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Fluorine in PDB 7z04: 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model)

Enzymatic activity of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model)

All present enzymatic activity of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model):
7.2.2.13;

Protein crystallography data

The structure of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model), PDB code: 7z04 was solved by M.U.Fruergaard, I.Dach, J.L.Andersen, M.Ozol, A.Shasavar, 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) 25.00 / 7.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119, 119.15, 498.24, 90, 90, 90
R / Rfree (%) 30.3 / 33.8

Other elements in 7z04:

The structure of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) (pdb code 7z04). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model), PDB code: 7z04:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7z04

Go back to Fluorine Binding Sites List in 7z04
Fluorine binding site 1 out of 6 in the 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:585.5
occ:1.00
F1 A:BEF1101 0.0 585.5 1.0
BE A:BEF1101 1.5 591.0 1.0
OD1 A:ASP369 2.4 566.4 1.0
NZ A:LYS691 2.4 446.0 1.0
F3 A:BEF1101 2.6 601.9 1.0
F2 A:BEF1101 2.6 586.9 1.0
CG A:ASP369 2.9 523.3 1.0
N A:GLY611 3.0 456.8 1.0
OD2 A:ASP369 3.2 569.1 1.0
CA A:THR610 3.2 464.4 1.0
OG1 A:THR610 3.4 448.4 1.0
C A:THR610 3.6 463.9 1.0
ND2 A:ASN713 3.6 449.8 1.0
CB A:THR610 3.7 454.0 1.0
CE A:LYS691 3.9 446.8 1.0
OD1 A:ASN713 3.9 440.0 1.0
CA A:GLY611 4.1 458.6 1.0
CB A:ASP369 4.1 462.3 1.0
CG A:ASN713 4.1 440.9 1.0
O A:VAL609 4.1 449.4 1.0
MG A:MG1102 4.2 539.5 1.0
N A:THR610 4.3 467.4 1.0
N A:LYS370 4.4 422.2 1.0
CA A:GLY213 4.6 449.6 1.0
O A:THR212 4.6 465.5 1.0
CA A:ASP369 4.6 431.2 1.0
C A:VAL609 4.6 449.1 1.0
O A:THR610 4.8 464.6 1.0
OG1 A:THR371 4.9 443.4 1.0
CD A:LYS691 4.9 438.1 1.0
C A:GLY611 4.9 457.5 1.0

Fluorine binding site 2 out of 6 in 7z04

Go back to Fluorine Binding Sites List in 7z04
Fluorine binding site 2 out of 6 in the 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:586.9
occ:1.00
F2 A:BEF1101 0.0 586.9 1.0
BE A:BEF1101 1.6 591.0 1.0
MG A:MG1102 1.9 539.5 1.0
OD2 A:ASP369 2.0 569.1 1.0
F3 A:BEF1101 2.5 601.9 1.0
OD1 A:ASP369 2.5 566.4 1.0
CG A:ASP369 2.6 523.3 1.0
F1 A:BEF1101 2.6 585.5 1.0
OG1 A:THR371 2.8 443.4 1.0
CA A:GLY213 3.4 449.6 1.0
OD1 A:ASP710 3.5 475.9 1.0
ND2 A:ASN713 3.6 449.8 1.0
O A:THR371 3.6 416.8 1.0
N A:THR371 3.9 428.8 1.0
CB A:THR371 4.0 426.1 1.0
OD1 A:ASN713 4.1 440.0 1.0
CB A:ASP369 4.1 462.3 1.0
O A:GLY213 4.2 420.2 1.0
C A:THR371 4.2 424.7 1.0
CA A:THR371 4.3 420.6 1.0
CG A:ASN713 4.3 440.9 1.0
C A:GLY213 4.3 441.4 1.0
N A:GLY213 4.4 454.7 1.0
CG A:ASP710 4.4 437.0 1.0
N A:LYS370 4.6 422.2 1.0
NZ A:LYS691 4.6 446.0 1.0
OG1 A:THR610 4.6 448.4 1.0
OD2 A:ASP710 4.6 439.2 1.0
C A:LYS370 4.7 428.4 1.0
OD2 A:ASP714 4.8 465.8 1.0
O A:THR212 4.9 465.5 1.0
O A:SER209 4.9 457.6 1.0
C A:THR212 5.0 456.1 1.0
OG1 A:THR373 5.0 411.0 1.0

Fluorine binding site 3 out of 6 in 7z04

Go back to Fluorine Binding Sites List in 7z04
Fluorine binding site 3 out of 6 in the 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:601.9
occ:1.00
F3 A:BEF1101 0.0 601.9 1.0
BE A:BEF1101 1.5 591.0 1.0
OD1 A:ASP369 2.2 566.4 1.0
OG1 A:THR610 2.3 448.4 1.0
F2 A:BEF1101 2.5 586.9 1.0
F1 A:BEF1101 2.6 585.5 1.0
OG1 A:THR371 3.1 443.4 1.0
N A:THR371 3.1 428.8 1.0
CG A:ASP369 3.3 523.3 1.0
CB A:THR610 3.3 454.0 1.0
N A:LYS370 3.4 422.2 1.0
CB A:LYS370 3.5 390.5 1.0
MG A:MG1102 3.6 539.5 1.0
O A:GLY213 3.6 420.2 1.0
OD2 A:ASP369 3.6 569.1 1.0
CA A:LYS370 3.8 414.3 1.0
N A:GLY611 3.8 456.8 1.0
CA A:THR610 3.8 464.4 1.0
C A:LYS370 3.9 428.4 1.0
CB A:THR371 4.0 426.1 1.0
CA A:THR371 4.1 420.6 1.0
CA A:GLY213 4.1 449.6 1.0
C A:THR610 4.3 463.9 1.0
CG2 A:THR371 4.3 419.0 1.0
C A:GLY213 4.3 441.4 1.0
CB A:ASP612 4.4 442.2 1.0
N A:ASP612 4.5 449.8 1.0
C A:ASP369 4.5 421.3 1.0
CG2 A:THR610 4.6 455.3 1.0
O A:THR371 4.6 416.8 1.0
CB A:ASP369 4.6 462.3 1.0
CA A:GLY611 4.7 458.6 1.0
C A:GLY611 4.8 457.5 1.0
CG A:LYS370 4.9 386.4 1.0
C A:THR371 4.9 424.7 1.0
CA A:ASP369 4.9 431.2 1.0
NZ A:LYS691 5.0 446.0 1.0
O A:VAL609 5.0 449.4 1.0
O A:LYS370 5.0 436.6 1.0

Fluorine binding site 4 out of 6 in 7z04

Go back to Fluorine Binding Sites List in 7z04
Fluorine binding site 4 out of 6 in the 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:520.7
occ:1.00
F1 C:BEF1101 0.0 520.7 1.0
BE C:BEF1101 1.5 530.2 1.0
MG C:MG1102 2.0 502.8 1.0
OD2 C:ASP369 2.1 548.5 1.0
OD1 C:ASN713 2.3 469.6 1.0
F3 C:BEF1101 2.6 535.0 1.0
CG C:ASP369 2.6 533.0 1.0
F2 C:BEF1101 2.6 542.6 1.0
OD1 C:ASP369 2.8 543.0 1.0
CG C:ASN713 3.3 474.8 1.0
OD1 C:ASP710 3.4 482.7 1.0
OG1 C:THR371 3.5 508.1 1.0
CA C:GLY213 3.7 494.0 1.0
ND2 C:ASN713 3.7 481.1 1.0
CB C:ASP369 3.8 504.6 1.0
NZ C:LYS691 4.0 467.0 1.0
OD2 C:ASP710 4.0 459.5 1.0
O C:THR212 4.1 510.3 1.0
OD2 C:ASP714 4.1 492.6 1.0
CG C:ASP710 4.2 461.4 1.0
N C:GLY213 4.2 499.2 1.0
C C:THR212 4.4 502.5 1.0
OD1 C:ASP714 4.4 493.7 1.0
OG1 C:THR610 4.5 479.5 1.0
N C:GLY611 4.6 445.8 1.0
CG C:ASP714 4.7 487.7 1.0
CB C:ASN713 4.7 473.8 1.0
O C:SER209 4.7 490.2 1.0
O C:THR371 4.7 500.6 1.0
O C:SER210 4.9 511.4 1.0
CB C:THR371 4.9 502.9 1.0
C C:GLY213 5.0 500.6 1.0

Fluorine binding site 5 out of 6 in 7z04

Go back to Fluorine Binding Sites List in 7z04
Fluorine binding site 5 out of 6 in the 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:542.6
occ:1.00
F2 C:BEF1101 0.0 542.6 1.0
BE C:BEF1101 1.5 530.2 1.0
OG1 C:THR610 2.1 479.5 1.0
OD1 C:ASP369 2.4 543.0 1.0
OD2 C:ASP369 2.4 548.5 1.0
F3 C:BEF1101 2.6 535.0 1.0
F1 C:BEF1101 2.6 520.7 1.0
N C:GLY611 2.7 445.8 1.0
CG C:ASP369 2.7 533.0 1.0
CB C:THR610 3.2 461.0 1.0
CA C:GLY213 3.2 494.0 1.0
CA C:THR610 3.2 459.5 1.0
OG1 C:THR371 3.3 508.1 1.0
C C:THR610 3.4 456.4 1.0
MG C:MG1102 3.5 502.8 1.0
CA C:GLY611 3.7 453.6 1.0
O C:GLY213 3.7 491.4 1.0
O C:THR212 3.7 510.3 1.0
N C:ASP612 3.9 458.5 1.0
C C:GLY213 3.9 500.6 1.0
CG2 C:THR610 4.0 455.2 1.0
N C:LYS370 4.1 498.1 1.0
C C:GLY611 4.2 465.0 1.0
CB C:ASP369 4.2 504.6 1.0
OD1 C:ASN713 4.2 469.6 1.0
N C:GLY213 4.2 499.2 1.0
N C:THR371 4.3 502.7 1.0
NZ C:LYS691 4.4 467.0 1.0
C C:THR212 4.4 502.5 1.0
CB C:THR371 4.5 502.9 1.0
CB C:LYS370 4.6 487.2 1.0
O C:THR610 4.6 461.6 1.0
N C:THR610 4.6 454.1 1.0
O C:VAL609 4.7 424.6 1.0
CB C:ASP612 4.8 446.8 1.0
CA C:LYS370 4.8 495.6 1.0
CA C:ASP369 4.8 489.4 1.0
CG2 C:THR371 4.9 504.2 1.0
CA C:ASP612 4.9 464.3 1.0
C C:ASP369 5.0 493.8 1.0
C C:LYS370 5.0 498.9 1.0

Fluorine binding site 6 out of 6 in 7z04

Go back to Fluorine Binding Sites List in 7z04
Fluorine binding site 6 out of 6 in the 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 10 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:535.0
occ:1.00
F3 C:BEF1101 0.0 535.0 1.0
BE C:BEF1101 1.6 530.2 1.0
OD1 C:ASN713 2.4 469.6 1.0
O C:THR212 2.5 510.3 1.0
F2 C:BEF1101 2.6 542.6 1.0
F1 C:BEF1101 2.6 520.7 1.0
N C:GLY611 2.6 445.8 1.0
OD2 C:ASP369 2.6 548.5 1.0
NZ C:LYS691 2.6 467.0 1.0
CA C:GLY611 3.2 453.6 1.0
CG C:ASN713 3.3 474.8 1.0
C C:THR212 3.4 502.5 1.0
C C:THR610 3.5 456.4 1.0
CE C:LYS691 3.6 466.3 1.0
CG C:ASP369 3.7 533.0 1.0
CA C:THR610 3.8 459.5 1.0
CA C:GLY213 3.8 494.0 1.0
N C:GLY213 4.0 499.2 1.0
CB C:ASN713 4.1 473.8 1.0
ND2 C:ASN713 4.2 481.1 1.0
OD1 C:ASP369 4.2 543.0 1.0
OG1 C:THR610 4.2 479.5 1.0
C C:GLY611 4.4 465.0 1.0
MG C:MG1102 4.4 502.8 1.0
O C:THR610 4.5 461.6 1.0
CA C:THR212 4.5 494.0 1.0
O C:THR686 4.6 436.9 1.0
CB C:THR610 4.7 461.0 1.0
OD1 C:ASP714 4.8 493.7 1.0
N C:ASP612 4.8 458.5 1.0
CD C:LYS691 4.8 455.4 1.0
N C:THR610 4.9 454.1 1.0
CB C:ASP369 5.0 504.6 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: Wed Jul 16 02:21:32 2025

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