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Fluorine in PDB 7efm: Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N in (Byk)E2BEF State

Protein crystallography data

The structure of Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N in (Byk)E2BEF State, PDB code: 7efm was solved by K.Abe, K.Yamamoto, K.Irie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.15 / 3.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.69, 104.69, 368.02, 90, 90, 120
R / Rfree (%) 22.8 / 29.3

Other elements in 7efm:

The structure of Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N in (Byk)E2BEF State also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N in (Byk)E2BEF State (pdb code 7efm). 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 K791S/E820D/Y340N in (Byk)E2BEF State, PDB code: 7efm:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7efm

Go back to Fluorine Binding Sites List in 7efm
Fluorine binding site 1 out of 3 in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N in (Byk)E2BEF State


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 K791S/E820D/Y340N in (Byk)E2BEF State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:69.0
occ:1.00
 F1 A:BFD385 0.0 69.0 1.0
BE A:BFD385 1.8 54.0 1.0
ND2 A:ASN729 2.4 58.6 1.0
NZ A:LYS707 2.7 42.4 1.0
F3 A:BFD385 2.8 46.7 1.0
N A:GLY627 2.9 57.3 1.0
OD1 A:BFD385 2.9 52.1 1.0
F2 A:BFD385 3.1 50.5 1.0
CA A:GLY229 3.2 60.1 1.0
CA A:THR626 3.4 60.1 1.0
C A:THR626 3.6 65.0 1.0
CG A:ASN729 3.6 61.7 1.0
N A:GLY229 3.7 57.5 1.0
CE A:LYS707 3.8 47.8 1.0
CG A:BFD385 3.8 49.8 1.0
CA A:GLY627 3.9 50.4 1.0
OD2 A:BFD385 4.0 52.3 1.0
CB A:THR626 4.1 60.0 1.0
C A:THR228 4.1 57.8 1.0
O A:THR228 4.2 63.6 1.0
O A:VAL625 4.2 64.3 1.0
OD1 A:ASN729 4.2 72.5 1.0
MG A:MG1101 4.4 53.5 1.0
N A:THR626 4.5 57.8 1.0
C A:GLY229 4.5 63.9 1.0
CB A:ASN729 4.7 47.8 1.0
OD1 A:ASP730 4.7 61.6 1.0
C A:VAL625 4.8 60.5 1.0
O A:THR626 4.8 74.0 1.0
C A:GLY627 4.8 56.1 1.0
O A:GLY229 4.9 62.1 1.0
N A:ASP628 4.9 53.2 1.0

Fluorine binding site 2 out of 3 in 7efm

Go back to Fluorine Binding Sites List in 7efm
Fluorine binding site 2 out of 3 in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N in (Byk)E2BEF State


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 K791S/E820D/Y340N in (Byk)E2BEF State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:50.5
occ:1.00
 F2 A:BFD385 0.0 50.5 1.0
BE A:BFD385 1.7 54.0 1.0
MG A:MG1101 1.8 53.5 1.0
F3 A:BFD385 2.6 46.7 1.0
OD2 A:BFD385 2.7 52.3 1.0
O A:THR387 3.0 62.1 1.0
OD1 A:BFD385 3.0 52.1 1.0
F1 A:BFD385 3.1 69.0 1.0
CG A:BFD385 3.3 49.8 1.0
CB A:THR387 3.3 66.0 1.0
O A:SER225 3.6 62.1 1.0
ND2 A:ASN729 3.6 58.6 1.0
C A:THR387 3.7 64.7 1.0
CA A:GLY229 3.7 60.1 1.0
N A:THR387 3.8 67.1 1.0
CA A:THR387 3.8 65.5 1.0
OD1 A:ASP726 3.9 61.0 1.0
O A:THR228 4.0 63.6 1.0
O A:GLY229 4.1 62.1 1.0
CG2 A:THR387 4.1 67.5 1.0
OG1 A:THR387 4.2 71.5 1.0
OD1 A:ASN729 4.2 72.5 1.0
C A:GLY229 4.3 63.9 1.0
CG A:ASN729 4.4 61.7 1.0
C A:SER225 4.7 63.5 1.0
N A:GLY229 4.7 57.5 1.0
C A:THR228 4.7 57.8 1.0
CG A:ASP726 4.8 65.6 1.0
C A:LYS386 4.8 61.1 1.0
CB A:BFD385 4.8 42.0 1.0
OD2 A:ASP726 4.8 71.5 1.0
N A:LYS386 4.8 57.8 1.0
O A:ASP726 4.9 76.9 1.0
N A:GLY388 4.9 65.1 1.0

Fluorine binding site 3 out of 3 in 7efm

Go back to Fluorine Binding Sites List in 7efm
Fluorine binding site 3 out of 3 in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N in (Byk)E2BEF State


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 K791S/E820D/Y340N in (Byk)E2BEF State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:46.7
occ:1.00
 F3 A:BFD385 0.0 46.7 1.0
BE A:BFD385 1.8 54.0 1.0
OD1 A:BFD385 2.5 52.1 1.0
F2 A:BFD385 2.6 50.5 1.0
F1 A:BFD385 2.8 69.0 1.0
N A:THR387 2.9 67.1 1.0
CB A:THR626 3.2 60.0 1.0
CA A:GLY229 3.4 60.1 1.0
CB A:THR387 3.5 66.0 1.0
N A:LYS386 3.5 57.8 1.0
O A:GLY229 3.5 62.1 1.0
OG1 A:THR387 3.5 71.5 1.0
CA A:THR626 3.6 60.1 1.0
CB A:LYS386 3.7 53.1 1.0
CG A:BFD385 3.7 49.8 1.0
CA A:THR387 3.7 65.5 1.0
C A:LYS386 3.9 61.1 1.0
CA A:LYS386 3.9 55.0 1.0
CG2 A:THR626 3.9 64.5 1.0
C A:GLY229 3.9 63.9 1.0
OD2 A:BFD385 4.0 52.3 1.0
N A:GLY627 4.1 57.3 1.0
MG A:MG1101 4.1 53.5 1.0
O A:THR387 4.2 62.1 1.0
OG1 A:THR626 4.3 64.8 1.0
CE A:LYS386 4.3 65.4 1.0
C A:THR626 4.4 65.0 1.0
C A:THR387 4.5 64.7 1.0
C A:BFD385 4.6 53.8 1.0
O A:VAL625 4.7 64.3 1.0
N A:GLY229 4.7 57.5 1.0
ND2 A:ASN729 4.8 58.6 1.0
CG A:LYS386 4.8 60.1 1.0
CB A:ASP628 4.8 62.3 1.0
N A:ASP628 4.8 53.2 1.0
CG2 A:THR387 4.8 67.5 1.0
NZ A:LYS707 4.8 42.4 1.0
CA A:BFD385 4.9 45.2 1.0
N A:THR626 4.9 57.8 1.0
CB A:BFD385 4.9 42.0 1.0
CD A:LYS386 4.9 63.4 1.0
O A:LYS386 5.0 58.0 1.0

Reference:

K.Abe, K.Yamamoto, K.Irie. Crystal Structure of the Gastric Proton Pump Mutants To Be Published.
Page generated: Tue Jul 15 19:17:24 2025

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