Magnesium in PDB 7wyv: Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+

The structure of Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+ also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+ (pdb code 7wyv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+, PDB code: 7wyv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:73.9 occ:1.00 OP3 A:PHD376 2.0 68.3 1.0 O A:HOH1202 2.0 73.3 1.0 O A:THR378 2.0 72.5 1.0 OD1 A:ASP717 2.1 70.0 1.0 O A:HOH1205 2.1 78.6 1.0 OD2 A:PHD376 2.2 68.3 1.0 CG A:ASP717 3.0 70.0 1.0 CG A:PHD376 3.2 68.3 1.0 C A:THR378 3.2 72.5 1.0 P A:PHD376 3.2 68.3 1.0 OD2 A:ASP717 3.3 70.0 1.0 OD1 A:PHD376 3.5 68.3 1.0 OD2 A:ASP721 3.8 73.2 1.0 N A:GLY718 3.9 73.2 1.0 OP1 A:PHD376 4.0 68.3 1.0 CA A:THR378 4.1 72.5 1.0 CB A:THR378 4.1 72.5 1.0 N A:GLY379 4.2 70.3 1.0 CA A:GLY379 4.3 70.3 1.0 OP2 A:PHD376 4.3 68.3 1.0 N A:THR378 4.4 72.5 1.0 CG2 A:THR378 4.4 72.5 1.0 CB A:ASP717 4.4 70.0 1.0 OD1 A:ASN720 4.4 76.0 1.0 CB A:PHD376 4.4 68.3 1.0 N A:ASP717 4.5 70.0 1.0 OG1 A:THR380 4.6 68.7 1.0 CA A:GLY718 4.6 73.2 1.0 ND2 A:ASN720 4.7 76.0 1.0 C A:ASP717 4.8 70.0 1.0 CA A:ASP717 4.8 70.0 1.0 O A:SER216 4.9 99.0 1.0 N A:THR380 4.9 68.7 1.0 C A:GLY379 4.9 70.3 1.0 CG A:ASP721 4.9 73.2 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:42.5 occ:1.00 OD2 A:ASP811 2.1 41.1 1.0 O A:HOH1204 2.2 39.4 1.0 O A:HOH1203 2.3 44.3 1.0 OE1 A:GLU786 2.4 36.1 1.0 CG A:ASP811 2.5 41.1 1.0 OD1 A:ASP811 2.5 41.1 1.0 O A:HOH1201 2.5 41.8 1.0 OE2 A:GLU334 3.1 47.0 1.0 CD A:GLU786 3.5 36.1 1.0 CB A:ASP811 3.8 41.1 1.0 OE2 A:GLU786 3.8 36.1 1.0 CG2 A:ILE807 4.2 39.5 1.0 OD1 A:ASN783 4.3 35.8 1.0 CD A:GLU334 4.4 47.0 1.0 O A:VAL332 4.4 46.4 1.0 O A:ALA330 4.6 43.9 1.0 CG A:GLU786 4.8 36.1 1.0 CB A:GLU786 5.0 36.1 1.0 CA A:ASP811 5.0 41.1 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:74.2 occ:1.00 OP3 C:PHD376 2.0 68.8 1.0 O C:HOH1202 2.0 73.8 1.0 O C:THR378 2.0 72.9 1.0 OD1 C:ASP717 2.1 70.5 1.0 O C:HOH1205 2.1 78.7 1.0 OD2 C:PHD376 2.2 68.8 1.0 CG C:ASP717 3.0 70.5 1.0 CG C:PHD376 3.2 68.8 1.0 C C:THR378 3.2 72.9 1.0 P C:PHD376 3.2 68.8 1.0 OD2 C:ASP717 3.3 70.5 1.0 OD1 C:PHD376 3.5 68.8 1.0 OD2 C:ASP721 3.8 73.7 1.0 N C:GLY718 3.9 73.5 1.0 OP1 C:PHD376 4.0 68.8 1.0 CA C:THR378 4.1 72.9 1.0 CB C:THR378 4.1 72.9 1.0 N C:GLY379 4.2 70.6 1.0 CA C:GLY379 4.3 70.6 1.0 OP2 C:PHD376 4.3 68.8 1.0 N C:THR378 4.4 72.9 1.0 CG2 C:THR378 4.4 72.9 1.0 CB C:ASP717 4.4 70.5 1.0 OD1 C:ASN720 4.4 76.3 1.0 CB C:PHD376 4.4 68.8 1.0 N C:ASP717 4.5 70.5 1.0 OG1 C:THR380 4.6 68.8 1.0 CA C:GLY718 4.6 73.5 1.0 ND2 C:ASN720 4.7 76.3 1.0 C C:ASP717 4.8 70.5 1.0 CA C:ASP717 4.8 70.5 1.0 O C:SER216 4.9 99.2 1.0 N C:THR380 4.9 68.8 1.0 C C:GLY379 4.9 70.6 1.0 CG C:ASP721 4.9 73.7 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Atp in the Presence of 40 Mm MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1103 b:42.8 occ:1.00 OD2 C:ASP811 2.1 41.0 1.0 O C:HOH1204 2.2 40.1 1.0 O C:HOH1203 2.3 44.1 1.0 OE1 C:GLU786 2.4 36.1 1.0 CG C:ASP811 2.5 41.0 1.0 OD1 C:ASP811 2.5 41.0 1.0 O C:HOH1201 2.5 41.9 1.0 OE2 C:GLU334 3.1 47.4 1.0 CD C:GLU786 3.5 36.1 1.0 CB C:ASP811 3.8 41.0 1.0 OE2 C:GLU786 3.8 36.1 1.0 CG2 C:ILE807 4.2 39.2 1.0 OD1 C:ASN783 4.3 35.5 1.0 CD C:GLU334 4.3 47.4 1.0 O C:VAL332 4.4 46.8 1.0 O C:ALA330 4.6 44.0 1.0 CG C:GLU786 4.8 36.1 1.0 CB C:GLU786 5.0 36.1 1.0 CA C:ASP811 5.0 41.0 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