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

Go back to Fluorine Binding Sites List in 7qtv
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

Go back to Fluorine Binding Sites List in 7qtv
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

Go back to Fluorine Binding Sites List in 7qtv
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

Go back to Fluorine Binding Sites List in 7qtv
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

Go back to Fluorine Binding Sites List in 7qtv
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

Go back to Fluorine Binding Sites List in 7qtv
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy