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

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

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin, PDB code: 7ddh 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 / 3.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	114.973, 118.493, 495.137, 90, 90, 90
R / Rfree (%)	24.1 / 27.2

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


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 Digoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:88.0 occ:1.00 O A:HOH1201 2.0 77.8 1.0 OD2 A:PHD369 2.0 101.1 1.0 O A:THR371 2.1 107.8 1.0 OD1 A:ASP710 2.1 112.0 1.0 OP3 A:PHD369 2.1 73.6 1.0 O A:HOH1202 2.2 87.6 1.0 OD2 A:ASP710 2.6 84.7 1.0 CG A:ASP710 2.6 96.7 1.0 CG A:PHD369 3.1 92.0 1.0 C A:THR371 3.3 87.3 1.0 P A:PHD369 3.4 80.2 1.0 N A:GLY711 3.5 83.7 1.0 OD1 A:PHD369 3.6 97.8 1.0 OD2 A:ASP714 3.9 76.2 1.0 CB A:ASP710 4.0 76.1 1.0 CA A:GLY372 4.0 82.4 1.0 N A:GLY372 4.1 80.9 1.0 N A:ASP710 4.2 76.1 1.0 CA A:GLY711 4.2 85.5 1.0 OP1 A:PHD369 4.2 73.6 1.0 CA A:THR371 4.3 85.2 1.0 CB A:PHD369 4.4 73.6 1.0 C A:ASP710 4.4 76.1 1.0 CA A:ASP710 4.4 76.1 1.0 OP2 A:PHD369 4.4 92.5 1.0 CB A:THR371 4.5 103.7 1.0 OG1 A:THR373 4.5 74.6 1.0 N A:THR373 4.6 74.6 1.0 OD1 A:ASN713 4.6 75.2 1.0 C A:GLY372 4.7 85.4 1.0 N A:THR371 4.7 89.8 1.0 O A:SER209 4.7 93.5 1.0 CG2 A:THR371 4.9 115.4 1.0

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


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 Digoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:67.2 occ:1.00 O A:HOH1203 2.0 75.5 1.0 OD2 A:ASP804 2.0 93.0 1.0 OD1 A:ASP804 2.2 74.3 1.0 OE2 A:GLU779 2.2 70.6 1.0 CG A:ASP804 2.3 98.0 1.0 OE2 A:GLU327 2.3 107.7 1.0 O A:HOH1204 2.4 75.2 1.0 O A:HOH1205 2.4 68.8 1.0 CD A:GLU779 3.1 83.7 1.0 OE1 A:GLU779 3.4 82.5 1.0 CD A:GLU327 3.4 86.7 1.0 CB A:ASP804 3.6 108.1 1.0 OE1 A:GLU327 3.9 83.6 1.0 ND2 A:ASN776 4.1 67.6 1.0 OD1 A:ASN776 4.4 108.1 1.0 CG A:GLU779 4.4 77.9 1.0 CG A:ASN776 4.4 79.0 1.0 O A:VAL325 4.6 88.3 1.0 O A:ALA323 4.6 89.2 1.0 CG2 A:ILE800 4.6 74.0 1.0 CG A:GLU327 4.7 72.0 1.0 CA A:ASP804 4.8 88.4 1.0 N A:GLU327 4.8 91.5 1.0 CB A:GLU779 4.8 85.2 1.0 CA A:PRO326 4.9 76.4 1.0 OG A:SER775 4.9 65.7 1.0

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


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 Digoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:87.4 occ:1.00 O C:HOH1205 2.0 86.0 1.0 O C:THR371 2.1 92.5 1.0 OD1 C:ASP710 2.2 98.3 1.0 OD2 C:PHD369 2.2 118.2 1.0 O C:HOH1201 2.3 86.3 1.0 OP3 C:PHD369 2.3 86.4 1.0 OD2 C:ASP710 2.5 89.0 1.0 CG C:ASP710 2.6 97.1 1.0 C C:THR371 3.3 92.5 1.0 CG C:PHD369 3.4 104.7 1.0 N C:GLY711 3.4 83.4 1.0 P C:PHD369 3.6 92.1 1.0 OD1 C:PHD369 3.9 97.5 1.0 OD2 C:ASP714 3.9 113.7 1.0 CB C:ASP710 3.9 96.4 1.0 CA C:GLY372 4.0 114.2 1.0 CA C:GLY711 4.0 83.4 1.0 N C:GLY372 4.1 101.7 1.0 N C:ASP710 4.1 83.3 1.0 C C:ASP710 4.3 83.3 1.0 CA C:ASP710 4.3 83.3 1.0 CA C:THR371 4.3 97.1 1.0 OG1 C:THR373 4.4 82.7 1.0 OP1 C:PHD369 4.4 86.4 1.0 CB C:THR371 4.5 122.2 1.0 N C:THR373 4.5 87.2 1.0 OD1 C:ASN713 4.6 134.1 1.0 C C:GLY372 4.6 104.4 1.0 CB C:PHD369 4.6 89.1 1.0 O C:SER209 4.6 95.3 1.0 OP2 C:PHD369 4.7 125.8 1.0 N C:THR371 4.7 92.5 1.0 CG2 C:THR371 4.9 134.8 1.0

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


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 Digoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1103 b:55.6 occ:1.00 O C:HOH1203 2.1 56.5 1.0 OD2 C:ASP804 2.1 78.1 1.0 OD1 C:ASP804 2.2 86.0 1.0 OE2 C:GLU779 2.3 92.2 1.0 OE2 C:GLU327 2.3 114.9 1.0 O C:HOH1202 2.4 92.0 1.0 CG C:ASP804 2.4 82.2 1.0 O C:HOH1204 2.5 58.0 1.0 CD C:GLU779 3.1 73.9 1.0 CD C:GLU327 3.4 116.4 1.0 OE1 C:GLU779 3.4 85.4 1.0 CB C:ASP804 3.8 81.6 1.0 OE1 C:GLU327 3.8 101.7 1.0 ND2 C:ASN776 4.2 60.6 1.0 CG2 C:ILE800 4.4 63.6 1.0 CG C:GLU779 4.5 59.5 1.0 CG C:ASN776 4.6 83.8 1.0 OD1 C:ASN776 4.6 95.0 1.0 CG C:GLU327 4.6 121.3 1.0 O C:VAL325 4.7 86.2 1.0 N C:GLU327 4.8 101.7 1.0 O C:ALA323 4.8 114.2 1.0 CB C:GLU779 4.9 59.5 1.0 CA C:PRO326 4.9 65.8 1.0 CA C:ASP804 4.9 77.2 1.0

R.Kanai, F.Cornelius, H.Ogawa, K.Motoyama, B.Vilsen, C.Toyoshima. Binding of Cardiotonic Steroids to Na + ,K + -Atpase in the E2P State. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33318128
DOI: 10.1073/PNAS.2020438118