Atomistry » Magnesium » PDB 7d86-7dhw » 7ddh
Atomistry »
  Magnesium »
    PDB 7d86-7dhw »
      7ddh »

Magnesium in PDB 7ddh: Crystal Structures of Na+,K+-Atpase in Complex with Digoxin

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

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

Protein crystallography data

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin, PDB code: 7ddh 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 / 3.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.973, 118.493, 495.137, 90, 90, 90
R / Rfree (%) 24.1 / 27.2

Other elements in 7ddh:

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

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structures of Na+,K+-Atpase in Complex with Digoxin (pdb code 7ddh). 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 Digoxin, PDB code: 7ddh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7ddh

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


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

b:88.0
occ:1.00
O A:HOH1201 2.0 77.8 1.0
OD2 A:PHD369 2.0 101.1 1.0
O A:THR371 2.1 107.8 1.0
OD1 A:ASP710 2.1 112.0 1.0
OP3 A:PHD369 2.1 73.6 1.0
O A:HOH1202 2.2 87.6 1.0
OD2 A:ASP710 2.6 84.7 1.0
CG A:ASP710 2.6 96.7 1.0
CG A:PHD369 3.1 92.0 1.0
C A:THR371 3.3 87.3 1.0
P A:PHD369 3.4 80.2 1.0
N A:GLY711 3.5 83.7 1.0
OD1 A:PHD369 3.6 97.8 1.0
OD2 A:ASP714 3.9 76.2 1.0
CB A:ASP710 4.0 76.1 1.0
CA A:GLY372 4.0 82.4 1.0
N A:GLY372 4.1 80.9 1.0
N A:ASP710 4.2 76.1 1.0
CA A:GLY711 4.2 85.5 1.0
OP1 A:PHD369 4.2 73.6 1.0
CA A:THR371 4.3 85.2 1.0
CB A:PHD369 4.4 73.6 1.0
C A:ASP710 4.4 76.1 1.0
CA A:ASP710 4.4 76.1 1.0
OP2 A:PHD369 4.4 92.5 1.0
CB A:THR371 4.5 103.7 1.0
OG1 A:THR373 4.5 74.6 1.0
N A:THR373 4.6 74.6 1.0
OD1 A:ASN713 4.6 75.2 1.0
C A:GLY372 4.7 85.4 1.0
N A:THR371 4.7 89.8 1.0
O A:SER209 4.7 93.5 1.0
CG2 A:THR371 4.9 115.4 1.0

Magnesium binding site 2 out of 4 in 7ddh

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


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

b:67.2
occ:1.00
O A:HOH1203 2.0 75.5 1.0
OD2 A:ASP804 2.0 93.0 1.0
OD1 A:ASP804 2.2 74.3 1.0
OE2 A:GLU779 2.2 70.6 1.0
CG A:ASP804 2.3 98.0 1.0
OE2 A:GLU327 2.3 107.7 1.0
O A:HOH1204 2.4 75.2 1.0
O A:HOH1205 2.4 68.8 1.0
CD A:GLU779 3.1 83.7 1.0
OE1 A:GLU779 3.4 82.5 1.0
CD A:GLU327 3.4 86.7 1.0
CB A:ASP804 3.6 108.1 1.0
OE1 A:GLU327 3.9 83.6 1.0
ND2 A:ASN776 4.1 67.6 1.0
OD1 A:ASN776 4.4 108.1 1.0
CG A:GLU779 4.4 77.9 1.0
CG A:ASN776 4.4 79.0 1.0
O A:VAL325 4.6 88.3 1.0
O A:ALA323 4.6 89.2 1.0
CG2 A:ILE800 4.6 74.0 1.0
CG A:GLU327 4.7 72.0 1.0
CA A:ASP804 4.8 88.4 1.0
N A:GLU327 4.8 91.5 1.0
CB A:GLU779 4.8 85.2 1.0
CA A:PRO326 4.9 76.4 1.0
OG A:SER775 4.9 65.7 1.0

Magnesium binding site 3 out of 4 in 7ddh

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


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

b:87.4
occ:1.00
O C:HOH1205 2.0 86.0 1.0
O C:THR371 2.1 92.5 1.0
OD1 C:ASP710 2.2 98.3 1.0
OD2 C:PHD369 2.2 118.2 1.0
O C:HOH1201 2.3 86.3 1.0
OP3 C:PHD369 2.3 86.4 1.0
OD2 C:ASP710 2.5 89.0 1.0
CG C:ASP710 2.6 97.1 1.0
C C:THR371 3.3 92.5 1.0
CG C:PHD369 3.4 104.7 1.0
N C:GLY711 3.4 83.4 1.0
P C:PHD369 3.6 92.1 1.0
OD1 C:PHD369 3.9 97.5 1.0
OD2 C:ASP714 3.9 113.7 1.0
CB C:ASP710 3.9 96.4 1.0
CA C:GLY372 4.0 114.2 1.0
CA C:GLY711 4.0 83.4 1.0
N C:GLY372 4.1 101.7 1.0
N C:ASP710 4.1 83.3 1.0
C C:ASP710 4.3 83.3 1.0
CA C:ASP710 4.3 83.3 1.0
CA C:THR371 4.3 97.1 1.0
OG1 C:THR373 4.4 82.7 1.0
OP1 C:PHD369 4.4 86.4 1.0
CB C:THR371 4.5 122.2 1.0
N C:THR373 4.5 87.2 1.0
OD1 C:ASN713 4.6 134.1 1.0
C C:GLY372 4.6 104.4 1.0
CB C:PHD369 4.6 89.1 1.0
O C:SER209 4.6 95.3 1.0
OP2 C:PHD369 4.7 125.8 1.0
N C:THR371 4.7 92.5 1.0
CG2 C:THR371 4.9 134.8 1.0

Magnesium binding site 4 out of 4 in 7ddh

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


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

b:55.6
occ:1.00
O C:HOH1203 2.1 56.5 1.0
OD2 C:ASP804 2.1 78.1 1.0
OD1 C:ASP804 2.2 86.0 1.0
OE2 C:GLU779 2.3 92.2 1.0
OE2 C:GLU327 2.3 114.9 1.0
O C:HOH1202 2.4 92.0 1.0
CG C:ASP804 2.4 82.2 1.0
O C:HOH1204 2.5 58.0 1.0
CD C:GLU779 3.1 73.9 1.0
CD C:GLU327 3.4 116.4 1.0
OE1 C:GLU779 3.4 85.4 1.0
CB C:ASP804 3.8 81.6 1.0
OE1 C:GLU327 3.8 101.7 1.0
ND2 C:ASN776 4.2 60.6 1.0
CG2 C:ILE800 4.4 63.6 1.0
CG C:GLU779 4.5 59.5 1.0
CG C:ASN776 4.6 83.8 1.0
OD1 C:ASN776 4.6 95.0 1.0
CG C:GLU327 4.6 121.3 1.0
O C:VAL325 4.7 86.2 1.0
N C:GLU327 4.8 101.7 1.0
O C:ALA323 4.8 114.2 1.0
CB C:GLU779 4.9 59.5 1.0
CA C:PRO326 4.9 65.8 1.0
CA C:ASP804 4.9 77.2 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 15:47:37 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy