Magnesium in PDB 3a3y: Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain

The structure of Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain, PDB code: 3a3y was solved by H.Ogawa, T.Shinoda, F.Cornelius, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	222.884, 50.720, 163.342, 90.00, 104.63, 90.00
R / Rfree (%)	24.7 / 29.3

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

Fluorine	(F)	4 atoms
Potassium	(K)	3 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain (pdb code 3a3y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain, PDB code: 3a3y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain


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 with Bound Potassium and Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:23.3 occ:1.00 MG A:MF42001 0.0 23.3 1.0 F3 A:MF42001 2.0 27.1 1.0 F1 A:MF42001 2.0 24.4 1.0 F2 A:MF42001 2.0 23.5 1.0 F4 A:MF42001 2.0 23.9 1.0 OD2 A:ASP376 2.5 26.1 1.0 OG1 A:THR617 3.5 23.1 1.0 O A:THR219 3.6 30.0 1.0 CG A:ASP376 3.7 27.0 1.0 MG A:MG2002 3.8 25.5 1.0 N A:GLY618 3.8 25.6 1.0 N A:THR378 3.9 26.3 1.0 OE1 A:GLU221 4.0 30.5 1.0 CB A:THR378 4.1 26.4 1.0 CA A:GLY220 4.1 28.9 1.0 OG1 A:THR378 4.1 26.3 1.0 O A:HOH5024 4.2 26.1 1.0 OD1 A:ASP376 4.3 28.4 1.0 O A:GLY220 4.3 28.3 1.0 ND2 A:ASN720 4.3 29.8 1.0 C A:GLY220 4.4 28.8 1.0 CA A:THR617 4.4 24.9 1.0 CB A:THR617 4.4 24.4 1.0 O A:HOH5026 4.4 24.7 1.0 N A:LYS377 4.4 26.6 1.0 CA A:THR378 4.5 26.3 1.0 NZ A:LYS698 4.5 27.9 1.0 C A:THR617 4.6 25.2 1.0 CA A:GLY618 4.6 26.2 1.0 C A:THR219 4.6 30.1 1.0 N A:ASP619 4.7 27.0 1.0 O A:THR378 4.7 26.1 1.0 CB A:ASP376 4.8 26.6 1.0 N A:GLY220 4.9 29.6 1.0 C A:LYS377 4.9 26.4 1.0 CD A:GLU221 4.9 30.3 1.0 CA A:LYS377 5.0 26.2 1.0 CB A:LYS377 5.0 26.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain


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 with Bound Potassium and Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:25.5 occ:1.00 F2 A:MF42001 1.9 23.5 1.0 O A:HOH5026 2.1 24.7 1.0 OD2 A:ASP717 2.1 31.2 1.0 O A:THR378 2.2 26.1 1.0 OD1 A:ASP376 2.3 28.4 1.0 O A:HOH5024 2.3 26.1 1.0 CG A:ASP376 3.1 27.0 1.0 OD2 A:ASP376 3.2 26.1 1.0 CG A:ASP717 3.2 29.7 1.0 C A:THR378 3.3 26.4 1.0 OD1 A:ASP717 3.6 30.6 1.0 MG A:MF42001 3.8 23.3 1.0 CA A:THR378 4.0 26.3 1.0 N A:THR378 4.1 26.3 1.0 OG1 A:THR380 4.1 27.1 1.0 OD2 A:ASP721 4.2 30.1 1.0 CB A:THR378 4.2 26.4 1.0 O A:GLY220 4.3 28.3 1.0 F4 A:MF42001 4.4 23.9 1.0 N A:GLY718 4.4 29.0 1.0 F1 A:MF42001 4.4 24.4 1.0 N A:GLY379 4.4 26.6 1.0 CB A:ASP717 4.5 28.9 1.0 N A:ASP717 4.5 28.8 1.0 CB A:ASP376 4.5 26.6 1.0 C A:ASP717 4.6 28.9 1.0 CA A:ASP717 4.7 28.9 1.0 CA A:GLY379 4.7 26.7 1.0 CA A:GLY220 4.8 28.9 1.0 CA A:GLY718 4.8 29.1 1.0 N A:THR380 4.9 27.3 1.0 C A:LYS377 4.9 26.4 1.0 OD1 A:ASN720 5.0 30.6 1.0 CG2 A:THR378 5.0 26.2 1.0 C A:GLY379 5.0 27.2 1.0 C A:GLY220 5.0 28.8 1.0

H.Ogawa, T.Shinoda, F.Cornelius, C.Toyoshima. Crystal Structure of the Sodium-Potassium Pump (Na+,K+-Atpase) with Bound Potassium and Ouabain. Proc.Natl.Acad.Sci.Usa V. 106 13742 2009.
ISSN: ISSN 0027-8424
PubMed: 19666591
DOI: 10.1073/PNAS.0907054106