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

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

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

Protein crystallography data

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin, PDB code: 7ddk 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) 16.00 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.357, 118.176, 494.668, 90, 90, 90
R / Rfree (%) 22 / 26.9

Other elements in 7ddk:

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

Magnesium binding site 1 out of 4 in 7ddk

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


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

b:84.5
occ:1.00
 O A:HOH1201 2.0 101.1 1.0
O A:THR371 2.0 64.2 1.0
OD2 A:PHD369 2.0 80.0 1.0
O A:HOH1202 2.1 67.0 1.0
OD1 A:ASP710 2.1 82.6 1.0
OP3 A:PHD369 2.3 68.4 1.0
OD2 A:ASP710 2.6 78.6 1.0
CG A:ASP710 2.6 76.5 1.0
CG A:PHD369 3.2 72.8 1.0
C A:THR371 3.2 50.3 1.0
N A:GLY711 3.5 73.7 1.0
P A:PHD369 3.5 55.7 1.0
OD1 A:PHD369 3.6 76.9 1.0
OD2 A:ASP714 3.7 59.5 1.0
CB A:ASP710 4.0 61.5 1.0
CA A:GLY372 4.0 67.8 1.0
N A:GLY372 4.0 61.0 1.0
CA A:GLY711 4.1 68.2 1.0
N A:ASP710 4.2 58.2 1.0
OP1 A:PHD369 4.3 54.4 1.0
CA A:THR371 4.3 65.7 1.0
C A:ASP710 4.4 61.9 1.0
CB A:THR371 4.4 80.7 1.0
CA A:ASP710 4.4 55.5 1.0
CB A:PHD369 4.4 64.5 1.0
N A:THR373 4.5 68.5 1.0
CG2 A:THR371 4.6 89.5 1.0
O A:SER209 4.6 41.0 1.0
OP2 A:PHD369 4.7 70.7 1.0
N A:THR371 4.7 85.8 1.0
OG1 A:THR373 4.7 60.1 1.0
C A:GLY372 4.7 70.5 1.0
OD1 A:ASN713 4.7 62.9 1.0
CG A:ASP714 4.9 60.5 1.0

Magnesium binding site 2 out of 4 in 7ddk

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


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

b:78.4
occ:1.00
 OD2 A:ASP804 2.1 74.6 1.0
O A:HOH1204 2.1 66.8 1.0
OD1 A:ASP804 2.1 78.0 1.0
O A:HOH1205 2.2 84.1 1.0
OE2 A:GLU779 2.3 56.9 1.0
CG A:ASP804 2.3 74.3 1.0
OE2 A:GLU327 2.4 92.6 1.0
O A:HOH1203 2.4 108.8 1.0
CD A:GLU779 3.0 54.4 1.0
OE1 A:GLU779 3.2 59.3 1.0
CD A:GLU327 3.5 80.7 1.0
CB A:ASP804 3.6 68.3 1.0
OE1 A:GLU327 3.9 81.6 1.0
ND2 A:ASN776 4.3 79.6 1.0
CG A:GLU779 4.3 46.0 1.0
CG2 A:ILE800 4.5 50.5 1.0
OD1 A:ASN776 4.5 108.4 1.0
O A:VAL325 4.6 69.1 1.0
CG A:ASN776 4.6 89.9 1.0
O A:ALA323 4.6 85.3 1.0
CA A:PRO326 4.7 62.8 1.0
CG A:GLU327 4.8 69.2 1.0
CA A:ASP804 4.8 64.3 1.0
N A:GLU327 4.8 70.8 1.0
CB A:GLU779 4.8 47.6 1.0

Magnesium binding site 3 out of 4 in 7ddk

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


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

b:61.9
occ:1.00
 O C:HOH1201 2.0 61.1 1.0
O C:THR371 2.1 67.1 1.0
OD1 C:ASP710 2.2 76.5 1.0
O C:HOH1205 2.2 54.9 1.0
OD2 C:PHD369 2.4 83.5 1.0
OP3 C:PHD369 2.5 60.0 1.0
OD2 C:ASP710 2.6 80.5 1.0
CG C:ASP710 2.6 76.8 1.0
N C:GLY711 3.2 60.8 1.0
C C:THR371 3.3 67.0 1.0
CG C:PHD369 3.5 77.0 1.0
CA C:GLY711 3.8 49.7 1.0
P C:PHD369 3.8 65.5 1.0
OD2 C:ASP714 3.9 58.5 1.0
CB C:ASP710 4.0 67.8 1.0
OD1 C:PHD369 4.0 75.2 1.0
CA C:GLY372 4.0 80.4 1.0
N C:GLY372 4.1 66.3 1.0
C C:ASP710 4.1 65.6 1.0
N C:ASP710 4.2 47.6 1.0
CA C:ASP710 4.3 59.5 1.0
CA C:THR371 4.4 78.0 1.0
O C:SER209 4.4 53.4 1.0
CB C:THR371 4.4 88.3 1.0
OD1 C:ASN713 4.5 82.4 1.0
OP1 C:PHD369 4.5 40.4 1.0
N C:THR373 4.6 77.3 1.0
OG1 C:THR373 4.7 79.0 1.0
CG2 C:THR371 4.7 108.8 1.0
C C:GLY372 4.7 85.3 1.0
CB C:PHD369 4.8 65.9 1.0
N C:THR371 4.8 66.2 1.0
OP2 C:PHD369 4.9 80.4 1.0
CG C:ASP714 5.0 56.1 1.0

Magnesium binding site 4 out of 4 in 7ddk

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


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

b:26.9
occ:1.00
 O C:HOH1204 2.1 35.1 1.0
OD2 C:ASP804 2.1 52.8 1.0
OD1 C:ASP804 2.2 57.1 1.0
OE2 C:GLU779 2.2 43.6 1.0
CG C:ASP804 2.3 62.6 1.0
OE2 C:GLU327 2.4 104.2 1.0
O C:HOH1203 2.4 34.7 1.0
O C:HOH1202 2.6 27.5 1.0
CD C:GLU779 3.0 35.2 1.0
OE1 C:GLU779 3.2 39.4 1.0
CD C:GLU327 3.5 89.4 1.0
CB C:ASP804 3.7 77.2 1.0
OE1 C:GLU327 4.0 86.5 1.0
ND2 C:ASN776 4.3 81.0 1.0
CG C:GLU779 4.3 25.0 1.0
CG2 C:ILE800 4.4 38.6 1.0
CG C:ASN776 4.6 78.4 1.0
O C:VAL325 4.6 42.6 1.0
OD1 C:ASN776 4.6 103.6 1.0
O C:ALA323 4.6 100.2 1.0
CG C:GLU327 4.7 72.3 1.0
CA C:PRO326 4.8 37.7 1.0
CB C:GLU779 4.8 35.8 1.0
N C:GLU327 4.8 51.1 1.0
CA C:ASP804 4.8 71.0 1.0
OG C:SER775 5.0 34.9 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 15:47:48 2024

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