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Sodium in PDB 7d93: Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry)

Enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry)

All present enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry):
7.2.2.13;

Protein crystallography data

The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry), PDB code: 7d93 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 / 3.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 115.62, 117.89, 494.3, 90, 90, 90
R / Rfree (%) 23.3 / 27.4

Other elements in 7d93:

The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry) also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry) (pdb code 7d93). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry), PDB code: 7d93:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7d93

Go back to Sodium Binding Sites List in 7d93
Sodium binding site 1 out of 2 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1102

b:84.0
occ:1.00
OD2 A:ASP740 2.5 90.2 1.0
O A:LYS719 3.0 135.1 1.0
CG A:ASP740 3.3 93.5 1.0
OD1 A:ASP740 3.3 90.1 1.0
O A:GLY272 3.5 158.2 1.0
O A:ALA721 3.5 95.1 1.0
CA A:GLY272 4.0 167.0 1.0
C A:LYS719 4.1 141.4 1.0
C A:GLY272 4.2 165.3 1.0
O A:SER718 4.3 106.1 1.0
CA A:LYS719 4.6 135.4 1.0
O A:ASP722 4.6 99.8 1.0
CB A:ASP740 4.7 101.7 1.0
C A:ALA721 4.8 113.1 1.0
CD A:LYS719 4.9 113.9 1.0
C A:ASP722 5.0 86.8 1.0

Sodium binding site 2 out of 2 in 7d93

Go back to Sodium Binding Sites List in 7d93
Sodium binding site 2 out of 2 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1102

b:75.0
occ:1.00
OD2 C:ASP740 2.5 93.5 1.0
O C:LYS719 3.1 131.7 1.0
OD1 C:ASP740 3.1 92.4 1.0
CG C:ASP740 3.1 94.2 1.0
O C:ALA721 3.6 115.0 1.0
O C:GLY272 3.7 141.5 1.0
C C:LYS719 4.2 128.2 1.0
O C:SER718 4.2 100.3 1.0
CA C:GLY272 4.4 125.3 1.0
C C:GLY272 4.5 140.4 1.0
O C:ASP722 4.6 94.2 1.0
CA C:LYS719 4.6 123.1 1.0
CB C:ASP740 4.6 88.3 1.0
C C:ALA721 4.8 120.5 1.0
C C:ASP722 4.9 94.2 1.0
O C:ALA738 5.0 108.7 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: Tue Oct 8 16:32:08 2024

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