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

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

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

Protein crystallography data

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain, PDB code: 7ddj 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 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 115.621, 117.81, 493.203, 90, 90, 90
R / Rfree (%) 27.1 / 30.8

Other elements in 7ddj:

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

Magnesium binding site 1 out of 4 in 7ddj

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


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

b:44.9
occ:1.00
O A:THR371 2.1 43.4 1.0
OD1 A:ASP710 2.1 48.1 1.0
O A:HOH1202 2.1 71.6 1.0
O A:HOH1204 2.2 38.4 1.0
OP3 A:PHD369 2.3 44.0 1.0
OD2 A:PHD369 2.4 40.7 1.0
CG A:ASP710 2.9 46.0 1.0
OD2 A:ASP710 3.0 46.0 1.0
C A:THR371 3.2 43.4 1.0
CG A:PHD369 3.4 42.9 1.0
P A:PHD369 3.5 37.5 1.0
N A:GLY711 3.6 44.0 1.0
OD1 A:PHD369 3.7 37.5 1.0
OD2 A:ASP714 4.0 35.4 1.0
CB A:THR371 4.0 65.6 1.0
CA A:THR371 4.1 44.4 1.0
OP1 A:PHD369 4.1 37.5 1.0
CA A:GLY711 4.1 39.3 1.0
N A:GLY372 4.2 43.3 1.0
O A:SER209 4.2 62.5 1.0
CG2 A:THR371 4.2 72.0 1.0
CB A:ASP710 4.2 36.1 1.0
CA A:GLY372 4.4 52.0 1.0
N A:ASP710 4.5 36.1 1.0
N A:THR371 4.5 52.3 1.0
C A:ASP710 4.5 55.7 1.0
OD1 A:ASN713 4.5 62.1 1.0
OG1 A:THR373 4.6 37.1 1.0
CA A:ASP710 4.6 36.1 1.0
OP2 A:PHD369 4.7 43.0 1.0
CB A:PHD369 4.7 48.7 1.0
N A:THR373 4.9 64.4 1.0
ND2 A:ASN713 4.9 58.5 1.0
C A:GLY372 4.9 72.8 1.0

Magnesium binding site 2 out of 4 in 7ddj

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


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

b:45.0
occ:1.00
OD2 A:ASP804 2.1 34.5 1.0
O A:HOH1201 2.2 27.2 1.0
OD1 A:ASP804 2.2 23.6 1.0
OE2 A:GLU779 2.2 44.1 1.0
O A:HOH1203 2.3 41.7 1.0
OE2 A:GLU327 2.3 85.5 1.0
CG A:ASP804 2.3 34.5 1.0
O A:HOH1205 2.3 41.0 1.0
CD A:GLU779 3.1 43.2 1.0
OE1 A:GLU779 3.3 47.3 1.0
CD A:GLU327 3.4 66.2 1.0
CB A:ASP804 3.7 40.8 1.0
OE1 A:GLU327 3.9 74.9 1.0
ND2 A:ASN776 4.0 27.1 1.0
O A:HOH1206 4.2 33.8 1.0
CG A:GLU779 4.3 33.0 1.0
O A:VAL325 4.5 54.3 1.0
O A:ALA323 4.6 38.1 1.0
CG A:ASN776 4.6 27.1 1.0
CG A:GLU327 4.7 39.8 1.0
CG2 A:ILE800 4.8 22.1 1.0
CB A:GLU779 4.8 37.6 1.0
N A:GLU327 4.8 38.1 1.0
OD1 A:ASN776 4.9 27.1 1.0
CA A:ASP804 4.9 39.2 1.0
CA A:PRO326 4.9 27.6 1.0
OG A:SER775 4.9 23.9 1.0

Magnesium binding site 3 out of 4 in 7ddj

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


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

b:42.5
occ:1.00
O C:HOH1201 2.0 36.0 1.0
O C:THR371 2.1 48.0 1.0
OD1 C:ASP710 2.1 36.2 1.0
OP3 C:PHD369 2.2 46.1 1.0
O C:HOH1202 2.2 44.3 1.0
OD2 C:PHD369 2.4 50.0 1.0
CG C:ASP710 2.9 39.5 1.0
OD2 C:ASP710 3.1 37.5 1.0
C C:THR371 3.3 36.0 1.0
CG C:PHD369 3.3 50.9 1.0
P C:PHD369 3.4 54.9 1.0
N C:GLY711 3.5 52.9 1.0
OD1 C:PHD369 3.6 61.2 1.0
OD2 C:ASP714 3.9 44.9 1.0
OP1 C:PHD369 4.0 61.6 1.0
CB C:THR371 4.0 35.4 1.0
CA C:GLY711 4.1 44.3 1.0
CA C:THR371 4.1 34.4 1.0
O C:SER209 4.2 72.4 1.0
CG2 C:THR371 4.3 34.3 1.0
CB C:ASP710 4.3 32.5 1.0
N C:GLY372 4.3 32.8 1.0
OD1 C:ASN713 4.3 75.9 1.0
N C:THR371 4.4 43.6 1.0
N C:ASP710 4.5 29.1 1.0
C C:ASP710 4.5 40.5 1.0
CA C:GLY372 4.5 37.9 1.0
OG1 C:THR373 4.5 54.8 1.0
OP2 C:PHD369 4.6 75.2 1.0
CB C:PHD369 4.6 44.5 1.0
CA C:ASP710 4.7 29.1 1.0
ND2 C:ASN713 4.8 32.6 1.0
CG C:ASP714 4.9 40.2 1.0
N C:THR373 5.0 51.8 1.0

Magnesium binding site 4 out of 4 in 7ddj

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


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

b:28.0
occ:1.00
O C:HOH1203 2.1 19.7 1.0
OD2 C:ASP804 2.1 43.4 1.0
O C:HOH1206 2.2 16.7 1.0
OD1 C:ASP804 2.2 44.6 1.0
O C:HOH1204 2.2 16.9 1.0
OE2 C:GLU779 2.2 25.5 1.0
OE2 C:GLU327 2.3 56.5 1.0
CG C:ASP804 2.3 45.0 1.0
CD C:GLU779 3.1 30.6 1.0
CD C:GLU327 3.3 62.2 1.0
OE1 C:GLU779 3.4 29.1 1.0
CB C:ASP804 3.7 39.1 1.0
OE1 C:GLU327 3.7 63.0 1.0
O C:HOH1205 4.3 21.4 1.0
O C:VAL325 4.3 64.4 1.0
CG C:GLU779 4.3 31.8 1.0
ND2 C:ASN776 4.4 53.4 1.0
O C:ALA323 4.6 47.9 1.0
CG C:GLU327 4.6 62.1 1.0
CA C:PRO326 4.7 33.4 1.0
N C:GLU327 4.7 37.7 1.0
CG2 C:ILE800 4.7 34.8 1.0
CB C:GLU779 4.8 36.5 1.0
CG C:ASN776 4.9 52.1 1.0
CA C:ASP804 4.9 23.4 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 Mar 3 15:03:05 2021

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