Fluorine in PDB 7qtv: Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)

Enzymatic activity of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)

All present enzymatic activity of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx):
7.2.2.13;

Protein crystallography data

The structure of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx), PDB code: 7qtv was solved by M.U.Fruergaard, I.Dach, J.L.Andersen, M.Ozol, A.Shahsavar, E.M.Quistgaard, H.Poulsen, N.U.Fedosova, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.67 / 4.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.47, 118.08, 494.66, 90, 90, 90
R / Rfree (%) 24.7 / 28.1

Other elements in 7qtv:

The structure of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) (pdb code 7qtv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx), PDB code: 7qtv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7qtv

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Fluorine binding site 1 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:191.6
occ:1.00
 F1 A:BEF1101 0.0 191.6 1.0
BE A:BEF1101 1.4 197.0 1.0
OD1 A:ASP369 2.2 158.9 1.0
F2 A:BEF1101 2.2 192.9 1.0
F3 A:BEF1101 2.3 208.0 1.0
CG A:ASP369 2.8 146.2 1.0
ND2 A:ASN713 2.8 151.4 1.0
OG1 A:THR610 2.8 148.4 1.0
OD2 A:ASP369 2.9 148.4 1.0
CA A:THR610 3.2 139.6 1.0
NZ A:LYS691 3.3 151.2 1.0
CB A:THR610 3.4 143.0 1.0
N A:GLY611 3.5 156.2 1.0
MG A:MG1106 3.8 145.6 1.0
C A:THR610 3.9 146.2 1.0
O A:VAL609 3.9 130.6 1.0
CE A:LYS691 4.0 142.7 1.0
OD1 A:ASP714 4.0 173.5 1.0
CG A:ASN713 4.1 146.6 1.0
CB A:ASP369 4.2 130.7 1.0
CA A:GLY213 4.3 150.9 1.0
N A:THR610 4.4 134.8 1.0
N A:LYS370 4.6 140.6 1.0
C A:VAL609 4.6 127.0 1.0
CA A:GLY611 4.7 158.5 1.0
OG1 A:THR371 4.7 159.7 1.0
CA A:ASP369 4.8 122.7 1.0
OD1 A:ASN713 4.8 145.8 1.0
CG2 A:THR610 4.9 132.4 1.0
N A:GLY213 4.9 152.7 1.0

Fluorine binding site 2 out of 6 in 7qtv

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Fluorine binding site 2 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:192.9
occ:1.00
 F2 A:BEF1101 0.0 192.9 1.0
BE A:BEF1101 1.4 197.0 1.0
MG A:MG1106 1.9 145.6 1.0
OD2 A:ASP369 2.1 148.4 1.0
F3 A:BEF1101 2.2 208.0 1.0
F1 A:BEF1101 2.2 191.6 1.0
OD1 A:ASP369 2.4 158.9 1.0
CG A:ASP369 2.6 146.2 1.0
OG1 A:THR371 3.0 159.7 1.0
ND2 A:ASN713 3.0 151.4 1.0
OD1 A:ASP710 3.1 142.2 1.0
CA A:GLY213 3.7 150.9 1.0
O A:THR371 3.9 146.9 1.0
CG A:ASN713 4.0 146.6 1.0
OG1 A:THR610 4.0 148.4 1.0
CB A:ASP369 4.1 130.7 1.0
OD1 A:ASN713 4.1 145.8 1.0
N A:THR371 4.2 140.3 1.0
CG A:ASP710 4.2 146.9 1.0
OD1 A:ASP714 4.3 173.5 1.0
CB A:THR371 4.3 142.7 1.0
O A:SER209 4.4 164.3 1.0
OD2 A:ASP714 4.4 180.8 1.0
N A:LYS370 4.5 140.6 1.0
OD2 A:ASP710 4.5 151.2 1.0
N A:GLY213 4.5 152.7 1.0
C A:THR371 4.5 153.8 1.0
CA A:THR371 4.6 142.5 1.0
NZ A:LYS691 4.6 151.2 1.0
CG A:ASP714 4.8 172.2 1.0
C A:GLY213 4.9 139.7 1.0
O A:GLY213 5.0 143.8 1.0
CB A:THR610 5.0 143.0 1.0

Fluorine binding site 3 out of 6 in 7qtv

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Fluorine binding site 3 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:208.0
occ:1.00
 F3 A:BEF1101 0.0 208.0 1.0
BE A:BEF1101 1.4 197.0 1.0
OG1 A:THR610 2.1 148.4 1.0
F2 A:BEF1101 2.2 192.9 1.0
OD1 A:ASP369 2.2 158.9 1.0
F1 A:BEF1101 2.3 191.6 1.0
OG1 A:THR371 3.0 159.7 1.0
CB A:THR610 3.2 143.0 1.0
MG A:MG1106 3.2 145.6 1.0
CG A:ASP369 3.3 146.2 1.0
N A:THR371 3.3 140.3 1.0
N A:LYS370 3.6 140.6 1.0
OD2 A:ASP369 3.6 148.4 1.0
CB A:LYS370 3.8 117.7 1.0
CA A:GLY213 3.9 150.9 1.0
O A:GLY213 3.9 143.8 1.0
CA A:THR610 4.0 139.6 1.0
CB A:THR371 4.0 142.7 1.0
CA A:LYS370 4.0 133.8 1.0
C A:LYS370 4.1 136.7 1.0
CG2 A:THR371 4.2 136.9 1.0
CA A:THR371 4.2 142.5 1.0
N A:GLY611 4.3 156.2 1.0
CG2 A:THR610 4.3 132.4 1.0
C A:GLY213 4.4 139.7 1.0
O A:THR371 4.5 146.9 1.0
ND2 A:ASN713 4.6 151.4 1.0
CB A:ASP369 4.6 130.7 1.0
C A:ASP369 4.6 129.6 1.0
C A:THR610 4.7 146.2 1.0
C A:THR371 4.8 153.8 1.0
CB A:ASP612 4.9 141.3 1.0
N A:ASP612 4.9 151.8 1.0
CA A:ASP369 4.9 122.7 1.0
O A:VAL609 5.0 130.6 1.0
CE A:LYS370 5.0 130.4 1.0

Fluorine binding site 4 out of 6 in 7qtv

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Fluorine binding site 4 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:155.8
occ:1.00
 F1 C:BEF1101 0.0 155.8 1.0
BE C:BEF1101 1.4 165.0 1.0
OD2 C:ASP369 2.2 155.7 1.0
F3 C:BEF1101 2.2 175.0 1.0
F2 C:BEF1101 2.3 173.8 1.0
ND2 C:ASN713 2.5 166.8 1.0
CG2 C:THR371 2.7 173.6 1.0
CG C:ASP369 2.9 157.4 1.0
OD1 C:ASP369 2.9 161.5 1.0
MG C:MG1105 3.1 163.3 1.0
CG C:ASN713 3.6 163.8 1.0
CA C:GLY213 3.6 166.9 1.0
OD1 C:ASP710 3.7 170.5 1.0
OG1 C:THR610 3.7 176.2 1.0
OD1 C:ASN713 3.8 168.8 1.0
CB C:THR371 3.9 172.6 1.0
O C:SER209 4.1 165.1 1.0
CB C:ASP369 4.3 150.0 1.0
OD1 C:ASP714 4.3 166.1 1.0
NZ C:LYS691 4.4 158.5 1.0
OD2 C:ASP714 4.5 163.8 1.0
N C:THR371 4.5 161.2 1.0
O C:GLY213 4.5 168.2 1.0
N C:GLY213 4.5 166.5 1.0
C C:GLY213 4.6 168.3 1.0
O C:THR371 4.6 177.8 1.0
CA C:THR371 4.7 169.2 1.0
CG C:ASP710 4.7 178.5 1.0
CB C:THR610 4.8 160.4 1.0
CG C:ASP714 4.8 164.9 1.0
CB C:ASN713 4.9 158.8 1.0
OG1 C:THR371 4.9 179.9 1.0
N C:GLY611 5.0 159.0 1.0
C C:THR371 5.0 177.4 1.0

Fluorine binding site 5 out of 6 in 7qtv

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Fluorine binding site 5 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:173.8
occ:1.00
 F2 C:BEF1101 0.0 173.8 1.0
BE C:BEF1101 1.4 165.0 1.0
OG1 C:THR610 1.9 176.2 1.0
F3 C:BEF1101 2.3 175.0 1.0
F1 C:BEF1101 2.3 155.8 1.0
CG2 C:THR371 2.9 173.6 1.0
CB C:THR371 3.1 172.6 1.0
CB C:THR610 3.1 160.4 1.0
N C:THR371 3.2 161.2 1.0
O C:GLY213 3.2 168.2 1.0
OD2 C:ASP369 3.3 155.7 1.0
OD1 C:ASP369 3.4 161.5 1.0
CG C:ASP369 3.6 157.4 1.0
CA C:GLY213 3.6 166.9 1.0
CA C:THR371 3.7 169.2 1.0
C C:GLY213 3.9 168.3 1.0
MG C:MG1105 3.9 163.3 1.0
CA C:THR610 4.1 154.2 1.0
CG2 C:THR610 4.2 152.9 1.0
N C:LYS370 4.2 165.2 1.0
N C:GLY611 4.2 159.0 1.0
C C:LYS370 4.3 164.5 1.0
NZ C:LYS370 4.4 171.4 1.0
OG1 C:THR371 4.4 179.9 1.0
ND2 C:ASN713 4.5 166.8 1.0
CA C:LYS370 4.6 164.0 1.0
CB C:LYS370 4.6 161.4 1.0
CB C:ASP612 4.7 161.0 1.0
O C:THR371 4.7 177.8 1.0
C C:THR610 4.7 157.1 1.0
C C:THR371 4.7 177.4 1.0
C C:ASP369 4.7 159.5 1.0
N C:ASP612 4.8 163.0 1.0
CB C:ASP369 4.8 150.0 1.0
CE C:LYS370 4.9 166.4 1.0

Fluorine binding site 6 out of 6 in 7qtv

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Fluorine binding site 6 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:175.0
occ:1.00
 F3 C:BEF1101 0.0 175.0 1.0
BE C:BEF1101 1.4 165.0 1.0
OG1 C:THR610 2.2 176.2 1.0
F1 C:BEF1101 2.2 155.8 1.0
F2 C:BEF1101 2.3 173.8 1.0
OD1 C:ASP369 2.4 161.5 1.0
N C:GLY611 2.9 159.0 1.0
CA C:THR610 3.0 154.2 1.0
CB C:THR610 3.0 160.4 1.0
ND2 C:ASN713 3.1 166.8 1.0
CG C:ASP369 3.2 157.4 1.0
OD2 C:ASP369 3.3 155.7 1.0
C C:THR610 3.4 157.1 1.0
NZ C:LYS691 3.7 158.5 1.0
CA C:GLY213 4.0 166.9 1.0
CA C:GLY611 4.1 155.6 1.0
CE C:LYS691 4.2 146.8 1.0
O C:VAL609 4.2 146.0 1.0
N C:THR610 4.3 149.3 1.0
CG2 C:THR610 4.4 152.9 1.0
CG C:ASN713 4.4 163.8 1.0
CG2 C:THR371 4.5 173.6 1.0
O C:GLY213 4.5 168.2 1.0
CB C:ASP369 4.6 150.0 1.0
OD1 C:ASP714 4.7 166.1 1.0
C C:VAL609 4.7 147.9 1.0
O C:THR610 4.7 156.0 1.0
N C:ASP612 4.7 163.0 1.0
MG C:MG1105 4.8 163.3 1.0
C C:GLY213 4.8 168.3 1.0
C C:GLY611 4.9 166.5 1.0
O C:THR212 5.0 166.0 1.0
N C:GLY213 5.0 166.5 1.0
N C:LYS370 5.0 165.2 1.0

Reference:

M.U.Fruergaard, I.Dach, J.L.Andersen, M.Ozol, A.Shahsavar, E.M.Quistgaard, H.Poulsen, N.U.Fedosova, P.Nissen. The Na + ,K + -Atpase in Complex with Beryllium Fluoride Mimics An Atpase Phosphorylated State. J.Biol.Chem. V. 298 02317 2022.
ISSN: ESSN 1083-351X
PubMed: 35926706
DOI: 10.1016/J.JBC.2022.102317
Page generated: Fri Aug 2 11:48:49 2024

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