Fluorine in PDB 7w47: Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan

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

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

Protein crystallography data

The structure of Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan, PDB code: 7w47 was solved by K.Abe, S.Tanaka, M.Morita, T.Yamagishi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.26 / 3.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.99, 104.99, 367.79, 90, 90, 120
R / Rfree (%) 22.2 / 28.5

Other elements in 7w47:

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

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan (pdb code 7w47). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan, PDB code: 7w47:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 7w47

Go back to Fluorine Binding Sites List in 7w47
Fluorine binding site 1 out of 5 in the Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan


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

b:42.9
occ:1.00
 F1 A:BFD385 0.0 42.9 1.0
BE A:BFD385 1.7 40.5 1.0
MG A:MG1101 2.1 21.9 1.0
F3 A:BFD385 2.7 43.9 1.0
OD1 A:BFD385 2.9 38.9 1.0
F2 A:BFD385 3.0 38.6 1.0
CA A:GLY229 3.1 32.0 1.0
O A:SER225 3.3 57.0 1.0
O A:THR387 3.4 32.2 1.0
CB A:THR387 3.5 40.3 1.0
O A:GLY229 3.7 43.1 1.0
ND2 A:ASN729 3.7 24.1 1.0
OD2 A:BFD385 3.8 58.9 1.0
C A:GLY229 3.8 37.1 1.0
O A:THR228 3.8 48.1 1.0
CG A:BFD385 3.9 45.9 1.0
N A:THR387 4.0 47.7 1.0
N A:GLY229 4.1 32.0 1.0
CA A:THR387 4.1 37.0 1.0
C A:THR387 4.2 37.2 1.0
OG1 A:THR387 4.2 56.6 1.0
OD1 A:ASP726 4.3 43.2 1.0
C A:THR228 4.3 34.2 1.0
CG2 A:THR387 4.4 19.9 1.0
OD1 A:ASN729 4.4 44.1 1.0
C A:SER225 4.5 62.1 1.0
CG A:ASN729 4.5 35.6 1.0
CA A:SER225 4.9 60.1 1.0
N A:GLU230 5.0 45.2 1.0
OD2 A:ASP726 5.0 46.4 1.0

Fluorine binding site 2 out of 5 in 7w47

Go back to Fluorine Binding Sites List in 7w47
Fluorine binding site 2 out of 5 in the Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan


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

b:38.6
occ:1.00
 F2 A:BFD385 0.0 38.6 1.0
BE A:BFD385 1.7 40.5 1.0
N A:LYS386 2.6 52.6 1.0
F3 A:BFD385 2.6 43.9 1.0
OG1 A:THR626 2.7 47.2 1.0
OD1 A:BFD385 3.0 38.9 1.0
F1 A:BFD385 3.0 42.9 1.0
N A:THR387 3.0 47.7 1.0
CB A:LYS386 3.2 35.4 1.0
CA A:LYS386 3.2 42.6 1.0
CG A:BFD385 3.3 45.9 1.0
CB A:THR626 3.4 48.5 1.0
CA A:THR626 3.4 49.5 1.0
OD2 A:BFD385 3.5 58.9 1.0
C A:LYS386 3.6 42.2 1.0
C A:BFD385 3.7 45.8 1.0
CA A:BFD385 3.9 28.8 1.0
N A:GLY627 4.0 35.3 1.0
CA A:THR387 4.1 37.0 1.0
MG A:MG1101 4.1 21.9 1.0
CB A:THR387 4.1 40.3 1.0
O A:VAL625 4.2 42.2 1.0
CB A:BFD385 4.2 39.6 1.0
OG1 A:THR387 4.2 56.6 1.0
CA A:GLY229 4.3 32.0 1.0
C A:THR626 4.3 46.5 1.0
O A:THR387 4.5 32.2 1.0
O A:GLY229 4.5 43.1 1.0
N A:THR626 4.5 52.0 1.0
CG A:LYS386 4.6 47.7 1.0
NZ A:LYS707 4.6 37.9 1.0
O A:LYS386 4.7 26.5 1.0
C A:THR387 4.7 37.2 1.0
C A:VAL625 4.8 50.0 1.0
CG2 A:THR626 4.8 60.5 1.0
O A:BFD385 4.8 38.1 1.0
CE A:LYS386 4.8 54.1 1.0
CD A:LYS386 4.9 55.0 1.0
C A:GLY229 4.9 37.1 1.0

Fluorine binding site 3 out of 5 in 7w47

Go back to Fluorine Binding Sites List in 7w47
Fluorine binding site 3 out of 5 in the Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan


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

b:43.9
occ:1.00
 F3 A:BFD385 0.0 43.9 1.0
BE A:BFD385 1.8 40.5 1.0
OD1 A:BFD385 2.5 38.9 1.0
F2 A:BFD385 2.6 38.6 1.0
F1 A:BFD385 2.7 42.9 1.0
NZ A:LYS707 2.8 37.9 1.0
ND2 A:ASN729 3.1 24.1 1.0
N A:GLY627 3.2 35.3 1.0
CA A:GLY229 3.6 32.0 1.0
CG A:BFD385 3.7 45.9 1.0
CA A:THR626 3.8 49.5 1.0
MG A:MG1101 3.9 21.9 1.0
C A:THR626 3.9 46.5 1.0
CG A:ASN729 3.9 35.6 1.0
CA A:GLY627 4.0 29.3 1.0
CE A:LYS707 4.0 51.2 1.0
N A:GLY229 4.1 32.0 1.0
O A:VAL625 4.1 42.2 1.0
OG1 A:THR626 4.2 47.2 1.0
OD1 A:ASN729 4.3 44.1 1.0
OD2 A:BFD385 4.4 58.9 1.0
CB A:BFD385 4.6 39.6 1.0
CB A:THR626 4.6 48.5 1.0
N A:LYS386 4.7 52.6 1.0
N A:THR626 4.7 52.0 1.0
C A:THR228 4.7 34.2 1.0
OD1 A:ASP730 4.8 14.5 1.0
CA A:BFD385 4.8 28.8 1.0
C A:VAL625 4.8 50.0 1.0
C A:GLY229 4.9 37.1 1.0
O A:THR228 4.9 48.1 1.0
CD A:LYS707 4.9 58.4 1.0

Fluorine binding site 4 out of 5 in 7w47

Go back to Fluorine Binding Sites List in 7w47
Fluorine binding site 4 out of 5 in the Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan


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 Tegoprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1105

b:78.6
occ:1.00
 F01 A:8BN1105 0.0 78.6 1.0
C13 A:8BN1105 1.3 54.8 1.0
C17 A:8BN1105 2.3 43.4 1.0
C11 A:8BN1105 2.5 46.7 1.0
C09 A:8BN1105 3.1 48.8 1.0
CB A:ALA335 3.2 43.6 1.0
OE1 A:GLN127 3.2 91.5 1.0
O A:HOH1261 3.5 40.0 1.0
CG1 A:VAL331 3.5 27.6 1.0
O04 A:8BN1105 3.5 59.5 1.0
C18 A:8BN1105 3.6 42.7 1.0
O A:VAL331 3.6 56.5 1.0
OH A:TYR799 3.7 42.7 1.0
C12 A:8BN1105 3.8 41.2 1.0
CA A:ALA335 4.0 36.6 1.0
C16 A:8BN1105 4.2 40.5 1.0
N A:ALA335 4.4 27.2 1.0
C A:VAL331 4.4 56.0 1.0
CD A:GLN127 4.4 89.6 1.0
C15 A:8BN1105 4.5 40.3 1.0
C05 A:8BN1105 4.5 68.1 1.0
CZ A:TYR799 4.6 48.7 1.0
F02 A:8BN1105 4.7 43.0 1.0
ND2 A:ASN138 4.8 42.3 1.0
CE1 A:TYR799 4.9 51.2 1.0
CB A:VAL331 4.9 49.1 1.0
CD2 A:PHE332 5.0 77.7 1.0

Fluorine binding site 5 out of 5 in 7w47

Go back to Fluorine Binding Sites List in 7w47
Fluorine binding site 5 out of 5 in the Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Gastric Proton Pump Complexed with Tegoprazan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1105

b:43.0
occ:1.00
 F02 A:8BN1105 0.0 43.0 1.0
C18 A:8BN1105 1.3 42.7 1.0
C17 A:8BN1105 2.3 43.4 1.0
C16 A:8BN1105 2.4 40.5 1.0
CB A:MET334 3.1 31.8 1.0
CB A:ALA123 3.2 47.0 1.0
C A:MET334 3.3 42.8 1.0
N A:ALA335 3.4 27.2 1.0
O A:MET334 3.6 50.8 1.0
C13 A:8BN1105 3.6 54.8 1.0
CG2 A:ILE119 3.6 19.1 1.0
C12 A:8BN1105 3.7 41.2 1.0
CA A:MET334 3.8 43.4 1.0
O A:ILE119 3.8 47.4 1.0
CA A:ALA335 3.9 36.6 1.0
C11 A:8BN1105 4.2 46.7 1.0
C A:ILE119 4.2 35.8 1.0
CA A:CYS120 4.3 54.7 1.0
CG A:MET334 4.3 38.3 1.0
CE A:MET334 4.3 40.1 1.0
N A:CYS120 4.4 41.1 1.0
O A:VAL331 4.5 56.5 1.0
CG2 A:VAL338 4.5 33.6 1.0
SD A:MET334 4.7 44.0 1.0
F01 A:8BN1105 4.7 78.6 1.0
CA A:ALA123 4.7 56.0 1.0
CB A:VAL338 4.7 48.3 1.0
O03 A:8BN1105 4.8 43.5 1.0
CB A:ILE119 4.8 19.3 1.0
CB A:ALA335 4.8 43.6 1.0
N A:MET334 4.9 52.9 1.0
ND2 A:ASN138 5.0 42.3 1.0

Reference:

K.Abe, S.Tanaka, M.Morita, T.Yamagishi. Crystal Structure of the Gastric Proton Pump with Pcab To Be Published.
Page generated: Fri Aug 2 14:43:39 2024

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