Magnesium in PDB 3b8e: Crystal Structure of the Sodium-Potassium Pump

All present enzymatic activity of Crystal Structure of the Sodium-Potassium Pump:
3.6.3.9;

The structure of Crystal Structure of the Sodium-Potassium Pump, PDB code: 3b8e was solved by J.P.Morth, P.B.Pedersen, M.S.Toustrup-Jensen, T.L.M.Soerensen, J.Petersen, J.P.Andersen, B.Vilsen, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.930, 261.500, 334.780, 90.00, 90.00, 90.00
R / Rfree (%)	27.7 / 31.3

The structure of Crystal Structure of the Sodium-Potassium Pump also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Rubidium	(Rb)	6 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Sodium-Potassium Pump (pdb code 3b8e). 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 the Sodium-Potassium Pump, PDB code: 3b8e:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Sodium-Potassium 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 the Sodium-Potassium Pump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:98.1 occ:1.00 O A:THR371 2.4 67.9 1.0 OD2 A:ASP710 2.4 85.9 1.0 OD1 A:ASP710 2.5 85.9 1.0 OD1 A:ASP369 2.5 88.3 1.0 F2 A:MF42001 2.5 98.1 1.0 CG A:ASP710 2.8 85.9 1.0 OD2 A:ASP369 3.0 88.3 1.0 CG A:ASP369 3.1 88.3 1.0 C A:THR371 3.5 67.9 1.0 O A:GLY213 3.5 65.8 1.0 MG A:MF42001 3.9 98.1 1.0 N A:GLY711 4.0 96.5 1.0 CB A:THR371 4.1 0.0 1.0 F4 A:MF42001 4.3 98.1 1.0 CB A:ASP710 4.3 85.9 1.0 CA A:THR371 4.3 67.9 1.0 CG2 A:THR371 4.3 0.0 1.0 C A:GLY213 4.3 65.8 1.0 N A:GLY372 4.4 85.1 1.0 CA A:GLY213 4.4 65.8 1.0 CA A:GLY372 4.5 85.1 1.0 CA A:GLY711 4.5 96.5 1.0 CB A:ASP369 4.5 88.3 1.0 OD1 A:ASN713 4.5 95.6 1.0 F1 A:MF42001 4.6 98.1 1.0 OD2 A:ASP714 4.8 89.9 1.0 N A:THR371 4.8 67.9 1.0 F3 A:MF42001 4.8 98.1 1.0 C A:ASP710 5.0 68.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Sodium-Potassium 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 the Sodium-Potassium Pump within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2002 b:98.1 occ:1.00 O C:THR371 2.3 75.8 1.0 OD2 C:ASP710 2.4 85.4 1.0 OD1 C:ASP369 2.5 72.4 1.0 F2 C:MF42001 2.5 98.1 1.0 OD1 C:ASP710 2.5 85.4 1.0 CG C:ASP710 2.8 85.4 1.0 OD2 C:ASP369 2.9 72.4 1.0 CG C:ASP369 3.0 72.4 1.0 C C:THR371 3.4 75.8 1.0 O C:GLY213 3.5 73.8 1.0 MG C:MF42001 3.9 98.1 1.0 N C:GLY711 4.0 86.1 1.0 CB C:THR371 4.1 0.5 1.0 F4 C:MF42001 4.3 98.1 1.0 CA C:THR371 4.3 75.8 1.0 CB C:ASP710 4.3 85.4 1.0 CG2 C:THR371 4.3 0.5 1.0 C C:GLY213 4.3 73.8 1.0 N C:GLY372 4.4 85.1 1.0 CA C:GLY213 4.4 73.8 1.0 CA C:GLY372 4.5 85.1 1.0 CB C:ASP369 4.5 72.4 1.0 CA C:GLY711 4.5 86.1 1.0 OD1 C:ASN713 4.5 74.0 1.0 F1 C:MF42001 4.6 98.1 1.0 OD2 C:ASP714 4.8 85.5 1.0 N C:THR371 4.8 75.8 1.0 F3 C:MF42001 4.8 98.1 1.0 C C:ASP710 5.0 61.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Sodium-Potassium 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 the Sodium-Potassium Pump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:98.1 occ:1.00 MG A:MF42001 0.0 98.1 1.0 F1 A:MF42001 1.5 98.1 1.0 F2 A:MF42001 1.5 98.1 1.0 F4 A:MF42001 1.5 98.1 1.0 F3 A:MF42001 1.5 98.1 1.0 OD2 A:ASP369 2.8 88.3 1.0 CG A:ASP369 3.2 88.3 1.0 OG1 A:THR610 3.2 51.1 1.0 OD1 A:ASP369 3.4 88.3 1.0 N A:GLY611 3.7 83.6 1.0 MG A:MG2002 3.9 98.1 1.0 CA A:THR610 3.9 78.1 1.0 ND2 A:ASN713 4.0 95.6 1.0 CB A:THR610 4.0 51.1 1.0 OE1 A:GLU214 4.1 0.5 1.0 NZ A:LYS691 4.3 68.6 1.0 CB A:ASP369 4.4 88.3 1.0 N A:THR371 4.4 67.9 1.0 O A:THR212 4.4 50.2 1.0 C A:THR610 4.4 78.1 1.0 CA A:GLY213 4.4 65.8 1.0 N A:LYS370 4.4 0.7 1.0 CB A:THR371 4.5 0.0 1.0 O A:THR371 4.5 67.9 1.0 CA A:ASP369 4.5 0.5 1.0 O A:VAL609 4.5 68.0 1.0 N A:ASP612 4.6 55.8 1.0 O A:GLY213 4.6 65.8 1.0 C A:GLY213 4.7 65.8 1.0 CA A:GLY611 4.7 83.6 1.0 C A:ASP369 4.7 0.5 1.0 CG A:ASN713 4.8 95.6 1.0 OD1 A:ASN713 4.8 95.6 1.0 CA A:THR371 4.9 67.9 1.0 OG1 A:THR371 4.9 0.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Sodium-Potassium 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 the Sodium-Potassium Pump within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2001 b:98.1 occ:1.00 MG C:MF42001 0.0 98.1 1.0 F2 C:MF42001 1.5 98.1 1.0 F4 C:MF42001 1.5 98.1 1.0 F1 C:MF42001 1.5 98.1 1.0 F3 C:MF42001 1.5 98.1 1.0 OD2 C:ASP369 2.8 72.4 1.0 CG C:ASP369 3.2 72.4 1.0 OG1 C:THR610 3.3 60.8 1.0 OD1 C:ASP369 3.4 72.4 1.0 N C:GLY611 3.7 71.3 1.0 MG C:MG2002 3.9 98.1 1.0 CA C:THR610 4.0 48.5 1.0 ND2 C:ASN713 4.0 74.0 1.0 CB C:THR610 4.1 60.8 1.0 OE1 C:GLU214 4.1 0.1 1.0 NZ C:LYS691 4.3 72.9 1.0 N C:THR371 4.4 75.8 1.0 CB C:ASP369 4.4 72.4 1.0 CA C:GLY213 4.4 73.8 1.0 O C:THR212 4.4 71.4 1.0 C C:THR610 4.4 48.5 1.0 N C:LYS370 4.4 0.1 1.0 CB C:THR371 4.4 0.5 1.0 O C:THR371 4.5 75.8 1.0 CA C:ASP369 4.5 97.3 1.0 O C:VAL609 4.6 66.4 1.0 N C:ASP612 4.6 40.1 1.0 O C:GLY213 4.6 73.8 1.0 C C:GLY213 4.7 73.8 1.0 CA C:GLY611 4.7 71.3 1.0 C C:ASP369 4.8 97.3 1.0 OD1 C:ASN713 4.8 74.0 1.0 CG C:ASN713 4.8 74.0 1.0 CA C:THR371 4.9 75.8 1.0 OG1 C:THR371 4.9 0.5 1.0

J.P.Morth, B.P.Pedersen, M.S.Toustrup-Jensen, T.L.Sorensen, J.Petersen, J.P.Andersen, B.Vilsen, P.Nissen. Crystal Structure of the Sodium-Potassium Pump. Nature V. 450 1043 2007.
ISSN: ISSN 0028-0836
PubMed: 18075585
DOI: 10.1038/NATURE06419