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

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 (pdb code 7wyw). 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, PDB code: 7wyw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7wyw

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:66.3
occ:1.00
 OP3 A:PHD376 1.9 62.3 1.0
O A:HOH1204 2.0 63.6 1.0
O A:THR378 2.0 63.5 1.0
OD1 A:ASP717 2.1 62.0 1.0
O A:HOH1205 2.2 72.0 1.0
OD2 A:PHD376 2.3 62.3 1.0
CG A:ASP717 3.0 62.0 1.0
C A:THR378 3.2 63.5 1.0
P A:PHD376 3.2 62.3 1.0
CG A:PHD376 3.2 62.3 1.0
OD2 A:ASP717 3.2 62.0 1.0
OD1 A:PHD376 3.5 62.3 1.0
OD2 A:ASP721 3.9 68.8 1.0
CB A:THR378 4.0 63.5 1.0
OP1 A:PHD376 4.0 62.3 1.0
CA A:THR378 4.0 63.5 1.0
N A:GLY718 4.0 65.4 1.0
N A:GLY379 4.1 59.8 1.0
OP2 A:PHD376 4.2 62.3 1.0
CG2 A:THR378 4.2 63.5 1.0
N A:THR378 4.3 63.5 1.0
CA A:GLY379 4.4 59.8 1.0
CB A:ASP717 4.4 62.0 1.0
OD1 A:ASN720 4.5 70.7 1.0
CB A:PHD376 4.5 62.3 1.0
N A:ASP717 4.6 62.0 1.0
OG1 A:THR380 4.6 60.8 1.0
CA A:GLY718 4.7 65.4 1.0
O A:SER216 4.8 85.6 1.0
ND2 A:ASN720 4.8 70.7 1.0
CA A:ASP717 4.8 62.0 1.0
C A:ASP717 4.8 62.0 1.0
N A:THR380 4.9 60.8 1.0
C A:GLY379 4.9 59.8 1.0
CG A:ASP721 5.0 68.8 1.0

Magnesium binding site 2 out of 6 in 7wyw

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:60.1
occ:1.00
 OD2 A:ASP747 2.1 47.5 1.0
CG A:ASP747 3.3 47.5 1.0
O A:LYS726 3.6 65.2 1.0
OD1 A:ASP747 3.9 47.5 1.0
O A:ALA728 4.1 56.5 1.0
O A:LEU725 4.3 60.6 1.0
O A:VAL279 4.4 72.5 1.0
CB A:ASP747 4.5 47.5 1.0
C A:LYS726 4.5 65.2 1.0
CA A:LYS726 4.7 65.2 1.0
O A:ASP729 4.7 53.3 1.0
CD A:LYS726 4.9 65.2 1.0
O A:ALA745 5.0 54.9 1.0

Magnesium binding site 3 out of 6 in 7wyw

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:26.6
occ:1.00
 OD2 A:ASP811 2.1 30.6 1.0
O A:HOH1202 2.2 26.7 1.0
O A:HOH1203 2.4 30.3 1.0
OE1 A:GLU786 2.5 24.1 1.0
CG A:ASP811 2.5 30.6 1.0
OD1 A:ASP811 2.6 30.6 1.0
O A:HOH1201 2.6 29.5 1.0
OE2 A:GLU334 3.2 39.2 1.0
CD A:GLU786 3.5 24.1 1.0
OE2 A:GLU786 3.8 24.1 1.0
CB A:ASP811 3.9 30.6 1.0
CG2 A:ILE807 4.2 31.2 1.0
OD1 A:ASN783 4.3 23.2 1.0
O A:VAL332 4.4 37.7 1.0
CD A:GLU334 4.5 39.2 1.0
O A:ALA330 4.5 34.0 1.0
CG A:GLU786 4.8 24.1 1.0
CB A:GLU786 5.0 24.1 1.0

Magnesium binding site 4 out of 6 in 7wyw

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:66.8
occ:1.00
 OP3 C:PHD376 1.9 62.0 1.0
O C:HOH1204 2.0 63.4 1.0
O C:THR378 2.0 63.4 1.0
OD1 C:ASP717 2.1 62.0 1.0
O C:HOH1205 2.1 71.8 1.0
OD2 C:PHD376 2.3 62.0 1.0
CG C:ASP717 3.0 62.0 1.0
C C:THR378 3.2 63.4 1.0
P C:PHD376 3.2 62.0 1.0
CG C:PHD376 3.2 62.0 1.0
OD2 C:ASP717 3.2 62.0 1.0
OD1 C:PHD376 3.5 62.0 1.0
OD2 C:ASP721 3.9 68.4 1.0
CB C:THR378 4.0 63.4 1.0
OP1 C:PHD376 4.0 62.0 1.0
CA C:THR378 4.0 63.4 1.0
N C:GLY718 4.0 65.7 1.0
N C:GLY379 4.1 60.1 1.0
OP2 C:PHD376 4.2 62.0 1.0
CG2 C:THR378 4.2 63.4 1.0
N C:THR378 4.3 63.4 1.0
CA C:GLY379 4.4 60.1 1.0
CB C:ASP717 4.4 62.0 1.0
OD1 C:ASN720 4.5 71.2 1.0
CB C:PHD376 4.5 62.0 1.0
N C:ASP717 4.6 62.0 1.0
OG1 C:THR380 4.6 60.9 1.0
CA C:GLY718 4.7 65.7 1.0
O C:SER216 4.8 85.1 1.0
ND2 C:ASN720 4.8 71.2 1.0
CA C:ASP717 4.8 62.0 1.0
C C:ASP717 4.8 62.0 1.0
N C:THR380 4.9 60.9 1.0
C C:GLY379 4.9 60.1 1.0
CG C:ASP721 5.0 68.4 1.0

Magnesium binding site 5 out of 6 in 7wyw

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1102

b:60.1
occ:1.00
 OD2 C:ASP747 2.1 47.8 1.0
CG C:ASP747 3.3 47.8 1.0
O C:LYS726 3.6 65.4 1.0
OD1 C:ASP747 3.9 47.8 1.0
O C:ALA728 4.1 57.4 1.0
O C:LEU725 4.3 60.9 1.0
O C:VAL279 4.4 72.8 1.0
CB C:ASP747 4.5 47.8 1.0
C C:LYS726 4.5 65.4 1.0
CA C:LYS726 4.7 65.4 1.0
O C:ASP729 4.7 54.1 1.0
CD C:LYS726 4.9 65.4 1.0
O C:ALA745 5.0 54.8 1.0

Magnesium binding site 6 out of 6 in 7wyw

Go back to Magnesium Binding Sites List in 7wyw
Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Na+,K+-Atpase in the E2P State Formed By Inorganic Phosphate


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:26.5
occ:1.00
 OD2 C:ASP811 2.1 30.9 1.0
O C:HOH1202 2.2 26.8 1.0
O C:HOH1203 2.4 31.4 1.0
OE1 C:GLU786 2.5 24.1 1.0
CG C:ASP811 2.5 30.9 1.0
OD1 C:ASP811 2.6 30.9 1.0
O C:HOH1201 2.6 29.1 1.0
OE2 C:GLU334 3.2 38.9 1.0
CD C:GLU786 3.5 24.1 1.0
OE2 C:GLU786 3.8 24.1 1.0
CB C:ASP811 3.9 30.9 1.0
CG2 C:ILE807 4.2 31.3 1.0
OD1 C:ASN783 4.3 23.8 1.0
O C:VAL332 4.4 37.7 1.0
CD C:GLU334 4.5 38.9 1.0
O C:ALA330 4.5 33.8 1.0
CG C:GLU786 4.8 24.1 1.0
CB C:GLU786 5.0 24.1 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: Fri Apr 7 01:54:23 2023

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