Magnesium in PDB 7wyt: Crystal Structures of Na+,K+-Atpase in Complex with Ouabain

All present enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain:
7.2.2.13;

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain, PDB code: 7wyt was solved by H.Ogawa, F.Cornelius, R.Kanai, K.Motoyama, B.Vilsen, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.99 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.621, 117.81, 493.203, 90, 90, 90
R / Rfree (%)	27 / 30.7

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain (pdb code 7wyt). 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 Structures of Na+,K+-Atpase in Complex with Ouabain, PDB code: 7wyt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:40.6 occ:1.00 O A:THR371 2.1 40.1 1.0 OD1 A:ASP710 2.1 42.7 1.0 O A:HOH1202 2.1 67.5 1.0 O A:HOH1204 2.2 35.5 1.0 OP3 A:PHD369 2.3 41.7 1.0 OD2 A:PHD369 2.4 37.2 1.0 CG A:ASP710 2.8 41.2 1.0 OD2 A:ASP710 3.0 41.0 1.0 C A:THR371 3.2 40.1 1.0 CG A:PHD369 3.4 38.7 1.0 P A:PHD369 3.5 34.6 1.0 N A:GLY711 3.6 41.3 1.0 OD1 A:PHD369 3.7 34.3 1.0 OD2 A:ASP714 4.0 35.0 1.0 CB A:THR371 4.0 60.5 1.0 CA A:THR371 4.1 40.8 1.0 OP1 A:PHD369 4.1 34.3 1.0 CA A:GLY711 4.1 36.0 1.0 N A:GLY372 4.2 40.0 1.0 O A:SER209 4.2 58.4 1.0 CG2 A:THR371 4.2 66.5 1.0 CB A:ASP710 4.2 32.9 1.0 CA A:GLY372 4.4 47.9 1.0 N A:ASP710 4.4 32.9 1.0 N A:THR371 4.5 49.2 1.0 C A:ASP710 4.5 53.1 1.0 OD1 A:ASN713 4.5 57.4 1.0 OG1 A:THR373 4.6 34.0 1.0 CA A:ASP710 4.6 32.9 1.0 OP2 A:PHD369 4.7 40.1 1.0 CB A:PHD369 4.7 44.4 1.0 N A:THR373 4.9 60.1 1.0 ND2 A:ASN713 4.9 53.6 1.0 C A:GLY372 4.9 68.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:40.2 occ:1.00 OD2 A:ASP804 2.1 29.7 1.0 O A:HOH1201 2.2 23.7 1.0 OD1 A:ASP804 2.2 19.0 1.0 OE2 A:GLU779 2.2 39.9 1.0 O A:HOH1203 2.3 40.4 1.0 OE2 A:GLU327 2.3 84.2 1.0 CG A:ASP804 2.3 29.2 1.0 O A:HOH1205 2.4 23.6 1.0 CD A:GLU779 3.0 39.0 1.0 OE1 A:GLU779 3.3 42.4 1.0 CD A:GLU327 3.4 65.2 1.0 CB A:ASP804 3.7 36.0 1.0 OE1 A:GLU327 3.9 73.9 1.0 ND2 A:ASN776 4.0 23.8 1.0 CG A:GLU779 4.3 29.1 1.0 O A:VAL325 4.5 50.1 1.0 O A:ALA323 4.6 34.8 1.0 CG A:ASN776 4.6 23.8 1.0 CG A:GLU327 4.7 37.6 1.0 CG2 A:ILE800 4.8 19.0 1.0 CB A:GLU779 4.8 32.9 1.0 N A:GLU327 4.8 36.2 1.0 OD1 A:ASN776 4.9 23.8 1.0 CA A:ASP804 4.9 35.0 1.0 CA A:PRO326 4.9 24.3 1.0 OG A:SER775 4.9 20.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:39.0 occ:1.00 O C:HOH1201 2.0 32.6 1.0 OD1 C:ASP710 2.1 32.3 1.0 O C:THR371 2.1 44.4 1.0 OP3 C:PHD369 2.2 44.1 1.0 O C:HOH1202 2.2 40.5 1.0 OD2 C:PHD369 2.4 48.9 1.0 CG C:ASP710 2.9 35.8 1.0 OD2 C:ASP710 3.1 33.9 1.0 C C:THR371 3.3 32.6 1.0 CG C:PHD369 3.3 49.1 1.0 P C:PHD369 3.4 53.1 1.0 N C:GLY711 3.5 48.5 1.0 OD1 C:PHD369 3.6 59.7 1.0 OD2 C:ASP714 3.9 39.8 1.0 OP1 C:PHD369 4.0 59.2 1.0 CB C:THR371 4.0 31.1 1.0 CA C:GLY711 4.0 40.1 1.0 CA C:THR371 4.1 31.1 1.0 O C:SER209 4.2 69.5 1.0 CG2 C:THR371 4.3 31.1 1.0 CB C:ASP710 4.3 29.3 1.0 N C:GLY372 4.3 29.7 1.0 OD1 C:ASN713 4.3 74.2 1.0 N C:THR371 4.4 40.0 1.0 N C:ASP710 4.5 25.9 1.0 C C:ASP710 4.5 36.6 1.0 CA C:GLY372 4.5 35.6 1.0 OG1 C:THR373 4.5 50.1 1.0 OP2 C:PHD369 4.6 71.6 1.0 CB C:PHD369 4.6 41.2 1.0 CA C:ASP710 4.6 25.9 1.0 ND2 C:ASN713 4.8 29.4 1.0 CG C:ASP714 4.9 35.5 1.0 N C:THR373 5.0 48.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1103 b:25.7 occ:1.00 O C:HOH1203 2.0 17.4 1.0 OD2 C:ASP804 2.1 41.5 1.0 O C:HOH1205 2.2 12.6 1.0 OD1 C:ASP804 2.2 42.0 1.0 OE2 C:GLU779 2.2 21.4 1.0 OE2 C:GLU327 2.3 59.4 1.0 O C:HOH1204 2.3 10.8 1.0 CG C:ASP804 2.3 42.3 1.0 CD C:GLU779 3.1 26.6 1.0 CD C:GLU327 3.3 63.0 1.0 OE1 C:GLU779 3.4 24.2 1.0 CB C:ASP804 3.7 35.5 1.0 OE1 C:GLU327 3.7 64.2 1.0 O C:VAL325 4.3 59.0 1.0 CG C:GLU779 4.3 28.8 1.0 ND2 C:ASN776 4.4 49.1 1.0 O C:ALA323 4.6 49.1 1.0 CG C:GLU327 4.6 60.3 1.0 CA C:PRO326 4.7 30.2 1.0 CG2 C:ILE800 4.7 32.6 1.0 N C:GLU327 4.7 35.7 1.0 CB C:GLU779 4.8 32.7 1.0 CG C:ASN776 4.9 47.0 1.0 CA C:ASP804 4.9 19.2 1.0

R.Kanai, F.Cornelius, B.Vilsen, C.Toyoshima. Cryoelectron Microscopy of Na + ,K + -Atpase in the Two E2P States with and Without Cardiotonic Steroids. Proc.Natl.Acad.Sci.Usa V. 119 26119 2022.
ISSN: ESSN 1091-6490
PubMed: 35380894
DOI: 10.1073/PNAS.2123226119