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Rubidium in PDB 7d94: Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin

Enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin

All present enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin:
7.2.2.13;

Protein crystallography data

The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin, PDB code: 7d94 was solved by R.Kanai, F.Cornelius, H.Ogawa, 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) 15.00 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 115.57, 117.31, 490.705, 90, 90, 90
R / Rfree (%) 22.4 / 26.3

Other elements in 7d94:

The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Sodium (Na) 2 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin (pdb code 7d94). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 2 binding sites of Rubidium where determined in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin, PDB code: 7d94:
Jump to Rubidium binding site number: 1; 2;

Rubidium binding site 1 out of 2 in 7d94

Go back to Rubidium Binding Sites List in 7d94
Rubidium binding site 1 out of 2 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb1104

b:101.8
occ:1.00
 OD2 A:ASP804 2.4 67.0 1.0
OG A:SER775 2.7 55.1 1.0
OD1 A:ASN776 2.9 125.0 1.0
OD1 A:ASP804 3.0 100.2 1.0
CG A:ASP804 3.0 77.4 1.0
OE2 A:GLU779 3.1 107.1 1.0
O A:THR772 3.1 94.8 1.0
MG A:MG1103 3.9 50.8 1.0
CD A:GLU779 3.9 94.0 1.0
N A:ASN776 3.9 63.9 1.0
OE1 A:GLU779 3.9 76.8 1.0
CG A:ASN776 3.9 92.7 1.0
CB A:SER775 4.0 46.3 1.0
C A:SER775 4.0 57.5 1.0
CA A:ASN776 4.2 60.9 1.0
CG2 A:THR772 4.2 94.6 1.0
C A:THR772 4.3 82.0 1.0
O A:SER775 4.4 62.2 1.0
CB A:ASN776 4.4 57.8 1.0
CB A:ASP804 4.5 66.6 1.0
CA A:SER775 4.5 53.0 1.0
OE1 A:GLU327 4.7 63.6 1.0
N A:SER775 4.9 59.9 1.0
O A:HOH1203 4.9 46.2 1.0
CA A:THR772 4.9 83.6 1.0
ND2 A:ASN776 5.0 92.1 1.0

Rubidium binding site 2 out of 2 in 7d94

Go back to Rubidium Binding Sites List in 7d94
Rubidium binding site 2 out of 2 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb1104

b:99.7
occ:1.00
 OD1 C:ASP804 2.3 50.7 1.0
OG C:SER775 2.7 33.1 1.0
OD1 C:ASN776 2.8 98.4 1.0
OD2 C:ASP804 2.9 52.9 1.0
CG C:ASP804 2.9 55.4 1.0
OE1 C:GLU779 3.0 112.6 1.0
O C:THR772 3.1 40.7 1.0
OE2 C:GLU779 3.7 105.6 1.0
N C:ASN776 3.7 67.4 1.0
CD C:GLU779 3.7 84.9 1.0
MG C:MG1103 3.7 28.3 1.0
C C:SER775 3.8 43.4 1.0
CG C:ASN776 3.8 53.8 1.0
CB C:SER775 3.9 50.2 1.0
CA C:ASN776 4.0 68.7 1.0
O C:SER775 4.2 35.1 1.0
CB C:ASN776 4.3 44.6 1.0
CA C:SER775 4.3 40.8 1.0
C C:THR772 4.3 45.7 1.0
CB C:ASP804 4.4 104.2 1.0
CG2 C:THR772 4.5 77.4 1.0
OE2 C:GLU327 4.7 43.5 1.0
N C:SER775 4.7 30.5 1.0
ND2 C:ASN776 5.0 47.4 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 15:43:22 2021

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