Fluorine in PDB 7efn: Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State

Protein crystallography data

The structure of Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State, PDB code: 7efn 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) 48.71 / 3.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.94, 105.94, 372.01, 90, 90, 120
R / Rfree (%) 26.8 / 30.8

Other elements in 7efn:

The structure of Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Rubidium (Rb) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State (pdb code 7efn). 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/E936V in (Byk)E2BEF State, PDB code: 7efn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7efn

Go back to Fluorine Binding Sites List in 7efn
Fluorine binding site 1 out of 3 in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V 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/E936V in (Byk)E2BEF State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:64.6
occ:1.00
F1 A:BFD385 0.0 64.6 1.0
BE A:BFD385 1.7 50.6 1.0
ND2 A:ASN729 2.4 48.6 1.0
F3 A:BFD385 2.7 46.9 1.0
OD1 A:BFD385 3.0 45.3 1.0
CA A:GLY229 3.0 47.8 1.0
F2 A:BFD385 3.1 57.7 1.0
N A:GLY229 3.1 54.4 1.0
N A:GLY627 3.2 52.8 1.0
NZ A:LYS707 3.6 47.3 1.0
CG A:ASN729 3.7 53.3 1.0
C A:THR228 3.8 57.8 1.0
CA A:GLY627 3.8 47.9 1.0
CG A:BFD385 4.0 44.7 1.0
C A:THR626 4.1 55.8 1.0
O A:THR228 4.2 62.0 1.0
CA A:THR626 4.2 52.8 1.0
OG1 A:THR626 4.3 61.4 1.0
OD2 A:BFD385 4.3 39.5 1.0
C A:GLY229 4.4 49.6 1.0
CB A:ASN729 4.4 49.0 1.0
CE A:LYS707 4.5 39.3 1.0
OD1 A:ASN729 4.5 61.9 1.0
CA A:THR228 4.7 49.9 1.0
C A:GLY627 4.7 48.7 1.0
N A:ASP628 4.8 53.8 1.0
O A:GLY229 4.9 51.1 1.0
CB A:THR626 4.9 57.3 1.0
O A:VAL625 4.9 47.8 1.0

Fluorine binding site 2 out of 3 in 7efn

Go back to Fluorine Binding Sites List in 7efn
Fluorine binding site 2 out of 3 in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V 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/E936V in (Byk)E2BEF State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:57.7
occ:1.00
F2 A:BFD385 0.0 57.7 1.0
BE A:BFD385 1.8 50.6 1.0
F3 A:BFD385 2.6 46.9 1.0
OD2 A:BFD385 2.8 39.5 1.0
MG A:MG1101 3.0 41.7 1.0
OD1 A:BFD385 3.0 45.3 1.0
F1 A:BFD385 3.1 64.6 1.0
CA A:GLY229 3.1 47.8 1.0
CB A:THR387 3.2 48.6 1.0
CG A:BFD385 3.3 44.7 1.0
O A:THR387 3.4 48.4 1.0
ND2 A:ASN729 3.6 48.6 1.0
N A:THR387 3.8 41.8 1.0
CA A:THR387 3.8 44.4 1.0
O A:SER225 3.9 58.4 1.0
OG1 A:THR387 3.9 50.1 1.0
C A:THR387 3.9 45.4 1.0
CG2 A:THR387 4.0 44.8 1.0
C A:GLY229 4.1 49.6 1.0
N A:GLY229 4.2 54.4 1.0
O A:THR228 4.2 62.0 1.0
O A:GLY229 4.2 51.1 1.0
OD1 A:ASP726 4.3 44.8 1.0
CG A:ASN729 4.5 53.3 1.0
OD1 A:ASN729 4.5 61.9 1.0
C A:THR228 4.6 57.8 1.0
CB A:BFD385 4.8 39.4 1.0
C A:SER225 5.0 58.9 1.0
C A:LYS386 5.0 43.7 1.0

Fluorine binding site 3 out of 3 in 7efn

Go back to Fluorine Binding Sites List in 7efn
Fluorine binding site 3 out of 3 in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V 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/E936V in (Byk)E2BEF State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F385

b:46.9
occ:1.00
F3 A:BFD385 0.0 46.9 1.0
BE A:BFD385 1.8 50.6 1.0
OG1 A:THR626 2.4 61.4 1.0
OD1 A:BFD385 2.5 45.3 1.0
F2 A:BFD385 2.6 57.7 1.0
F1 A:BFD385 2.7 64.6 1.0
CA A:GLY229 3.0 47.8 1.0
N A:THR387 3.4 41.8 1.0
O A:GLY229 3.5 51.1 1.0
CB A:THR626 3.6 57.3 1.0
OG1 A:THR387 3.6 50.1 1.0
N A:GLY627 3.6 52.8 1.0
CA A:THR626 3.7 52.8 1.0
C A:GLY229 3.7 49.6 1.0
CG A:BFD385 3.7 44.7 1.0
CB A:THR387 3.8 48.6 1.0
N A:LYS386 3.9 48.6 1.0
OD2 A:BFD385 4.1 39.5 1.0
N A:GLY229 4.1 54.4 1.0
CB A:LYS386 4.1 50.4 1.0
CA A:THR387 4.2 44.4 1.0
C A:THR626 4.2 55.8 1.0
N A:ASP628 4.3 53.8 1.0
CA A:LYS386 4.3 48.9 1.0
C A:LYS386 4.4 43.7 1.0
ND2 A:ASN729 4.6 48.6 1.0
CA A:GLY627 4.6 47.9 1.0
C A:BFD385 4.7 45.3 1.0
CB A:ASP628 4.8 44.4 1.0
CG2 A:THR626 4.8 55.8 1.0
O A:THR387 4.8 48.4 1.0
CE A:LYS386 4.8 57.0 1.0
O A:VAL625 4.9 47.8 1.0
C A:GLY627 5.0 48.7 1.0
CB A:BFD385 5.0 39.4 1.0

Reference:

K.Abe, K.Yamamoto, K.Irie. Crystal Structure of the Gastric Proton Pump Mutants To Be Published.
Page generated: Fri Sep 24 13:22:49 2021

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