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Magnesium in PDB 7ddf: Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride

Enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride

All present enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride:
7.2.2.13;

Protein crystallography data

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride, PDB code: 7ddf was solved by H.Ogawa, F.Cornelius, R.Kanai, K.Motoyama, B.Vilsen, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.99 / 4.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.481, 118.371, 495.388, 90, 90, 90
R / Rfree (%) 19.4 / 24.2

Other elements in 7ddf:

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 7ddf

Go back to Magnesium Binding Sites List in 7ddf
Magnesium binding site 1 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:96.0
occ:1.00
 OD1 A:ASP710 2.0 86.7 1.0
F2 A:BFD369 2.0 93.9 1.0
O A:THR371 2.1 91.9 1.0
O A:HOH1203 2.1 87.1 1.0
O A:HOH1205 2.1 87.4 1.0
OD2 A:BFD369 2.2 85.0 1.0
CG A:ASP710 3.0 88.0 1.0
CG A:BFD369 3.1 86.5 1.0
BE A:BFD369 3.2 92.5 1.0
C A:THR371 3.3 100.0 1.0
OD2 A:ASP710 3.3 85.6 1.0
OD1 A:BFD369 3.5 89.8 1.0
N A:GLY711 3.7 100.1 1.0
OD2 A:ASP714 3.8 102.8 1.0
F3 A:BFD369 4.1 97.8 1.0
N A:GLY372 4.2 99.8 1.0
CA A:THR371 4.2 110.1 1.0
CB A:THR371 4.3 118.3 1.0
CB A:ASP710 4.3 92.1 1.0
CA A:GLY372 4.3 100.0 1.0
F1 A:BFD369 4.3 91.1 1.0
CA A:GLY711 4.4 99.6 1.0
CB A:BFD369 4.4 87.1 1.0
N A:ASP710 4.4 89.4 1.0
N A:THR371 4.5 110.4 1.0
O A:SER209 4.5 128.2 1.0
OD1 A:ASN713 4.5 95.5 1.0
C A:ASP710 4.6 99.4 1.0
CA A:ASP710 4.7 93.8 1.0
OG1 A:THR373 4.7 105.9 1.0
N A:THR373 4.7 101.2 1.0
CG2 A:THR371 4.8 122.1 1.0
CG A:ASP714 4.9 102.5 1.0
C A:GLY372 4.9 101.1 1.0
ND2 A:ASN713 4.9 93.4 1.0

Magnesium binding site 2 out of 4 in 7ddf

Go back to Magnesium Binding Sites List in 7ddf
Magnesium binding site 2 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:113.8
occ:1.00
 O A:HOH1204 2.0 114.0 1.0
OD2 A:ASP804 2.0 111.3 1.0
OE2 A:GLU779 2.2 116.0 1.0
OD1 A:ASP804 2.2 111.4 1.0
OE2 A:GLU327 2.2 100.7 1.0
CG A:ASP804 2.3 109.6 1.0
O A:HOH1201 2.3 85.3 1.0
O A:HOH1202 2.6 83.2 1.0
CD A:GLU779 3.0 115.6 1.0
OE1 A:GLU779 3.2 117.0 1.0
CD A:GLU327 3.3 100.2 1.0
CB A:ASP804 3.7 105.7 1.0
OE1 A:GLU327 3.8 100.9 1.0
ND2 A:ASN776 4.2 88.5 1.0
CG A:GLU779 4.4 112.3 1.0
OD1 A:ASN776 4.4 90.9 1.0
CG A:ASN776 4.5 89.6 1.0
CG2 A:ILE800 4.5 103.7 1.0
CG A:GLU327 4.6 98.5 1.0
O A:VAL325 4.7 112.7 1.0
N A:GLU327 4.8 91.3 1.0
CB A:GLU779 4.8 109.4 1.0
CA A:ASP804 4.8 101.8 1.0
O A:ALA323 4.8 113.3 1.0
OG A:SER775 4.9 70.3 1.0

Magnesium binding site 3 out of 4 in 7ddf

Go back to Magnesium Binding Sites List in 7ddf
Magnesium binding site 3 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:113.2
occ:1.00
 O C:THR371 2.0 109.5 1.0
OD1 C:ASP710 2.0 106.9 1.0
F2 C:BFD369 2.1 113.3 1.0
O C:HOH1201 2.1 111.3 1.0
O C:HOH1204 2.1 105.9 1.0
OD2 C:BFD369 2.1 107.8 1.0
CG C:ASP710 3.0 107.3 1.0
CG C:BFD369 3.1 108.4 1.0
C C:THR371 3.2 113.7 1.0
OD2 C:ASP710 3.3 105.0 1.0
BE C:BFD369 3.3 113.2 1.0
OD1 C:BFD369 3.6 111.5 1.0
N C:GLY711 3.7 123.8 1.0
OD2 C:ASP714 4.0 120.4 1.0
F3 C:BFD369 4.1 115.2 1.0
CA C:THR371 4.1 122.0 1.0
CA C:GLY711 4.2 125.7 1.0
N C:GLY372 4.2 112.2 1.0
CB C:THR371 4.2 127.3 1.0
CB C:ASP710 4.3 112.2 1.0
O C:SER209 4.3 134.6 1.0
CA C:GLY372 4.4 107.0 1.0
N C:THR371 4.4 124.0 1.0
CB C:BFD369 4.4 107.2 1.0
OD1 C:ASN713 4.4 125.2 1.0
F1 C:BFD369 4.4 114.1 1.0
N C:ASP710 4.5 117.4 1.0
OG1 C:THR373 4.6 99.5 1.0
C C:ASP710 4.6 121.7 1.0
CA C:ASP710 4.7 117.3 1.0
N C:THR373 4.7 100.7 1.0
CG2 C:THR371 4.8 129.2 1.0
C C:GLY372 4.9 102.8 1.0
ND2 C:ASN713 4.9 125.1 1.0

Magnesium binding site 4 out of 4 in 7ddf

Go back to Magnesium Binding Sites List in 7ddf
Magnesium binding site 4 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

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

b:104.7
occ:1.00
 OD2 C:ASP804 2.1 100.2 1.0
OD1 C:ASP804 2.2 99.9 1.0
OE2 C:GLU779 2.2 102.8 1.0
O C:HOH1202 2.3 84.7 1.0
O C:HOH1203 2.3 163.2 1.0
OE2 C:GLU327 2.4 96.0 1.0
CG C:ASP804 2.4 96.6 1.0
O C:HOH1205 2.8 86.2 1.0
CD C:GLU779 3.0 102.7 1.0
OE1 C:GLU779 3.3 102.4 1.0
CD C:GLU327 3.5 94.3 1.0
CB C:ASP804 3.7 89.5 1.0
OE1 C:GLU327 4.0 94.3 1.0
CG C:GLU779 4.4 102.9 1.0
O C:VAL325 4.5 121.4 1.0
ND2 C:ASN776 4.6 91.5 1.0
CA C:PRO326 4.6 102.0 1.0
CG2 C:ILE800 4.6 84.9 1.0
N C:GLU327 4.6 94.1 1.0
CG C:GLU327 4.7 93.9 1.0
OD1 C:ASN776 4.7 92.7 1.0
CG C:ASN776 4.8 92.3 1.0
CB C:GLU779 4.9 102.8 1.0
CA C:ASP804 4.9 82.9 1.0
O C:ALA323 5.0 91.5 1.0

Reference:

R.Kanai, F.Cornelius, H.Ogawa, K.Motoyama, B.Vilsen, C.Toyoshima. Binding of Cardiotonic Steroids to Na + ,K + -Atpase in the E2P State. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33318128
DOI: 10.1073/PNAS.2020438118
Page generated: Wed Oct 2 15:47:27 2024

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