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

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

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime, PDB code: 7wys 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)	15.98 / 3.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.109, 117.47, 491.339, 90, 90, 90
R / Rfree (%)	19.3 / 23.8

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime 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 Istaroxime (pdb code 7wys). 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 Istaroxime, PDB code: 7wys:
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 Istaroxime


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 Istaroxime within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:160.8 occ:1.00 OD1 A:ASP710 2.1 163.4 1.0 O A:HOH1205 2.2 154.7 1.0 O A:THR371 2.3 121.7 1.0 O A:HOH1201 2.3 114.3 1.0 OD2 A:PHD369 2.3 115.7 1.0 OD2 A:ASP710 2.4 164.4 1.0 OP3 A:PHD369 2.5 129.8 1.0 CG A:ASP710 2.5 157.4 1.0 N A:GLY711 3.2 112.2 1.0 C A:THR371 3.5 127.0 1.0 CG A:PHD369 3.5 111.8 1.0 OD2 A:ASP714 3.7 125.6 1.0 P A:PHD369 3.7 125.7 1.0 CB A:ASP710 3.8 141.2 1.0 CA A:GLY711 3.9 107.6 1.0 OD1 A:PHD369 3.9 119.0 1.0 N A:ASP710 4.1 117.5 1.0 C A:ASP710 4.1 118.5 1.0 CA A:GLY372 4.1 107.6 1.0 CA A:ASP710 4.2 124.6 1.0 N A:GLY372 4.2 112.2 1.0 OP1 A:PHD369 4.4 131.0 1.0 OG1 A:THR373 4.4 75.2 1.0 CA A:THR371 4.5 144.2 1.0 N A:THR373 4.6 93.1 1.0 O A:SER209 4.6 141.6 1.0 CB A:THR371 4.6 178.6 1.0 OD1 A:ASN713 4.6 132.8 1.0 C A:GLY372 4.7 104.8 1.0 CB A:PHD369 4.7 104.7 1.0 CG2 A:THR371 4.8 195.7 1.0 CG A:ASP714 4.8 124.8 1.0 OP2 A:PHD369 4.8 134.4 1.0 N A:THR371 4.9 123.4 1.0

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


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 Istaroxime within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:176.5 occ:1.00 OD2 A:ASP804 2.2 173.6 1.0 O A:HOH1202 2.2 249.7 1.0 OE2 A:GLU779 2.2 157.8 1.0 OD1 A:ASP804 2.2 171.0 1.0 CG A:ASP804 2.4 166.0 1.0 O A:HOH1203 2.5 63.0 1.0 O A:HOH1204 2.5 138.5 1.0 OE2 A:GLU327 2.6 174.9 1.0 CD A:GLU779 3.0 144.8 1.0 OE1 A:GLU779 3.2 148.8 1.0 CD A:GLU327 3.6 164.3 1.0 CB A:ASP804 3.7 152.0 1.0 OE1 A:GLU327 3.9 165.7 1.0 ND2 A:ASN776 4.2 136.1 1.0 CG A:GLU779 4.3 130.4 1.0 O A:ALA323 4.6 137.6 1.0 CG2 A:ILE800 4.6 106.6 1.0 CA A:PRO326 4.6 114.2 1.0 CG A:ASN776 4.6 130.9 1.0 O A:VAL325 4.7 117.1 1.0 OG A:SER775 4.7 56.0 1.0 OD1 A:ASN776 4.8 138.1 1.0 CB A:GLU779 4.8 119.9 1.0 N A:GLU327 4.8 109.5 1.0 CA A:ASP804 4.9 135.5 1.0 CG A:GLU327 5.0 151.8 1.0

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


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 Istaroxime within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:126.2 occ:1.00 OD1 C:ASP710 2.1 131.6 1.0 OD2 C:PHD369 2.1 110.4 1.0 O C:HOH1201 2.2 128.0 1.0 O C:THR371 2.2 136.9 1.0 O C:HOH1204 2.3 106.6 1.0 OP3 C:PHD369 2.4 106.4 1.0 CG C:ASP710 2.7 129.2 1.0 OD2 C:ASP710 2.8 135.0 1.0 N C:GLY711 3.3 113.7 1.0 CG C:PHD369 3.3 103.3 1.0 C C:THR371 3.4 136.1 1.0 P C:PHD369 3.6 89.7 1.0 OD2 C:ASP714 3.6 87.7 1.0 OD1 C:PHD369 3.8 112.5 1.0 CA C:GLY711 3.9 115.4 1.0 CB C:ASP710 4.0 116.2 1.0 N C:ASP710 4.1 110.4 1.0 CA C:GLY372 4.2 126.2 1.0 C C:ASP710 4.2 108.7 1.0 N C:GLY372 4.2 131.6 1.0 OP1 C:PHD369 4.3 100.2 1.0 CA C:ASP710 4.3 110.0 1.0 CA C:THR371 4.5 141.4 1.0 O C:SER209 4.5 123.0 1.0 OG1 C:THR373 4.5 101.5 1.0 OD1 C:ASN713 4.5 113.9 1.0 CB C:PHD369 4.6 98.4 1.0 N C:THR373 4.6 109.8 1.0 CB C:THR371 4.7 156.2 1.0 OP2 C:PHD369 4.7 109.6 1.0 CG C:ASP714 4.7 87.7 1.0 N C:THR371 4.8 128.0 1.0 C C:GLY372 4.8 119.2 1.0 CG2 C:THR371 5.0 154.9 1.0

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


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 Istaroxime within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1103 b:168.8 occ:1.00 OD2 C:ASP804 2.2 155.8 1.0 OE2 C:GLU779 2.2 202.0 1.0 O C:HOH1202 2.3 235.4 1.0 OD1 C:ASP804 2.3 150.7 1.0 CG C:ASP804 2.4 142.2 1.0 O C:HOH1203 2.5 163.7 1.0 O C:HOH1205 2.5 76.6 1.0 OE2 C:GLU327 2.5 140.9 1.0 CD C:GLU779 3.0 181.0 1.0 OE1 C:GLU779 3.2 189.3 1.0 CD C:GLU327 3.6 130.8 1.0 CB C:ASP804 3.7 119.2 1.0 OE1 C:GLU327 4.0 135.1 1.0 ND2 C:ASN776 4.1 108.0 1.0 CG C:GLU779 4.3 151.4 1.0 CG2 C:ILE800 4.5 116.0 1.0 O C:VAL325 4.6 88.0 1.0 CG C:ASN776 4.7 102.9 1.0 O C:ALA323 4.8 110.7 1.0 OG C:SER775 4.8 57.7 1.0 CA C:PRO326 4.8 70.5 1.0 CB C:GLU779 4.8 123.8 1.0 N C:GLU327 4.9 92.5 1.0 OD1 C:ASN776 4.9 99.0 1.0 CG C:GLU327 4.9 117.8 1.0 CA C:ASP804 4.9 100.2 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