Magnesium in PDB 7yzr: 50 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model)

All present enzymatic activity of 50 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model):
7.2.2.13;

The structure of 50 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model), PDB code: 7yzr 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)	24.99 / 6.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.94, 118.92, 496.9, 90, 90, 90
R / Rfree (%)	28.9 / 30.9

The structure of 50 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the 50 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model) (pdb code 7yzr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 50 Mm Rb+ Soak of Beryllium Fluoride Inhibited Na+,K+-Atpase, E2-Befx (Rigid Body Model), PDB code: 7yzr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 50 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 Magnesium with other atoms in the Mg binding site number 1 of 50 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:Mg1101 b:393.9 occ:1.00 HG1 A:THR371 1.7 368.5 1.0 OD2 A:ASP710 2.0 364.7 1.0 OD1 A:ASP710 2.0 401.4 1.0 F2 A:BEF1102 2.0 463.1 1.0 OD2 A:ASP369 2.0 494.5 1.0 CG A:ASP710 2.2 362.5 1.0 OG1 A:THR371 2.4 368.9 1.0 O A:THR371 2.5 342.3 1.0 HD21 A:ASN713 2.6 374.9 1.0 CG A:ASP369 3.0 448.8 1.0 C A:THR371 3.2 350.2 1.0 ND2 A:ASN713 3.4 375.3 1.0 CB A:THR371 3.4 351.5 1.0 HG1 A:THR373 3.5 336.0 1.0 H A:THR371 3.5 353.9 1.0 BE A:BEF1102 3.5 467.2 1.0 HA2 A:GLY213 3.6 357.5 1.0 OD1 A:ASP369 3.6 491.9 1.0 CA A:THR371 3.6 346.0 1.0 HB A:THR371 3.7 351.1 1.0 H A:GLY711 3.7 337.5 1.0 N A:THR371 3.7 354.2 1.0 HA3 A:GLY213 3.7 357.5 1.0 CB A:ASP710 3.7 349.1 1.0 HB3 A:ASP369 4.0 387.4 1.0 HD22 A:ASN713 4.0 374.9 1.0 HB3 A:ASP710 4.0 348.8 1.0 CB A:ASP369 4.1 387.8 1.0 OD1 A:ASN713 4.1 365.5 1.0 CA A:GLY213 4.1 357.9 1.0 H A:ASP710 4.1 363.0 1.0 HB2 A:ASP710 4.2 348.8 1.0 OG1 A:THR373 4.2 336.4 1.0 N A:GLY372 4.2 368.0 1.0 CG A:ASN713 4.2 366.3 1.0 F3 A:BEF1102 4.3 478.2 1.0 HA3 A:GLY372 4.3 364.6 1.0 F1 A:BEF1102 4.4 461.8 1.0 H A:THR373 4.5 354.2 1.0 N A:GLY711 4.5 337.9 1.0 HB2 A:ASP369 4.5 387.4 1.0 HA A:THR371 4.5 345.6 1.0 C A:LYS370 4.7 353.9 1.0 O A:GLY213 4.7 328.4 1.0 N A:ASP710 4.7 363.4 1.0 CA A:ASP710 4.7 352.6 1.0 CA A:GLY372 4.7 365.0 1.0 CG2 A:THR371 4.8 344.4 1.0 HZ3 A:LYS691 4.8 371.0 1.0 H A:GLY372 4.8 367.6 1.0 HZ1 A:LYS691 4.9 371.0 1.0 C A:GLY213 4.9 349.6 1.0 HG23 A:THR371 4.9 344.0 1.0 H A:LYS370 4.9 347.2 1.0 N A:THR373 5.0 354.6 1.0

Magnesium binding site 2 out of 2 in the 50 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 Magnesium with other atoms in the Mg binding site number 2 of 50 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:Mg1101 b:357.1 occ:1.00 F1 C:BEF1102 2.0 403.7 1.0 OD1 C:ASP369 2.0 476.7 1.0 OD1 C:ASP710 2.0 416.4 1.0 CG C:ASP369 2.1 466.7 1.0 O C:THR371 2.3 434.2 1.0 OG1 C:THR371 2.3 441.8 1.0 OD2 C:ASP369 2.3 482.1 1.0 BE C:BEF1102 2.4 440.2 1.0 H C:THR371 2.7 436.2 1.0 HG1 C:THR371 2.8 441.6 1.0 N C:THR371 2.9 436.4 1.0 HB3 C:ASP369 3.1 438.1 1.0 C C:THR371 3.1 428.6 1.0 F2 C:BEF1102 3.1 474.5 1.0 CG C:ASP710 3.1 395.0 1.0 HD21 C:ASN713 3.2 414.6 1.0 CB C:ASP369 3.2 438.2 1.0 CA C:THR371 3.3 433.2 1.0 CB C:THR371 3.3 436.6 1.0 C C:LYS370 3.6 432.6 1.0 HD22 C:ASN713 3.6 414.6 1.0 ND2 C:ASN713 3.7 414.8 1.0 OD2 C:ASP710 3.7 393.1 1.0 HB2 C:ASP369 3.7 438.1 1.0 H C:LYS370 3.8 431.7 1.0 H C:THR373 3.8 417.9 1.0 HB C:THR371 3.8 436.5 1.0 F3 C:BEF1102 3.8 459.7 1.0 N C:LYS370 3.9 431.8 1.0 OG1 C:THR610 4.0 413.2 1.0 HB3 C:ASP710 4.0 385.8 1.0 OG1 C:THR373 4.0 394.5 1.0 O C:LYS370 4.0 429.3 1.0 CB C:ASP710 4.2 386.0 1.0 HA C:THR371 4.2 433.1 1.0 HG1 C:THR373 4.2 394.4 1.0 HG23 C:THR371 4.3 437.7 1.0 C C:ASP369 4.3 427.4 1.0 CA C:LYS370 4.3 429.2 1.0 N C:GLY372 4.3 427.5 1.0 CG2 C:THR371 4.4 437.8 1.0 CA C:ASP369 4.4 423.0 1.0 H C:GLY711 4.4 368.9 1.0 HB3 C:LYS370 4.5 420.7 1.0 HA3 C:GLY372 4.5 424.5 1.0 N C:THR373 4.6 418.1 1.0 HA2 C:GLY213 4.6 410.4 1.0 CG C:ASN713 4.7 408.5 1.0 HA C:ASP369 4.8 422.9 1.0 HB2 C:ASP710 4.8 385.8 1.0 HG21 C:THR371 4.8 437.7 1.0 CA C:GLY372 4.9 424.7 1.0 H C:ASP710 4.9 396.9 1.0 CB C:LYS370 4.9 420.8 1.0 HB C:THR610 5.0 394.5 1.0 OD1 C:ASN713 5.0 403.3 1.0

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