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

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

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digitoxin, PDB code: 7ddi 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)	16.00 / 3.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.27, 117.715, 491.243, 90, 90, 90
R / Rfree (%)	18.6 / 23.3

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


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 Digitoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:160.1 occ:1.00 O A:THR371 2.2 151.4 1.0 OD1 A:ASP710 2.2 172.1 1.0 OP3 A:PHD369 2.2 148.3 1.0 O A:HOH2002 2.3 114.6 1.0 O A:HOH2003 2.3 117.9 1.0 OD2 A:PHD369 2.4 159.4 1.0 OD2 A:ASP710 2.6 179.5 1.0 CG A:ASP710 2.6 174.8 1.0 C A:THR371 3.3 146.3 1.0 CG A:PHD369 3.4 151.8 1.0 N A:GLY711 3.5 141.9 1.0 P A:PHD369 3.5 153.4 1.0 OD1 A:PHD369 3.8 162.5 1.0 OD2 A:ASP714 4.0 211.0 1.0 CA A:GLY372 4.1 137.8 1.0 CB A:ASP710 4.1 166.7 1.0 CA A:GLY711 4.1 132.6 1.0 N A:GLY372 4.1 133.7 1.0 OP1 A:PHD369 4.2 168.3 1.0 O A:SER209 4.3 201.2 1.0 CA A:THR371 4.3 160.3 1.0 C A:ASP710 4.4 148.1 1.0 N A:ASP710 4.4 147.0 1.0 CB A:THR371 4.4 169.3 1.0 CA A:ASP710 4.5 155.0 1.0 OG1 A:THR373 4.6 107.3 1.0 N A:THR373 4.6 139.9 1.0 OP2 A:PHD369 4.6 156.9 1.0 CG2 A:THR371 4.7 160.4 1.0 CB A:PHD369 4.7 124.7 1.0 N A:THR371 4.8 164.1 1.0 C A:GLY372 4.8 145.1 1.0 OD1 A:ASN713 4.8 140.2 1.0 OG A:SER209 4.9 246.2 1.0

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


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 Digitoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:174.2 occ:1.00 OD2 A:ASP804 2.1 167.0 1.0 O A:HOH2004 2.1 188.5 1.0 OD1 A:ASP804 2.2 168.5 1.0 OE2 A:GLU779 2.2 101.9 1.0 CG A:ASP804 2.3 155.6 1.0 OE2 A:GLU327 2.3 131.0 1.0 O A:HOH2005 2.4 116.0 1.0 O A:HOH2001 2.6 117.3 1.0 CD A:GLU779 3.0 115.4 1.0 OE1 A:GLU779 3.3 122.7 1.0 CD A:GLU327 3.4 132.8 1.0 CB A:ASP804 3.6 140.3 1.0 OE1 A:GLU327 3.8 134.9 1.0 ND2 A:ASN776 4.2 107.4 1.0 CG A:GLU779 4.3 123.3 1.0 OD1 A:ASN776 4.4 131.9 1.0 O A:VAL325 4.4 135.6 1.0 CG A:ASN776 4.4 112.1 1.0 O A:ALA323 4.5 155.8 1.0 CG A:GLU327 4.6 138.6 1.0 CG2 A:ILE800 4.6 84.8 1.0 N A:GLU327 4.7 138.5 1.0 CA A:PRO326 4.8 138.5 1.0 CA A:ASP804 4.8 128.1 1.0 CB A:GLU779 4.8 122.2 1.0

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


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 Digitoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:152.9 occ:1.00 OD2 C:PHD369 2.1 141.1 1.0 OD1 C:ASP710 2.1 149.1 1.0 O C:THR371 2.2 130.6 1.0 O C:HOH1202 2.2 113.5 1.0 OP3 C:PHD369 2.3 123.4 1.0 O C:HOH1201 2.4 123.2 1.0 CG C:ASP710 2.7 140.1 1.0 OD2 C:ASP710 2.8 143.2 1.0 CG C:PHD369 3.2 123.6 1.0 N C:GLY711 3.3 115.2 1.0 C C:THR371 3.4 133.5 1.0 OD2 C:ASP714 3.5 147.8 1.0 P C:PHD369 3.5 105.8 1.0 OD1 C:PHD369 3.7 126.9 1.0 CA C:GLY711 3.9 118.1 1.0 CB C:ASP710 4.0 123.5 1.0 CA C:GLY372 4.1 141.5 1.0 N C:ASP710 4.1 107.2 1.0 N C:GLY372 4.1 138.6 1.0 OP1 C:PHD369 4.2 122.6 1.0 C C:ASP710 4.2 108.2 1.0 CA C:ASP710 4.3 111.7 1.0 OG1 C:THR373 4.3 92.4 1.0 CB C:PHD369 4.4 104.4 1.0 N C:THR373 4.5 133.5 1.0 CA C:THR371 4.5 141.7 1.0 O C:SER209 4.5 171.4 1.0 OD1 C:ASN713 4.6 143.0 1.0 CB C:THR371 4.6 161.6 1.0 CG C:ASP714 4.6 145.8 1.0 C C:GLY372 4.7 142.3 1.0 OP2 C:PHD369 4.7 127.2 1.0 N C:THR371 4.8 138.8 1.0

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


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 Digitoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1103 b:128.5 occ:1.00 OD2 C:ASP804 2.1 134.0 1.0 OD1 C:ASP804 2.1 135.4 1.0 OE2 C:GLU779 2.2 110.2 1.0 O C:HOH1203 2.2 82.3 1.0 O C:HOH1205 2.3 118.6 1.0 CG C:ASP804 2.3 140.1 1.0 OE2 C:GLU327 2.3 122.8 1.0 O C:HOH1204 2.6 101.7 1.0 CD C:GLU779 3.0 111.4 1.0 OE1 C:GLU779 3.3 108.7 1.0 CD C:GLU327 3.4 119.3 1.0 CB C:ASP804 3.6 143.0 1.0 OE1 C:GLU327 3.8 120.9 1.0 ND2 C:ASN776 4.2 100.8 1.0 CG C:GLU779 4.3 122.5 1.0 O C:VAL325 4.3 128.2 1.0 OD1 C:ASN776 4.5 126.0 1.0 CG C:ASN776 4.5 102.8 1.0 CA C:PRO326 4.5 110.4 1.0 N C:GLU327 4.5 126.3 1.0 O C:ALA323 4.6 101.5 1.0 CG2 C:ILE800 4.6 91.8 1.0 CG C:GLU327 4.7 116.7 1.0 CB C:GLU779 4.8 124.3 1.0 CA C:ASP804 4.8 132.1 1.0 OG C:SER775 4.9 81.0 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