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Magnesium in PDB 7wyy: Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime (pdb code 7wyy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime, PDB code: 7wyy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7wyy

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime


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 Inorganic Phosphate with Istaroxime within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:39.6
occ:1.00
 OP3 A:PHD376 1.9 30.4 1.0
O A:HOH1203 2.0 38.0 1.0
O A:THR378 2.0 34.6 1.0
OD1 A:ASP717 2.1 35.7 1.0
O A:HOH1204 2.2 43.4 1.0
OD2 A:PHD376 2.3 30.4 1.0
CG A:ASP717 3.0 35.7 1.0
C A:THR378 3.2 34.6 1.0
P A:PHD376 3.2 30.4 1.0
OD2 A:ASP717 3.2 35.7 1.0
CG A:PHD376 3.2 30.4 1.0
OD1 A:PHD376 3.5 30.4 1.0
OD2 A:ASP721 3.9 41.2 1.0
CB A:THR378 4.0 34.6 1.0
OP1 A:PHD376 4.0 30.4 1.0
N A:GLY718 4.0 39.8 1.0
CA A:THR378 4.0 34.6 1.0
N A:GLY379 4.1 32.8 1.0
CG2 A:THR378 4.2 34.6 1.0
OP2 A:PHD376 4.2 30.4 1.0
N A:THR378 4.4 34.6 1.0
CA A:GLY379 4.4 32.8 1.0
CB A:ASP717 4.4 35.7 1.0
OD1 A:ASN720 4.5 43.6 1.0
CB A:PHD376 4.5 30.4 1.0
N A:ASP717 4.6 35.7 1.0
OG1 A:THR380 4.6 30.7 1.0
CA A:GLY718 4.7 39.8 1.0
ND2 A:ASN720 4.8 43.6 1.0
CA A:ASP717 4.8 35.7 1.0
C A:ASP717 4.8 35.7 1.0
O A:SER216 4.8 62.4 1.0
N A:THR380 4.9 30.7 1.0
C A:GLY379 4.9 32.8 1.0
CG A:ASP721 4.9 41.2 1.0

Magnesium binding site 2 out of 6 in 7wyy

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime


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 Inorganic Phosphate with Istaroxime within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:21.9
occ:1.00
 OD2 A:ASP747 2.1 26.6 1.0
CG A:ASP747 3.3 26.6 1.0
O A:LYS726 3.6 38.6 1.0
OD1 A:ASP747 3.9 26.6 1.0
O A:ALA728 4.1 29.2 1.0
O A:LEU725 4.3 36.1 1.0
O A:VAL279 4.4 53.2 1.0
CB A:ASP747 4.5 26.6 1.0
C A:LYS726 4.5 38.6 1.0
CA A:LYS726 4.7 38.6 1.0
O A:ASP729 4.7 26.2 1.0
CD A:LYS726 4.9 38.6 1.0
CG1 A:VAL279 5.0 53.2 1.0
O A:ALA745 5.0 34.9 1.0

Magnesium binding site 3 out of 6 in 7wyy

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime


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 Inorganic Phosphate with Istaroxime within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:18.3
occ:1.00
 OD2 A:ASP811 2.0 22.1 1.0
O A:HOH1201 2.1 19.8 1.0
OD1 A:ASP811 2.2 22.1 1.0
O A:HOH1202 2.2 16.1 1.0
CG A:ASP811 2.4 22.1 1.0
OE1 A:GLU786 2.4 14.9 1.0
NAZ A:7Q21104 3.3 21.6 1.0
OE2 A:GLU334 3.6 22.2 1.0
CD A:GLU786 3.6 14.9 1.0
CB A:ASP811 3.9 22.1 1.0
OD1 A:ASN783 4.0 13.6 1.0
CG2 A:ILE807 4.3 20.4 1.0
CG A:GLU786 4.4 14.9 1.0
CAY A:7Q21104 4.5 21.6 1.0
CAX A:7Q21104 4.5 21.6 1.0
OE2 A:GLU786 4.6 14.9 1.0
OG A:SER782 4.6 11.4 1.0
CB A:GLU786 4.6 14.9 1.0
O A:ALA330 4.8 18.9 1.0
CA A:ASP811 4.8 22.1 1.0
CD A:GLU334 4.8 22.2 1.0
O A:VAL332 5.0 21.3 1.0

Magnesium binding site 4 out of 6 in 7wyy

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime


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 Inorganic Phosphate with Istaroxime within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:39.0
occ:1.00
 OP3 C:PHD376 1.9 30.0 1.0
O C:HOH1202 2.0 37.5 1.0
O C:THR378 2.0 34.3 1.0
OD1 C:ASP717 2.1 35.1 1.0
O C:HOH1204 2.2 42.4 1.0
OD2 C:PHD376 2.3 30.0 1.0
CG C:ASP717 3.0 35.1 1.0
C C:THR378 3.2 34.3 1.0
P C:PHD376 3.2 30.0 1.0
OD2 C:ASP717 3.2 35.1 1.0
CG C:PHD376 3.2 30.0 1.0
OD1 C:PHD376 3.5 30.0 1.0
OD2 C:ASP721 3.9 40.2 1.0
CB C:THR378 4.0 34.3 1.0
OP1 C:PHD376 4.0 30.0 1.0
CA C:THR378 4.0 34.3 1.0
N C:GLY718 4.0 39.3 1.0
N C:GLY379 4.1 32.3 1.0
CG2 C:THR378 4.2 34.3 1.0
OP2 C:PHD376 4.2 30.0 1.0
N C:THR378 4.4 34.3 1.0
CA C:GLY379 4.4 32.3 1.0
CB C:ASP717 4.4 35.1 1.0
OD1 C:ASN720 4.5 43.6 1.0
CB C:PHD376 4.5 30.0 1.0
N C:ASP717 4.6 35.1 1.0
OG1 C:THR380 4.6 30.2 1.0
CA C:GLY718 4.7 39.3 1.0
ND2 C:ASN720 4.8 43.6 1.0
CA C:ASP717 4.8 35.1 1.0
C C:ASP717 4.8 35.1 1.0
O C:SER216 4.8 61.9 1.0
N C:THR380 4.9 30.2 1.0
C C:GLY379 4.9 32.3 1.0
CG C:ASP721 4.9 40.2 1.0

Magnesium binding site 5 out of 6 in 7wyy

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1102

b:22.5
occ:1.00
 OD2 C:ASP747 2.1 26.4 1.0
CG C:ASP747 3.3 26.4 1.0
O C:LYS726 3.6 37.8 1.0
OD1 C:ASP747 3.9 26.4 1.0
O C:ALA728 4.1 29.2 1.0
O C:LEU725 4.3 36.2 1.0
O C:VAL279 4.4 54.0 1.0
CB C:ASP747 4.5 26.4 1.0
C C:LYS726 4.5 37.8 1.0
CA C:LYS726 4.7 37.8 1.0
O C:ASP729 4.7 26.2 1.0
CD C:LYS726 4.9 37.8 1.0
CG1 C:VAL279 5.0 54.0 1.0
O C:ALA745 5.0 34.8 1.0

Magnesium binding site 6 out of 6 in 7wyy

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Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate with Istaroxime within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:17.7
occ:1.00
 OD2 C:ASP811 2.0 22.0 1.0
O C:HOH1201 2.1 19.2 1.0
OD1 C:ASP811 2.2 22.0 1.0
O C:HOH1203 2.3 16.3 1.0
CG C:ASP811 2.4 22.0 1.0
OE1 C:GLU786 2.4 14.6 1.0
NAZ C:7Q21104 3.3 21.8 1.0
OE2 C:GLU334 3.6 21.9 1.0
CD C:GLU786 3.6 14.6 1.0
CB C:ASP811 3.9 22.0 1.0
OD1 C:ASN783 4.0 13.5 1.0
CG2 C:ILE807 4.3 20.8 1.0
CG C:GLU786 4.4 14.6 1.0
CAY C:7Q21104 4.5 21.8 1.0
CAX C:7Q21104 4.5 21.8 1.0
OE2 C:GLU786 4.6 14.6 1.0
OG C:SER782 4.6 11.4 1.0
CB C:GLU786 4.6 14.6 1.0
O C:ALA330 4.8 19.0 1.0
CA C:ASP811 4.8 22.0 1.0
CD C:GLU334 4.8 21.9 1.0
O C:VAL332 5.0 21.4 1.0

Reference:

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
Page generated: Thu Oct 3 11:42:14 2024

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