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

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

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Bufalin, PDB code: 7ddl 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)	14.99 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.721, 117.646, 492.068, 90, 90, 90
R / Rfree (%)	24.1 / 28.1

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


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 Bufalin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:101.6 occ:1.00 OD1 A:ASP710 2.1 83.7 1.0 O A:THR371 2.1 105.2 1.0 O A:HOH1201 2.2 112.5 1.0 O A:HOH1205 2.4 67.0 1.0 OP3 A:PHD369 2.4 76.0 1.0 OD2 A:PHD369 2.5 83.9 1.0 CG A:ASP710 2.9 72.1 1.0 OD2 A:ASP710 3.1 74.9 1.0 C A:THR371 3.3 88.8 1.0 CG A:PHD369 3.4 85.0 1.0 N A:GLY711 3.5 98.8 1.0 P A:PHD369 3.6 89.9 1.0 OD1 A:PHD369 3.7 80.6 1.0 OD2 A:ASP714 4.0 62.1 1.0 CB A:THR371 4.0 78.7 1.0 CA A:GLY711 4.0 89.3 1.0 CA A:THR371 4.1 79.4 1.0 O A:SER209 4.2 77.5 1.0 CG2 A:THR371 4.2 89.5 1.0 N A:GLY372 4.2 85.5 1.0 CB A:ASP710 4.3 61.1 1.0 OP1 A:PHD369 4.3 68.6 1.0 CA A:GLY372 4.4 89.8 1.0 N A:ASP710 4.4 55.7 1.0 C A:ASP710 4.4 87.9 1.0 OD1 A:ASN713 4.5 74.7 1.0 N A:THR371 4.5 86.6 1.0 CA A:ASP710 4.6 65.2 1.0 OP2 A:PHD369 4.7 77.9 1.0 CB A:PHD369 4.7 85.2 1.0 OG1 A:THR373 4.7 82.0 1.0 ND2 A:ASN713 4.9 88.5 1.0 C A:GLY372 5.0 96.7 1.0 N A:THR373 5.0 84.6 1.0

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


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 Bufalin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:91.2 occ:1.00 OD2 A:ASP804 2.1 89.1 1.0 OD1 A:ASP804 2.2 74.9 1.0 OE2 A:GLU779 2.2 77.0 1.0 OE2 A:GLU327 2.2 107.1 1.0 CG A:ASP804 2.3 86.3 1.0 O A:HOH1204 2.4 114.8 1.0 O A:HOH1203 2.4 78.2 1.0 O A:HOH1202 2.4 124.0 1.0 CD A:GLU779 3.1 80.6 1.0 OE1 A:GLU779 3.3 77.1 1.0 CD A:GLU327 3.4 101.1 1.0 CB A:ASP804 3.7 87.5 1.0 OE1 A:GLU327 3.9 105.1 1.0 ND2 A:ASN776 4.2 88.3 1.0 CG A:GLU779 4.5 82.7 1.0 CG A:GLU327 4.6 88.2 1.0 O A:ALA323 4.6 75.5 1.0 O A:VAL325 4.7 72.9 1.0 CG A:ASN776 4.7 84.6 1.0 N A:GLU327 4.7 76.9 1.0 CA A:PRO326 4.7 65.3 1.0 OD1 A:ASN776 4.9 105.8 1.0 OG A:SER775 4.9 47.5 1.0 CA A:ASP804 4.9 65.9 1.0 CG2 A:ILE800 4.9 61.5 1.0 CB A:GLU779 5.0 80.7 1.0

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


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 Bufalin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:96.2 occ:1.00 OD1 C:ASP710 2.1 80.9 1.0 O C:HOH1201 2.1 86.5 1.0 O C:THR371 2.1 110.0 1.0 OP3 C:PHD369 2.3 83.6 1.0 O C:HOH1205 2.3 63.7 1.0 OD2 C:PHD369 2.4 82.8 1.0 CG C:ASP710 2.9 83.7 1.0 OD2 C:ASP710 3.1 80.0 1.0 C C:THR371 3.3 105.0 1.0 CG C:PHD369 3.4 77.7 1.0 N C:GLY711 3.5 83.5 1.0 P C:PHD369 3.5 70.9 1.0 OD1 C:PHD369 3.7 76.7 1.0 OD2 C:ASP714 4.0 68.7 1.0 CA C:GLY711 4.0 69.7 1.0 O C:SER209 4.1 74.1 1.0 CB C:THR371 4.1 123.5 1.0 OP1 C:PHD369 4.2 62.5 1.0 CA C:THR371 4.2 111.9 1.0 CB C:ASP710 4.3 87.7 1.0 N C:GLY372 4.3 94.0 1.0 CG2 C:THR371 4.3 108.4 1.0 OD1 C:ASN713 4.3 81.6 1.0 CA C:GLY372 4.4 97.1 1.0 C C:ASP710 4.5 80.7 1.0 N C:ASP710 4.5 71.1 1.0 N C:THR371 4.5 99.9 1.0 OG1 C:THR373 4.6 72.5 1.0 CA C:ASP710 4.6 78.1 1.0 OP2 C:PHD369 4.7 82.4 1.0 CB C:PHD369 4.7 73.1 1.0 ND2 C:ASN713 4.8 81.2 1.0 N C:THR373 4.9 79.6 1.0 C C:GLY372 5.0 97.2 1.0

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


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 Bufalin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1103 b:62.6 occ:1.00 O C:HOH1202 2.1 40.6 1.0 OD2 C:ASP804 2.1 93.2 1.0 OE2 C:GLU779 2.2 61.6 1.0 OD1 C:ASP804 2.3 103.0 1.0 OE2 C:GLU327 2.3 108.3 1.0 O C:HOH1203 2.3 51.4 1.0 CG C:ASP804 2.3 97.8 1.0 O C:HOH1204 2.6 28.3 1.0 CD C:GLU779 3.1 62.5 1.0 CD C:GLU327 3.4 108.0 1.0 OE1 C:GLU779 3.4 54.2 1.0 CB C:ASP804 3.7 85.9 1.0 OE1 C:GLU327 3.8 122.9 1.0 CG C:GLU779 4.5 55.4 1.0 ND2 C:ASN776 4.5 56.0 1.0 CA C:PRO326 4.5 68.8 1.0 N C:GLU327 4.5 76.4 1.0 O C:VAL325 4.6 91.2 1.0 OG C:SER775 4.6 65.9 1.0 CG C:GLU327 4.7 97.6 1.0 O C:ALA323 4.7 74.8 1.0 CG2 C:ILE800 4.7 39.9 1.0 CG C:ASN776 4.8 63.3 1.0 CA C:ASP804 4.9 70.2 1.0 CB C:GLU779 4.9 51.1 1.0 OD1 C:ASN776 4.9 80.9 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