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Fluorine in PDB 7vh6: Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)

Enzymatic activity of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)

All present enzymatic activity of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry):
7.1.2.1;

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) (pdb code 7vh6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry), PDB code: 7vh6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 7vh6

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Fluorine binding site 1 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:59.8
occ:1.00
 F1 A:BEF1001 0.0 59.8 1.0
BE A:BEF1001 1.5 59.8 1.0
OD1 A:ASP634 2.4 44.1 1.0
F3 A:BEF1001 2.5 59.8 1.0
F2 A:BEF1001 2.6 59.8 1.0
OG1 A:THR380 2.7 52.6 1.0
CG A:ASP634 3.1 44.1 1.0
OD2 A:ASP634 3.1 44.1 1.0
O A:SER228 3.2 46.7 1.0
N A:GLY635 3.7 45.5 1.0
CA A:GLY635 3.8 45.5 1.0
O A:ALA229 3.8 48.6 1.0
OD2 A:ASP378 3.9 48.5 1.0
CA A:GLY232 3.9 47.6 1.0
CB A:THR380 4.0 52.6 1.0
N A:GLY381 4.3 51.0 1.0
N A:GLY232 4.4 47.6 1.0
C A:ALA229 4.4 48.6 1.0
O A:ILE230 4.4 46.0 1.0
C A:SER228 4.5 46.7 1.0
CB A:ASP634 4.5 44.1 1.0
C A:ASP634 4.6 44.1 1.0
CG2 A:THR380 4.6 52.6 1.0
ND2 A:ASN637 4.7 52.2 1.0
CA A:GLY381 4.8 51.0 1.0
C A:ILE230 4.8 46.0 1.0
CG A:ASP378 4.9 48.5 1.0
C A:THR231 4.9 41.6 1.0
CA A:ASP634 5.0 44.1 1.0

Fluorine binding site 2 out of 18 in 7vh6

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Fluorine binding site 2 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:59.8
occ:1.00
 F2 A:BEF1001 0.0 59.8 1.0
BE A:BEF1001 1.6 59.8 1.0
OD2 A:ASP378 2.2 48.5 1.0
F3 A:BEF1001 2.5 59.8 1.0
F1 A:BEF1001 2.6 59.8 1.0
OD1 A:ASP634 2.7 44.1 1.0
N A:GLY635 2.9 45.5 1.0
OD1 A:ASN637 3.0 52.2 1.0
CA A:GLY635 3.3 45.5 1.0
ND2 A:ASN637 3.4 52.2 1.0
CG A:ASP378 3.5 48.5 1.0
CG A:ASN637 3.6 52.2 1.0
OD1 A:ASP638 3.8 47.9 1.0
OD2 A:ASP638 3.8 47.9 1.0
CG A:ASP634 3.9 44.1 1.0
N A:ASP634 4.0 44.1 1.0
OG1 A:THR380 4.0 52.6 1.0
CG A:ASP638 4.1 47.9 1.0
C A:ASP634 4.1 44.1 1.0
C A:GLY635 4.2 45.5 1.0
OD1 A:ASP378 4.3 48.5 1.0
CB A:ASP378 4.3 48.5 1.0
O A:ILE230 4.4 46.0 1.0
CA A:ASP634 4.5 44.1 1.0
O A:GLY635 4.5 45.5 1.0
OD2 A:ASP634 4.6 44.1 1.0
NZ A:LYS615 4.7 50.9 1.0
CB A:ASP634 4.8 44.1 1.0
C A:GLY633 5.0 43.7 1.0

Fluorine binding site 3 out of 18 in 7vh6

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Fluorine binding site 3 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:59.8
occ:1.00
 F3 A:BEF1001 0.0 59.8 1.0
BE A:BEF1001 1.5 59.8 1.0
OG1 A:THR380 2.1 52.6 1.0
OD1 A:ASP634 2.2 44.1 1.0
OD2 A:ASP378 2.4 48.5 1.0
F2 A:BEF1001 2.5 59.8 1.0
F1 A:BEF1001 2.5 59.8 1.0
N A:GLY381 2.9 51.0 1.0
CG A:ASP378 3.0 48.5 1.0
CG A:ASP634 3.1 44.1 1.0
CB A:THR380 3.5 52.6 1.0
CA A:GLY381 3.6 51.0 1.0
OD2 A:ASP634 3.6 44.1 1.0
CB A:ASP378 3.6 48.5 1.0
OD1 A:ASP378 3.7 48.5 1.0
C A:THR380 3.8 52.6 1.0
CA A:THR380 4.0 52.6 1.0
N A:THR380 4.0 52.6 1.0
CG2 A:THR380 4.0 52.6 1.0
N A:THR382 4.2 48.0 1.0
N A:ASP634 4.2 44.1 1.0
N A:GLY635 4.3 45.5 1.0
CB A:ASP634 4.3 44.1 1.0
C A:GLY381 4.4 51.0 1.0
CG2 A:THR382 4.7 48.0 1.0
CA A:ASP634 4.7 44.1 1.0
C A:ASP378 4.7 48.5 1.0
CA A:ASP378 4.8 48.5 1.0
O A:ASP378 4.8 48.5 1.0
O A:THR380 5.0 52.6 1.0

Fluorine binding site 4 out of 18 in 7vh6

Go back to Fluorine Binding Sites List in 7vh6
Fluorine binding site 4 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:59.8
occ:1.00
 F1 B:BEF1001 0.0 59.8 1.0
BE B:BEF1001 1.5 59.8 1.0
OD1 B:ASP634 2.4 44.1 1.0
F3 B:BEF1001 2.5 59.8 1.0
F2 B:BEF1001 2.6 59.8 1.0
OG1 B:THR380 2.7 52.6 1.0
CG B:ASP634 3.1 44.1 1.0
OD2 B:ASP634 3.1 44.1 1.0
O B:SER228 3.2 46.7 1.0
N B:GLY635 3.7 45.5 1.0
CA B:GLY635 3.8 45.5 1.0
O B:ALA229 3.8 48.6 1.0
OD2 B:ASP378 3.9 48.5 1.0
CA B:GLY232 3.9 47.6 1.0
CB B:THR380 4.0 52.6 1.0
N B:GLY381 4.3 51.0 1.0
N B:GLY232 4.4 47.6 1.0
C B:ALA229 4.4 48.6 1.0
O B:ILE230 4.4 46.0 1.0
C B:SER228 4.5 46.7 1.0
CB B:ASP634 4.5 44.1 1.0
C B:ASP634 4.6 44.1 1.0
CG2 B:THR380 4.6 52.6 1.0
ND2 B:ASN637 4.7 52.2 1.0
CA B:GLY381 4.8 51.0 1.0
C B:ILE230 4.8 46.0 1.0
CG B:ASP378 4.9 48.5 1.0
C B:THR231 4.9 41.6 1.0
CA B:ASP634 5.0 44.1 1.0

Fluorine binding site 5 out of 18 in 7vh6

Go back to Fluorine Binding Sites List in 7vh6
Fluorine binding site 5 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:59.8
occ:1.00
 F2 B:BEF1001 0.0 59.8 1.0
BE B:BEF1001 1.6 59.8 1.0
OD2 B:ASP378 2.2 48.5 1.0
F3 B:BEF1001 2.5 59.8 1.0
F1 B:BEF1001 2.6 59.8 1.0
OD1 B:ASP634 2.7 44.1 1.0
N B:GLY635 2.9 45.5 1.0
OD1 B:ASN637 3.0 52.2 1.0
CA B:GLY635 3.3 45.5 1.0
ND2 B:ASN637 3.4 52.2 1.0
CG B:ASP378 3.5 48.5 1.0
CG B:ASN637 3.6 52.2 1.0
OD1 B:ASP638 3.8 47.9 1.0
OD2 B:ASP638 3.8 47.9 1.0
CG B:ASP634 3.9 44.1 1.0
N B:ASP634 4.0 44.1 1.0
OG1 B:THR380 4.0 52.6 1.0
CG B:ASP638 4.1 47.9 1.0
C B:ASP634 4.1 44.1 1.0
C B:GLY635 4.2 45.5 1.0
OD1 B:ASP378 4.3 48.5 1.0
CB B:ASP378 4.3 48.5 1.0
O B:ILE230 4.4 46.0 1.0
CA B:ASP634 4.5 44.1 1.0
O B:GLY635 4.5 45.5 1.0
OD2 B:ASP634 4.6 44.1 1.0
NZ B:LYS615 4.7 50.9 1.0
CB B:ASP634 4.8 44.1 1.0
C B:GLY633 5.0 43.7 1.0

Fluorine binding site 6 out of 18 in 7vh6

Go back to Fluorine Binding Sites List in 7vh6
Fluorine binding site 6 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:59.8
occ:1.00
 F3 B:BEF1001 0.0 59.8 1.0
BE B:BEF1001 1.5 59.8 1.0
OG1 B:THR380 2.1 52.6 1.0
OD1 B:ASP634 2.2 44.1 1.0
OD2 B:ASP378 2.4 48.5 1.0
F2 B:BEF1001 2.5 59.8 1.0
F1 B:BEF1001 2.5 59.8 1.0
N B:GLY381 2.8 51.0 1.0
CG B:ASP378 3.0 48.5 1.0
CG B:ASP634 3.1 44.1 1.0
CB B:THR380 3.5 52.6 1.0
CA B:GLY381 3.6 51.0 1.0
OD2 B:ASP634 3.6 44.1 1.0
CB B:ASP378 3.6 48.5 1.0
OD1 B:ASP378 3.7 48.5 1.0
C B:THR380 3.8 52.6 1.0
CA B:THR380 4.0 52.6 1.0
N B:THR380 4.0 52.6 1.0
CG2 B:THR380 4.0 52.6 1.0
N B:THR382 4.2 48.0 1.0
N B:ASP634 4.2 44.1 1.0
N B:GLY635 4.3 45.5 1.0
CB B:ASP634 4.3 44.1 1.0
C B:GLY381 4.4 51.0 1.0
CG2 B:THR382 4.7 48.0 1.0
CA B:ASP634 4.7 44.1 1.0
C B:ASP378 4.7 48.5 1.0
CA B:ASP378 4.8 48.5 1.0
O B:ASP378 4.8 48.5 1.0
O B:THR380 5.0 52.6 1.0

Fluorine binding site 7 out of 18 in 7vh6

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Fluorine binding site 7 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1001

b:59.8
occ:1.00
 F1 C:BEF1001 0.0 59.8 1.0
BE C:BEF1001 1.5 59.8 1.0
OD1 C:ASP634 2.4 44.1 1.0
F3 C:BEF1001 2.5 59.8 1.0
F2 C:BEF1001 2.6 59.8 1.0
OG1 C:THR380 2.7 52.6 1.0
CG C:ASP634 3.1 44.1 1.0
OD2 C:ASP634 3.1 44.1 1.0
O C:SER228 3.2 46.7 1.0
N C:GLY635 3.7 45.5 1.0
CA C:GLY635 3.8 45.5 1.0
O C:ALA229 3.8 48.6 1.0
OD2 C:ASP378 3.9 48.5 1.0
CA C:GLY232 3.9 47.6 1.0
CB C:THR380 4.0 52.6 1.0
N C:GLY381 4.3 51.0 1.0
N C:GLY232 4.4 47.6 1.0
C C:ALA229 4.4 48.6 1.0
O C:ILE230 4.4 46.0 1.0
C C:SER228 4.5 46.7 1.0
CB C:ASP634 4.5 44.1 1.0
C C:ASP634 4.6 44.1 1.0
CG2 C:THR380 4.6 52.6 1.0
ND2 C:ASN637 4.7 52.2 1.0
CA C:GLY381 4.8 51.0 1.0
C C:ILE230 4.8 46.0 1.0
CG C:ASP378 4.9 48.5 1.0
C C:THR231 4.9 41.6 1.0
CA C:ASP634 5.0 44.1 1.0

Fluorine binding site 8 out of 18 in 7vh6

Go back to Fluorine Binding Sites List in 7vh6
Fluorine binding site 8 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1001

b:59.8
occ:1.00
 F2 C:BEF1001 0.0 59.8 1.0
BE C:BEF1001 1.6 59.8 1.0
OD2 C:ASP378 2.2 48.5 1.0
F3 C:BEF1001 2.5 59.8 1.0
F1 C:BEF1001 2.6 59.8 1.0
OD1 C:ASP634 2.7 44.1 1.0
N C:GLY635 2.9 45.5 1.0
OD1 C:ASN637 3.0 52.2 1.0
CA C:GLY635 3.4 45.5 1.0
ND2 C:ASN637 3.4 52.2 1.0
CG C:ASP378 3.5 48.5 1.0
CG C:ASN637 3.6 52.2 1.0
OD1 C:ASP638 3.8 47.9 1.0
OD2 C:ASP638 3.8 47.9 1.0
CG C:ASP634 3.9 44.1 1.0
N C:ASP634 4.0 44.1 1.0
OG1 C:THR380 4.0 52.6 1.0
CG C:ASP638 4.1 47.9 1.0
C C:ASP634 4.1 44.1 1.0
C C:GLY635 4.2 45.5 1.0
OD1 C:ASP378 4.3 48.5 1.0
CB C:ASP378 4.3 48.5 1.0
O C:ILE230 4.4 46.0 1.0
CA C:ASP634 4.5 44.1 1.0
O C:GLY635 4.5 45.5 1.0
OD2 C:ASP634 4.6 44.1 1.0
NZ C:LYS615 4.7 50.9 1.0
CB C:ASP634 4.8 44.1 1.0
C C:GLY633 5.0 43.7 1.0

Fluorine binding site 9 out of 18 in 7vh6

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Fluorine binding site 9 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1001

b:59.8
occ:1.00
 F3 C:BEF1001 0.0 59.8 1.0
BE C:BEF1001 1.5 59.8 1.0
OG1 C:THR380 2.1 52.6 1.0
OD1 C:ASP634 2.2 44.1 1.0
OD2 C:ASP378 2.4 48.5 1.0
F2 C:BEF1001 2.5 59.8 1.0
F1 C:BEF1001 2.5 59.8 1.0
N C:GLY381 2.8 51.0 1.0
CG C:ASP378 3.0 48.5 1.0
CG C:ASP634 3.1 44.1 1.0
CB C:THR380 3.5 52.6 1.0
CA C:GLY381 3.6 51.0 1.0
OD2 C:ASP634 3.6 44.1 1.0
CB C:ASP378 3.6 48.5 1.0
OD1 C:ASP378 3.7 48.5 1.0
C C:THR380 3.8 52.6 1.0
CA C:THR380 4.0 52.6 1.0
N C:THR380 4.0 52.6 1.0
CG2 C:THR380 4.0 52.6 1.0
N C:THR382 4.2 48.0 1.0
N C:ASP634 4.2 44.1 1.0
N C:GLY635 4.3 45.5 1.0
CB C:ASP634 4.3 44.1 1.0
C C:GLY381 4.4 51.0 1.0
CG2 C:THR382 4.7 48.0 1.0
CA C:ASP634 4.7 44.1 1.0
C C:ASP378 4.7 48.5 1.0
CA C:ASP378 4.8 48.5 1.0
O C:ASP378 4.8 48.5 1.0
O C:THR380 5.0 52.6 1.0

Fluorine binding site 10 out of 18 in 7vh6

Go back to Fluorine Binding Sites List in 7vh6
Fluorine binding site 10 out of 18 in the Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Cryo-Em Structure of the Hexameric Plasma Membrane H+-Atpase in the Active State (pH 6.0, BEF3-, Conformation 1, C1 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1001

b:59.8
occ:1.00
 F1 D:BEF1001 0.0 59.8 1.0
BE D:BEF1001 1.5 59.8 1.0
OD1 D:ASP634 2.4 44.1 1.0
F3 D:BEF1001 2.5 59.8 1.0
F2 D:BEF1001 2.6 59.8 1.0
OG1 D:THR380 2.7 52.6 1.0
CG D:ASP634 3.1 44.1 1.0
OD2 D:ASP634 3.1 44.1 1.0
O D:SER228 3.2 46.7 1.0
N D:GLY635 3.7 45.5 1.0
CA D:GLY635 3.8 45.5 1.0
O D:ALA229 3.8 48.6 1.0
OD2 D:ASP378 3.9 48.5 1.0
CA D:GLY232 3.9 47.6 1.0
CB D:THR380 4.0 52.6 1.0
N D:GLY381 4.3 51.0 1.0
N D:GLY232 4.4 47.6 1.0
C D:ALA229 4.4 48.6 1.0
O D:ILE230 4.4 46.0 1.0
C D:SER228 4.5 46.7 1.0
CB D:ASP634 4.5 44.1 1.0
C D:ASP634 4.6 44.1 1.0
CG2 D:THR380 4.6 52.6 1.0
ND2 D:ASN637 4.7 52.2 1.0
CA D:GLY381 4.8 51.0 1.0
C D:ILE230 4.8 46.0 1.0
CG D:ASP378 4.9 48.5 1.0
C D:THR231 4.9 41.6 1.0
CA D:ASP634 5.0 44.1 1.0

Reference:

P.Zhao, C.Zhao, D.Chen, C.Yun, H.Li, L.Bai. Structure and Activation Mechanism of the Hexameric Plasma Membrane H+-Atpase Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-26782-Y
Page generated: Wed Jul 16 01:13:58 2025

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