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Magnesium in PDB 7qtv: Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)

Enzymatic activity of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)

All present enzymatic activity of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx):
7.2.2.13;

Protein crystallography data

The structure of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx), PDB code: 7qtv was solved by M.U.Fruergaard, I.Dach, J.L.Andersen, M.Ozol, A.Shahsavar, E.M.Quistgaard, H.Poulsen, N.U.Fedosova, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.67 / 4.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.47, 118.08, 494.66, 90, 90, 90
R / Rfree (%) 24.7 / 28.1

Other elements in 7qtv:

The structure of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) (pdb code 7qtv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx), PDB code: 7qtv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7qtv

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Magnesium binding site 1 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:160.4
occ:1.00
 OE1 A:GLU779 1.9 145.0 1.0
OD1 A:ASN776 2.0 128.2 1.0
O A:HOH1203 2.1 156.7 1.0
OD2 A:ASP804 2.2 154.3 1.0
O A:HOH1204 2.3 127.4 1.0
OD1 A:ASP804 2.5 156.2 1.0
CG A:ASP804 2.6 143.3 1.0
OE2 A:GLU327 2.6 151.8 1.0
O A:HOH1201 2.6 168.1 1.0
CD A:GLU779 2.7 138.5 1.0
OE2 A:GLU779 2.8 135.2 1.0
CG A:ASN776 3.2 114.2 1.0
CD A:GLU327 3.5 131.6 1.0
OE1 A:GLU327 3.7 126.1 1.0
O A:ALA323 4.0 127.1 1.0
ND2 A:ASN776 4.0 121.1 1.0
CB A:ASP804 4.0 126.8 1.0
CG A:GLU779 4.1 129.2 1.0
CB A:ASN776 4.3 94.1 1.0
O A:VAL325 4.4 130.4 1.0
CA A:ASN776 4.4 101.4 1.0
OG A:SER775 4.4 124.1 1.0
CB A:GLU779 4.5 124.5 1.0
CG2 A:ILE800 4.7 120.0 1.0
N A:ASN776 4.9 108.6 1.0
CG A:GLU327 4.9 121.7 1.0
N A:GLU327 5.0 123.5 1.0

Magnesium binding site 2 out of 6 in 7qtv

Go back to Magnesium Binding Sites List in 7qtv
Magnesium binding site 2 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1106

b:145.6
occ:1.00
 F2 A:BEF1101 1.9 192.9 1.0
OD1 A:ASP710 1.9 142.2 1.0
OD2 A:ASP369 2.1 148.4 1.0
O A:THR371 2.1 146.9 1.0
CG A:ASP369 2.5 146.2 1.0
BE A:BEF1101 2.6 197.0 1.0
CG A:ASP710 2.8 146.9 1.0
OD1 A:ASP369 2.8 158.9 1.0
OG1 A:THR371 2.9 159.7 1.0
C A:THR371 3.1 153.8 1.0
F3 A:BEF1101 3.2 208.0 1.0
OD2 A:ASP710 3.3 151.2 1.0
N A:THR371 3.4 140.3 1.0
CB A:ASP369 3.5 130.7 1.0
CA A:THR371 3.6 142.5 1.0
F1 A:BEF1101 3.8 191.6 1.0
CB A:THR371 3.8 142.7 1.0
CB A:ASP710 3.9 145.7 1.0
OG1 A:THR373 4.0 128.0 1.0
N A:LYS370 4.1 140.6 1.0
C A:LYS370 4.1 136.7 1.0
OD2 A:ASP714 4.1 180.8 1.0
N A:GLY372 4.2 219.6 1.0
C A:ASP369 4.4 129.6 1.0
N A:ASP710 4.4 129.2 1.0
N A:THR373 4.5 151.6 1.0
ND2 A:ASN713 4.5 151.4 1.0
CA A:ASP369 4.6 122.7 1.0
N A:GLY711 4.6 137.9 1.0
CA A:ASP710 4.7 134.4 1.0
O A:LYS370 4.7 159.0 1.0
CA A:GLY372 4.7 217.9 1.0
CA A:LYS370 4.7 133.8 1.0
OD1 A:ASP714 4.8 173.5 1.0
CB A:THR373 4.8 122.3 1.0
CG A:ASP714 4.9 172.2 1.0
OD1 A:ASN713 4.9 145.8 1.0
O A:ASP369 5.0 124.4 1.0

Magnesium binding site 3 out of 6 in 7qtv

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Magnesium binding site 3 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1107

b:116.0
occ:1.00
 O A:HOH1205 2.0 135.0 1.0
O A:HOH1202 2.0 117.2 1.0
OD2 A:ASP740 2.0 111.0 1.0
OD1 A:ASP740 2.2 132.4 1.0
CG A:ASP740 2.3 124.9 1.0
CB A:ASP740 3.7 120.1 1.0
O A:ASP722 3.7 116.9 1.0
O A:ALA721 3.8 127.8 1.0
O A:LYS719 3.9 121.7 1.0
O A:GLY272 3.9 120.8 1.0
CA A:ILE723 4.1 112.6 1.0
C A:ASP722 4.3 113.6 1.0
O A:SER718 4.4 145.1 1.0
N A:ILE723 4.5 105.0 1.0
N A:GLY724 4.5 125.3 1.0
N A:ASP740 4.6 121.1 1.0
CA A:ASP740 4.7 112.7 1.0
C A:ILE723 4.8 103.8 1.0
O A:ALA738 4.8 121.1 1.0
C A:LYS719 4.9 116.2 1.0
C A:GLY272 4.9 134.3 1.0
C A:ALA721 4.9 121.3 1.0
CA A:GLY272 4.9 146.5 1.0

Magnesium binding site 4 out of 6 in 7qtv

Go back to Magnesium Binding Sites List in 7qtv
Magnesium binding site 4 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:187.3
occ:1.00
 OE1 C:GLU779 1.8 175.9 1.0
O C:HOH1202 1.9 252.5 1.0
OD2 C:ASP804 1.9 192.6 1.0
OD1 C:ASN776 2.2 156.2 1.0
O C:HOH1203 2.3 149.4 1.0
O C:HOH1201 2.7 159.0 1.0
CD C:GLU779 2.7 164.2 1.0
CG C:ASP804 2.8 168.3 1.0
OE1 C:GLU327 2.8 174.8 1.0
OE2 C:GLU779 3.0 170.9 1.0
OD1 C:ASP804 3.0 174.9 1.0
CG C:ASN776 3.4 141.4 1.0
OE2 C:GLU327 3.5 154.3 1.0
CD C:GLU327 3.5 162.0 1.0
O C:ALA323 3.9 114.6 1.0
CG C:GLU779 4.1 148.7 1.0
CB C:ASP804 4.2 144.9 1.0
ND2 C:ASN776 4.3 135.1 1.0
CG2 C:ILE800 4.4 169.2 1.0
CB C:ASN776 4.5 133.9 1.0
O C:VAL325 4.5 132.5 1.0
CB C:GLU779 4.5 146.0 1.0
CA C:ASN776 4.6 130.6 1.0
OG C:SER775 4.7 130.6 1.0
CG C:GLU327 4.9 147.1 1.0

Magnesium binding site 5 out of 6 in 7qtv

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Magnesium binding site 5 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1104

b:144.6
occ:1.00
 O C:HOH1204 2.0 154.9 1.0
OD2 C:ASP740 2.1 159.4 1.0
OD1 C:ASP740 2.2 136.8 1.0
CG C:ASP740 2.4 145.4 1.0
O C:LYS719 3.4 126.3 1.0
CB C:ASP740 3.9 141.2 1.0
O C:SER718 3.9 139.6 1.0
O C:GLY272 3.9 173.7 1.0
O C:ALA721 4.0 131.3 1.0
C C:LYS719 4.3 125.9 1.0
O C:ALA738 4.3 143.3 1.0
CA C:LYS719 4.4 121.8 1.0
O C:ASP722 4.5 138.8 1.0
CA C:GLY272 4.5 178.9 1.0
N C:ASP740 4.7 154.0 1.0
C C:GLY272 4.7 181.8 1.0
CA C:ILE723 4.7 134.7 1.0
N C:GLY724 4.8 170.3 1.0
CA C:ASP740 4.8 142.2 1.0
C C:ASP722 4.9 128.2 1.0
C C:SER718 4.9 133.8 1.0
CD C:LYS719 5.0 148.3 1.0

Magnesium binding site 6 out of 6 in 7qtv

Go back to Magnesium Binding Sites List in 7qtv
Magnesium binding site 6 out of 6 in the Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Beryllium Fluoride Form of the Na+,K+-Atpase (E2-Befx) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1105

b:163.3
occ:1.00
 O C:THR371 1.7 177.8 1.0
OD1 C:ASP710 1.7 170.5 1.0
OD2 C:ASP369 1.8 155.7 1.0
CG C:ASP710 2.6 178.5 1.0
CG2 C:THR371 2.6 173.6 1.0
C C:THR371 2.6 177.4 1.0
CG C:ASP369 2.8 157.4 1.0
F1 C:BEF1101 3.1 155.8 1.0
CB C:ASP369 3.2 150.0 1.0
CA C:THR371 3.3 169.2 1.0
OD2 C:ASP710 3.3 182.1 1.0
N C:THR371 3.3 161.2 1.0
CB C:ASP710 3.4 174.0 1.0
CB C:THR371 3.5 172.6 1.0
BE C:BEF1101 3.5 165.0 1.0
OG1 C:THR373 3.7 151.6 1.0
OD2 C:ASP714 3.7 163.8 1.0
N C:GLY372 3.7 184.2 1.0
N C:THR373 3.8 164.1 1.0
O C:ASP369 3.8 161.2 1.0
OD1 C:ASP369 3.9 161.5 1.0
F2 C:BEF1101 3.9 173.8 1.0
C C:ASP369 4.0 159.5 1.0
N C:ASP710 4.0 165.1 1.0
CA C:GLY372 4.2 168.9 1.0
C C:LYS370 4.2 164.5 1.0
CA C:ASP369 4.2 151.2 1.0
CA C:ASP710 4.2 169.6 1.0
OG1 C:THR371 4.2 179.9 1.0
C C:GLY372 4.5 160.3 1.0
N C:LYS370 4.5 165.2 1.0
CB C:THR373 4.5 148.9 1.0
N C:GLY711 4.7 158.5 1.0
CG C:ASP714 4.7 164.9 1.0
O C:LYS370 4.7 170.2 1.0
C C:ASP710 4.7 167.9 1.0
F3 C:BEF1101 4.8 175.0 1.0
CA C:THR373 4.8 155.4 1.0
OD1 C:ASP714 4.9 166.1 1.0

Reference:

M.U.Fruergaard, I.Dach, J.L.Andersen, M.Ozol, A.Shahsavar, E.M.Quistgaard, H.Poulsen, N.U.Fedosova, P.Nissen. The Na + ,K + -Atpase in Complex with Beryllium Fluoride Mimics An Atpase Phosphorylated State. J.Biol.Chem. V. 298 02317 2022.
ISSN: ESSN 1083-351X
PubMed: 35926706
DOI: 10.1016/J.JBC.2022.102317
Page generated: Thu Apr 6 21:01:38 2023

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