Magnesium in PDB 8jbl: Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State

The structure of Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State, PDB code: 8jbl was solved by R.Kanai, B.Vilsen, F.Cornelius, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.99 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	196.797, 74.319, 163.553, 90, 116.29, 90
R / Rfree (%)	23.3 / 28.2

The binding sites of Magnesium atom in the Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State (pdb code 8jbl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State, PDB code: 8jbl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:66.9 occ:1.00 OD1 A:ASP710 2.2 102.5 1.0 O A:HOH1212 2.2 45.3 1.0 CG A:ASP710 3.2 95.0 1.0 OD2 A:ASP710 3.5 101.4 1.0 OD1 A:ASP714 3.6 63.7 1.0 OD2 A:ASP369 3.7 35.7 1.0 OD2 A:ASP714 4.1 51.8 1.0 NZ A:LYS691 4.1 49.7 1.0 CG A:ASP714 4.2 49.8 1.0 O A:HOH1204 4.3 81.3 1.0 N A:GLY711 4.3 80.8 1.0 N A:ASP710 4.4 49.9 1.0 CG A:ASP369 4.5 39.3 1.0 CB A:ASP710 4.5 72.8 1.0 CG A:PRO688 4.6 92.1 1.0 CB A:PRO688 4.7 84.3 1.0 CA A:ASP710 4.9 53.4 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:89.6 occ:1.00 OE2 A:GLU779 2.2 69.5 1.0 OG A:SER775 2.2 63.0 1.0 O A:HOH1208 2.2 59.2 1.0 OD1 A:ASP804 2.2 77.5 1.0 CB A:SER775 2.7 46.1 1.0 CD A:GLU779 3.1 54.7 1.0 CG A:ASP804 3.2 61.5 1.0 OE1 A:GLU779 3.3 59.3 1.0 OD2 A:ASP804 3.6 73.3 1.0 CA A:SER775 4.0 55.5 1.0 C A:SER775 4.1 53.4 1.0 O A:SER775 4.2 36.1 1.0 NE2 A:GLN923 4.2 56.4 1.0 CB A:ASP804 4.4 49.3 1.0 CG A:GLU779 4.5 58.0 1.0 CA A:ASP804 4.5 37.9 1.0 O A:THR772 4.6 50.1 1.0 ND2 A:ASN776 4.6 73.2 1.0 CG2 A:ILE803 4.7 46.2 1.0 N A:ASN776 4.7 56.9 1.0 O A:HOH1209 4.8 77.0 1.0 N A:ASP804 4.8 42.1 1.0 N A:SER775 4.9 63.4 1.0 CB A:ASP808 5.0 66.3 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:34.5 occ:1.00 O A:HOH1206 2.0 44.9 1.0 OD2 A:ASP740 2.1 54.6 1.0 O A:ALA721 2.8 58.5 1.0 CG A:ASP740 3.2 56.0 1.0 O A:LYS719 3.6 49.4 1.0 O A:ASP722 3.6 60.8 1.0 OD1 A:ASP740 3.8 58.7 1.0 O A:LEU718 4.0 47.3 1.0 C A:ALA721 4.1 43.3 1.0 C A:ASP722 4.1 54.5 1.0 C A:LYS719 4.4 51.1 1.0 CB A:ASP740 4.4 45.1 1.0 CA A:ASP722 4.5 45.4 1.0 N A:GLY724 4.6 56.8 1.0 CA A:LYS719 4.7 60.2 1.0 N A:ILE723 4.8 49.8 1.0 N A:ASP722 4.8 23.3 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:95.6 occ:1.00 OD1 C:ASP710 2.2 94.7 1.0 O C:HOH1209 2.2 80.9 1.0 O C:HOH1211 2.3 76.5 1.0 CG C:ASP710 3.0 79.3 1.0 OD2 C:ASP710 3.3 94.0 1.0 OD2 C:ASP369 3.6 73.3 1.0 OD2 C:ASP714 4.2 84.8 1.0 NZ C:LYS691 4.4 55.9 1.0 CB C:ASP710 4.4 55.0 1.0 N C:GLY711 4.4 76.8 1.0 N C:ASP710 4.5 63.0 1.0 CG C:ASP369 4.7 60.5 1.0 CA C:ASP710 4.8 54.0 1.0 C C:ASP710 5.0 64.1 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1102 b:64.1 occ:1.00 OE2 C:GLU779 2.1 68.3 1.0 OD1 C:ASP804 2.1 82.7 1.0 OG C:SER775 2.1 72.9 1.0 O C:HOH1204 2.2 76.2 1.0 CB C:SER775 2.6 68.3 1.0 CD C:GLU779 3.0 62.8 1.0 OE1 C:GLU779 3.2 59.6 1.0 CG C:ASP804 3.2 81.7 1.0 OD2 C:ASP804 3.7 82.9 1.0 CA C:SER775 3.9 71.3 1.0 C C:SER775 4.0 66.5 1.0 O C:SER775 4.1 67.9 1.0 CG2 C:ILE803 4.3 63.8 1.0 NE2 C:GLN923 4.3 47.9 1.0 OD2 C:ASP808 4.4 99.1 1.0 CG C:GLU779 4.4 62.2 1.0 ND2 C:ASN776 4.4 84.7 1.0 CB C:ASP804 4.5 75.3 1.0 N C:ASN776 4.6 68.9 1.0 CG C:ASP808 4.6 91.8 1.0 O C:THR772 4.7 51.2 1.0 CA C:ASP804 4.7 64.5 1.0 N C:SER775 4.8 75.7 1.0 N C:ASP804 5.0 74.2 1.0 OD1 C:ASP808 5.0 101.6 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Na+,K+-Atpase in the E1.MG2+ State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1103 b:44.5 occ:1.00 OD1 C:ASP740 2.2 82.8 1.0 O C:HOH1201 2.3 94.5 1.0 O C:HOH1205 2.3 68.0 1.0 O C:LYS719 2.7 68.6 1.0 CG C:ASP740 3.3 80.0 1.0 O C:LEU718 3.3 45.1 1.0 C C:LYS719 3.5 62.2 1.0 CA C:LYS719 3.6 78.5 1.0 O C:ALA721 3.6 72.7 1.0 OD2 C:ASP740 3.7 78.3 1.0 CD C:LYS719 4.1 106.4 1.0 C C:LEU718 4.3 75.3 1.0 N C:LYS719 4.4 72.4 1.0 NZ C:LYS719 4.5 85.8 1.0 CE C:LYS719 4.5 96.3 1.0 CB C:ASP740 4.6 73.2 1.0 CG C:LYS719 4.6 98.5 1.0 N C:LYS720 4.7 55.6 1.0 CB C:LYS719 4.7 88.0 1.0 O C:ALA738 4.8 78.3 1.0 C C:ALA721 4.8 46.8 1.0 O C:ASP722 4.9 59.0 1.0 N C:ASP740 5.0 69.7 1.0

R.Kanai, B.Vilsen, F.Cornelius, C.Toyoshima. Crystal Structures of Na + ,K + -Atpase Reveal the Mechanism That Converts the K + -Bound Form to Na + -Bound Form and Opens and Closes the Cytoplasmic Gate. Febs Lett. 2023.
ISSN: ISSN 0014-5793
PubMed: 37357620
DOI: 10.1002/1873-3468.14689