Magnesium in PDB 3kdp: 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: 3kdp was solved by J.P.Morth, B.P.Pedersen, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.86 / 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 (%)	24.2 / 28.6

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 3kdp). 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: 3kdp:
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:Mg2001 b:93.0 occ:1.00 MG A:MF42001 0.0 93.0 1.0 F1 A:MF42001 1.5 91.1 1.0 F2 A:MF42001 1.5 97.2 1.0 F3 A:MF42001 1.5 92.7 1.0 F4 A:MF42001 1.5 88.8 1.0 OD1 A:ASP369 2.6 83.3 1.0 CG A:ASP369 3.2 84.2 1.0 OG1 A:THR610 3.3 75.0 1.0 OD2 A:ASP369 3.4 86.4 1.0 MG A:MG2002 3.8 33.1 1.0 N A:GLY611 3.8 60.0 1.0 CB A:THR371 3.9 74.5 1.0 OE1 A:GLU214 4.0 66.7 1.0 N A:THR371 4.1 67.8 1.0 O A:THR212 4.1 61.9 1.0 CA A:THR610 4.1 72.5 1.0 ND2 A:ASN713 4.2 60.3 1.0 CB A:THR610 4.2 72.8 1.0 CA A:GLY213 4.2 67.6 1.0 N A:LYS370 4.3 0.8 1.0 NZ A:LYS691 4.3 57.5 1.0 CB A:ASP369 4.4 81.7 1.0 OD1 A:ASN713 4.5 74.4 1.0 C A:THR610 4.5 71.9 1.0 CA A:THR371 4.5 73.3 1.0 O A:THR371 4.5 79.8 1.0 CG2 A:THR371 4.5 80.3 1.0 CA A:ASP369 4.6 75.8 1.0 C A:GLY213 4.7 71.3 1.0 CG A:ASN713 4.8 69.8 1.0 OG1 A:THR371 4.8 72.9 1.0 CA A:GLY611 4.8 61.3 1.0 O A:GLY213 4.8 74.6 1.0 C A:ASP369 4.9 74.9 1.0 N A:ASP612 4.9 75.2 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 A:Mg2002 b:33.1 occ:1.00 OD2 A:ASP710 2.3 64.9 1.0 F2 A:MF42001 2.4 97.2 1.0 OD2 A:ASP369 2.5 86.4 1.0 O A:THR371 2.5 79.8 1.0 CG A:ASP710 3.0 74.1 1.0 OD1 A:ASP369 3.0 83.3 1.0 CG A:ASP369 3.1 84.2 1.0 OD1 A:ASP710 3.1 82.5 1.0 CG2 A:THR371 3.4 80.3 1.0 C A:THR371 3.5 78.3 1.0 MG A:MF42001 3.8 93.0 1.0 O A:GLY213 3.9 74.6 1.0 CB A:THR371 3.9 74.5 1.0 N A:GLY711 4.2 67.1 1.0 CA A:THR371 4.2 73.3 1.0 OD1 A:ASN713 4.3 74.4 1.0 F4 A:MF42001 4.4 88.8 1.0 CA A:GLY711 4.4 68.4 1.0 OD2 A:ASP714 4.4 82.1 1.0 N A:GLY372 4.5 65.2 1.0 F1 A:MF42001 4.5 91.1 1.0 CB A:ASP369 4.5 81.7 1.0 CB A:ASP710 4.5 84.6 1.0 CA A:GLY213 4.6 67.6 1.0 F3 A:MF42001 4.6 92.7 1.0 CA A:GLY372 4.6 73.6 1.0 N A:THR371 4.6 67.8 1.0 C A:GLY213 4.7 71.3 1.0 C A:ASP710 4.7 93.8 1.0 OG1 A:THR373 4.8 0.7 1.0 N A:ASP710 4.8 74.5 1.0 CA A:ASP710 4.9 88.8 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 C:Mg2001 b:97.6 occ:1.00 MG C:MF42001 0.0 97.6 1.0 F2 C:MF42001 1.5 0.8 1.0 F1 C:MF42001 1.5 95.5 1.0 F3 C:MF42001 1.5 99.2 1.0 F4 C:MF42001 1.5 91.9 1.0 OD1 C:ASP369 2.6 80.8 1.0 CG C:ASP369 3.2 82.4 1.0 OG1 C:THR610 3.3 73.9 1.0 OD2 C:ASP369 3.5 86.8 1.0 MG C:MG2002 3.8 32.5 1.0 CB C:THR371 3.9 72.1 1.0 N C:GLY611 3.9 75.9 1.0 N C:THR371 4.0 62.9 1.0 OE1 C:GLU214 4.1 42.0 1.0 O C:THR212 4.1 62.6 1.0 CA C:THR610 4.2 71.4 1.0 CB C:THR610 4.2 71.2 1.0 CA C:GLY213 4.2 63.7 1.0 ND2 C:ASN713 4.2 49.7 1.0 N C:LYS370 4.3 74.0 1.0 NZ C:LYS691 4.4 70.0 1.0 CB C:ASP369 4.4 78.2 1.0 O C:THR371 4.5 77.0 1.0 CA C:THR371 4.5 69.1 1.0 CG2 C:THR371 4.5 79.9 1.0 OD1 C:ASN713 4.5 64.9 1.0 C C:THR610 4.6 72.9 1.0 CA C:ASP369 4.6 71.4 1.0 OG1 C:THR371 4.7 70.5 1.0 C C:GLY213 4.8 67.4 1.0 CG C:ASN713 4.8 61.2 1.0 O C:GLY213 4.8 69.5 1.0 CA C:GLY611 4.9 79.7 1.0 C C:ASP369 4.9 69.8 1.0 N C:ASP612 5.0 61.3 1.0 C C:THR371 5.0 74.6 1.0 C C:LYS370 5.0 77.2 1.0 O C:VAL609 5.0 62.8 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:Mg2002 b:32.5 occ:1.00 OD2 C:ASP710 2.2 68.1 1.0 F2 C:MF42001 2.3 0.8 1.0 O C:THR371 2.4 77.0 1.0 OD2 C:ASP369 2.4 86.8 1.0 CG C:ASP710 3.0 78.7 1.0 OD1 C:ASP369 3.0 80.8 1.0 CG C:ASP369 3.0 82.4 1.0 OD1 C:ASP710 3.1 88.2 1.0 CG2 C:THR371 3.3 79.9 1.0 C C:THR371 3.4 74.6 1.0 MG C:MF42001 3.8 97.6 1.0 CB C:THR371 3.9 72.1 1.0 O C:GLY213 3.9 69.5 1.0 CA C:THR371 4.2 69.1 1.0 N C:GLY711 4.2 59.6 1.0 OD1 C:ASN713 4.3 64.9 1.0 F4 C:MF42001 4.4 91.9 1.0 OD2 C:ASP714 4.4 75.2 1.0 N C:GLY372 4.4 60.8 1.0 CA C:GLY711 4.4 63.3 1.0 CB C:ASP710 4.4 87.6 1.0 CB C:ASP369 4.5 78.2 1.0 F1 C:MF42001 4.5 95.5 1.0 F3 C:MF42001 4.6 99.2 1.0 CA C:GLY372 4.6 69.9 1.0 N C:THR371 4.6 62.9 1.0 CA C:GLY213 4.6 63.7 1.0 C C:GLY213 4.7 67.4 1.0 C C:ASP710 4.7 99.8 1.0 OG1 C:THR373 4.8 82.1 1.0 N C:ASP710 4.8 77.3 1.0 CA C:ASP710 4.9 92.6 1.0 N C:THR373 5.0 81.0 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