4.5 25.5 1.0
CA A:GLY229 4.5 35.0 1.0
CB A:BFD385 4.6 23.9 1.0
O A:VAL625 4.6 22.4 1.0
O A:LYS386 4.6 32.8 1.0
C A:THR387 4.7 30.0 1.0
CD A:LYS386 4.7 24.1 1.0
N A:THR626 4.7 28.8 1.0
N A:ASP628 4.8 31.6 1.0
C A:GLY229 4.9 32.9 1.0
CB A:ASP628 4.9 28.1 1.0
O A:BFD385 4.9 27.5 1.0
OD2 A:ASP726 5.0 31.7 1.0

Fluorine binding site 2 out of 4 in 5ylu

Go back to Fluorine Binding Sites List in 5ylu
Fluorine binding site 2 out of 4 in the Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan


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 Vonoprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:33.1
occ:1.00
 F2 A:BFD385 0.0 33.1 1.0
BE A:BFD385 1.7 26.9 1.0
F3 A:BFD385 2.6 32.9 1.0
ND2 A:ASN729 2.8 30.2 1.0
CA A:GLY229 2.8 35.0 1.0
OD1 A:BFD385 3.0 25.8 1.0
F1 A:BFD385 3.0 28.7 1.0
MG A:MG1104 3.1 56.1 1.0
O A:THR228 3.3 30.7 1.0
N A:GLY627 3.6 27.8 1.0
NZ A:LYS707 3.6 27.1 1.0
N A:GLY229 3.7 25.4 1.0
C A:GLY229 3.7 32.9 1.0
O A:GLY229 3.7 30.7 1.0
C A:THR228 3.8 27.0 1.0
CG A:ASN729 3.8 29.7 1.0
CG A:BFD385 4.1 25.1 1.0
CA A:GLY627 4.2 27.4 1.0
OD1 A:ASP730 4.2 26.0 1.0
O A:SER225 4.2 29.1 1.0
OD1 A:ASN729 4.3 32.7 1.0
OD2 A:BFD385 4.4 24.9 1.0
OG1 A:THR626 4.4 26.8 1.0
OD2 A:ASP726 4.5 31.7 1.0
OD2 A:ASP730 4.5 34.9 1.0
OD1 A:ASP726 4.6 35.0 1.0
C A:THR626 4.6 28.5 1.0
CE A:LYS707 4.7 23.7 1.0
CA A:THR626 4.7 27.5 1.0
CG A:ASP730 4.7 25.4 1.0
N A:ASP628 4.8 31.6 1.0
C A:GLY627 4.8 31.6 1.0
CB A:THR387 4.8 25.5 1.0
N A:GLU230 4.9 33.7 1.0
N A:THR387 4.9 26.3 1.0
CB A:ASN729 5.0 26.4 1.0
O A:THR387 5.0 30.6 1.0

Fluorine binding site 3 out of 4 in 5ylu

Go back to Fluorine Binding Sites List in 5ylu
Fluorine binding site 3 out of 4 in the Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan


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 Vonoprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:32.9
occ:1.00
 F3 A:BFD385 0.0 32.9 1.0
BE A:BFD385 1.8 26.9 1.0
MG A:MG1104 1.8 56.1 1.0
OD2 A:BFD385 2.4 24.9 1.0
OD2 A:ASP726 2.4 31.7 1.0
O A:THR387 2.5 30.6 1.0
F2 A:BFD385 2.6 33.1 1.0
OD1 A:BFD385 2.6 25.8 1.0
F1 A:BFD385 2.6 28.7 1.0
CG A:BFD385 2.8 25.1 1.0
N A:THR387 3.0 26.3 1.0
CG A:ASP726 3.2 32.2 1.0
CB A:THR387 3.3 25.5 1.0
C A:THR387 3.3 30.0 1.0
OD1 A:ASP726 3.3 35.0 1.0
CA A:THR387 3.3 26.8 1.0
N A:LYS386 3.9 26.8 1.0
C A:LYS386 4.0 29.7 1.0
OG1 A:THR387 4.2 25.0 1.0
O A:GLY229 4.2 30.7 1.0
OD2 A:ASP730 4.3 34.9 1.0
CG2 A:THR387 4.3 22.4 1.0
CB A:BFD385 4.3 23.9 1.0
O A:SER225 4.4 29.1 1.0
ND2 A:ASN729 4.5 30.2 1.0
CA A:LYS386 4.5 23.7 1.0
N A:GLY388 4.6 30.4 1.0
CA A:GLY229 4.6 35.0 1.0
CB A:ASP726 4.7 25.9 1.0
C A:BFD385 4.7 26.2 1.0
O A:LYS386 4.8 32.8 1.0
NZ A:LYS707 4.9 27.1 1.0
C A:GLY229 4.9 32.9 1.0
CA A:BFD385 4.9 23.4 1.0
O A:THR228 5.0 30.7 1.0
CG A:ASP730 5.0 25.4 1.0

Fluorine binding site 4 out of 4 in 5ylu

Go back to Fluorine Binding Sites List in 5ylu
Fluorine binding site 4 out of 4 in the Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:51.1
occ:1.00
 FAB A:HKT1101 0.0 51.1 1.0
CAR A:HKT1101 1.4 48.5 1.0
CAW A:HKT1101 2.4 50.3 1.0
CAM A:HKT1101 2.4 44.5 1.0
CAL A:HKT1101 2.9 45.6 1.0
CAQ A:HKT1101 3.3 44.2 1.0
CB A:CYS813 3.3 45.4 1.0
SG A:CYS813 3.4 37.4 1.0
CAZ A:HKT1101 3.6 51.4 1.0
CAS A:HKT1101 3.7 40.6 1.0
CD1 A:LEU141 3.7 46.3 1.0
CA A:CYS813 3.9 42.2 1.0
NAI A:HKT1101 4.0 51.5 1.0
CD2 A:LEU141 4.0 36.5 1.0
CAX A:HKT1101 4.2 40.3 1.0
CAT A:HKT1101 4.2 50.7 1.0
CG A:LEU141 4.2 44.1 1.0
CB A:LEU141 4.3 47.5 1.0
CAN A:HKT1101 4.3 48.5 1.0
CAP A:HKT1101 4.4 48.4 1.0
NAJ A:HKT1101 4.5 45.1 1.0
CAU A:HKT1101 4.8 44.9 1.0
CAO A:HKT1101 4.8 49.8 1.0
SAA A:HKT1101 4.8 59.9 1.0
C A:CYS813 4.8 38.0 1.0
CG2 A:ILE816 4.9 36.5 1.0
N A:CYS813 4.9 46.9 1.0
O A:CYS813 4.9 41.6 1.0
CBA A:HKT1101 4.9 42.2 1.0

Reference:

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
Page generated: Tue Jul 15 09:30:40 2025

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