Magnesium in PDB 5ksd: Crystal Structure of A Plasma Membrane Proton Pump

All present enzymatic activity of Crystal Structure of A Plasma Membrane Proton Pump:
3.6.3.6;

The structure of Crystal Structure of A Plasma Membrane Proton Pump, PDB code: 5ksd was solved by T.Croll, B.P.Pedersen, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.02 / 3.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.290, 144.420, 312.110, 90.00, 90.00, 90.00
R / Rfree (%)	28.7 / 32.4

The structure of Crystal Structure of A Plasma Membrane Proton Pump also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Plasma Membrane Proton Pump (pdb code 5ksd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Plasma Membrane Proton Pump, PDB code: 5ksd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Plasma Membrane Proton Pump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Plasma Membrane Proton Pump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:0.1 occ:1.00 OD2 A:ASP588 2.2 0.3 1.0 O1B A:ACP904 2.5 0.1 1.0 O1G A:ACP904 2.5 85.9 1.0 CG A:ASP588 3.3 0.6 1.0 PB A:ACP904 3.8 0.5 1.0 PG A:ACP904 3.8 0.8 1.0 OD1 A:ASP588 3.8 0.8 1.0 C3B A:ACP904 4.2 0.4 1.0 O2G A:ACP904 4.4 0.5 1.0 CB A:ASP588 4.5 0.8 1.0 O2B A:ACP904 4.8 94.2 1.0 O3A A:ACP904 4.8 91.1 1.0 CB A:THR331 5.0 84.8 1.0 O1A A:ACP904 5.0 91.5 1.0 O3G A:ACP904 5.0 0.4 1.0 OD2 A:ASP329 5.0 0.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Plasma Membrane Proton Pump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Plasma Membrane Proton Pump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:0.2 occ:1.00 OD2 A:ASP372 2.1 0.1 1.0 OD1 A:ASP372 2.1 0.4 1.0 CG A:ASP372 2.4 0.3 1.0 CB A:ASP372 3.8 0.5 1.0 N7 A:ACP904 4.1 0.6 1.0 N6 A:ACP904 4.6 95.9 1.0 CA A:ASP372 4.7 0.5 1.0 N A:ALA373 4.8 0.1 1.0 O1A A:ACP904 4.9 91.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Plasma Membrane Proton Pump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Plasma Membrane Proton Pump within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:0.5 occ:1.00 OD2 B:ASP588 2.2 0.7 1.0 O2B B:ACP904 2.3 0.6 1.0 O2G B:ACP904 2.7 0.5 1.0 CG B:ASP588 3.2 0.9 1.0 OD1 B:ASP588 3.5 0.4 1.0 PB B:ACP904 3.6 0.1 1.0 PG B:ACP904 3.9 0.8 1.0 C3B B:ACP904 3.9 95.0 1.0 O1B B:ACP904 4.3 74.8 1.0 OG1 B:THR331 4.4 0.4 1.0 CB B:ASP588 4.5 93.6 1.0 O3G B:ACP904 4.8 97.8 1.0 O3A B:ACP904 4.8 0.6 1.0 OD1 B:ASP329 4.8 0.3 1.0 MG B:MG902 4.8 0.5 1.0 CG B:ASP329 5.0 0.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A Plasma Membrane Proton Pump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Plasma Membrane Proton Pump within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:0.5 occ:1.00 O2A B:ACP904 2.3 0.7 1.0 PA B:ACP904 3.6 0.0 1.0 O3A B:ACP904 4.1 0.6 1.0 O2B B:ACP904 4.1 0.6 1.0 O1A B:ACP904 4.4 0.4 1.0 PB B:ACP904 4.7 0.1 1.0 O5' B:ACP904 4.7 0.3 1.0 MG B:MG901 4.8 0.5 1.0 C8 B:ACP904 4.9 0.8 1.0

D.Focht, T.I.Croll, B.P.Pedersen, P.Nissen. Improved Model of Proton Pump Crystal Structure Obtained By Interactive Molecular Dynamics Flexible Fitting Expands the Mechanistic Model For Proton Translocation in P-Type Atpases. Front Physiol V. 8 202 2017.
ISSN: ESSN 1664-042X
PubMed: 28443028
DOI: 10.3389/FPHYS.2017.00202