Magnesium in PDB 7z04: 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;

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

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:

Fluorine

(F)

6 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg1102 b:539.5 occ:1.00 O A:THR371 1.8 416.8 1.0 OD2 A:ASP369 1.8 569.1 1.0 F2 A:BEF1101 1.9 586.9 1.0 OD1 A:ASP710 2.1 475.9 1.0 CG A:ASP369 2.6 523.3 1.0 C A:THR371 2.7 424.7 1.0 OG1 A:THR371 2.7 443.4 1.0 BE A:BEF1101 2.9 591.0 1.0 CG A:ASP710 3.0 437.0 1.0 OD1 A:ASP369 3.0 566.4 1.0 N A:THR371 3.2 428.8 1.0 CA A:THR371 3.2 420.6 1.0 OD2 A:ASP710 3.3 439.2 1.0 OG1 A:THR373 3.5 411.0 1.0 CB A:THR371 3.5 426.1 1.0 F3 A:BEF1101 3.6 601.9 1.0 N A:GLY372 3.8 442.6 1.0 CB A:ASP369 3.8 462.3 1.0 C A:LYS370 3.9 428.4 1.0 CB A:ASP710 4.1 423.7 1.0 F1 A:BEF1101 4.2 585.5 1.0 N A:THR373 4.2 429.2 1.0 O A:LYS370 4.3 436.6 1.0 N A:LYS370 4.4 422.2 1.0 CA A:GLY372 4.4 439.6 1.0 CB A:THR373 4.4 401.4 1.0 N A:ASP710 4.7 438.0 1.0 CA A:GLY213 4.7 449.6 1.0 C A:GLY372 4.7 436.1 1.0 C A:ASP369 4.7 421.3 1.0 OD2 A:ASP714 4.7 465.8 1.0 CA A:LYS370 4.7 414.3 1.0 CG2 A:THR371 4.8 419.0 1.0 N A:GLY711 4.9 412.4 1.0 CA A:ASP369 4.9 431.2 1.0 CA A:ASP710 4.9 427.1 1.0 CA A:THR373 5.0 411.3 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 C:Mg1102 b:502.8 occ:1.00 F1 C:BEF1101 2.0 520.7 1.0 OD1 C:ASP710 2.1 482.7 1.0 OD1 C:ASP369 2.2 543.0 1.0 CG C:ASP369 2.4 533.0 1.0 OD2 C:ASP710 2.6 459.5 1.0 CG C:ASP710 2.6 461.4 1.0 O C:THR371 2.8 500.6 1.0 OG1 C:THR371 2.8 508.1 1.0 OD2 C:ASP369 2.9 548.5 1.0 BE C:BEF1101 3.0 530.2 1.0 CB C:ASP369 3.1 504.6 1.0 F2 C:BEF1101 3.5 542.6 1.0 C C:THR371 3.7 494.9 1.0 OG1 C:THR373 3.7 460.9 1.0 CB C:THR371 3.9 502.9 1.0 N C:THR371 3.9 502.7 1.0 CA C:THR371 4.0 499.6 1.0 CB C:ASP710 4.1 452.3 1.0 OD1 C:ASN713 4.1 469.6 1.0 OD2 C:ASP714 4.2 492.6 1.0 N C:LYS370 4.4 498.1 1.0 F3 C:BEF1101 4.4 535.0 1.0 CA C:ASP369 4.4 489.4 1.0 C C:LYS370 4.4 498.9 1.0 C C:ASP369 4.6 493.8 1.0 CA C:GLY213 4.7 494.0 1.0 OG1 C:THR610 4.7 479.5 1.0 N C:GLY372 4.8 493.9 1.0 N C:THR373 4.8 484.4 1.0 O C:LYS370 4.9 495.7 1.0 N C:GLY711 4.9 435.4 1.0 N C:ASP710 4.9 463.4 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