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Magnesium 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:

Sodium (Na) 2 atoms
Rubidium (Rb) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7d94

Go back to Magnesium Binding Sites List in 7d94
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg1101

b:70.9
occ:1.00
 OD1 A:ASP710 2.1 64.3 1.0
O A:HOH1201 2.1 101.7 1.0
OP3 A:PHD369 2.1 65.7 1.0
O A:THR371 2.2 97.3 1.0
OD2 A:PHD369 2.3 64.8 1.0
O A:HOH1204 2.4 68.4 1.0
CG A:ASP710 2.9 68.0 1.0
OD2 A:ASP710 3.1 69.1 1.0
CG A:PHD369 3.3 67.8 1.0
P A:PHD369 3.3 69.4 1.0
C A:THR371 3.4 70.4 1.0
OD1 A:PHD369 3.5 83.8 1.0
N A:GLY711 3.6 84.0 1.0
OD2 A:ASP714 3.8 79.8 1.0
OP1 A:PHD369 4.0 70.8 1.0
CB A:THR371 4.1 72.0 1.0
CA A:GLY711 4.1 80.8 1.0
CA A:THR371 4.2 65.1 1.0
O A:SER209 4.2 72.8 1.0
CB A:ASP710 4.3 81.8 1.0
CG2 A:THR371 4.3 83.4 1.0
OD1 A:ASN713 4.3 91.2 1.0
N A:GLY372 4.4 75.5 1.0
N A:ASP710 4.4 52.6 1.0
OP2 A:PHD369 4.5 78.6 1.0
N A:THR371 4.5 73.5 1.0
C A:ASP710 4.5 69.8 1.0
CA A:GLY372 4.5 111.9 1.0
CB A:PHD369 4.6 60.4 1.0
OG1 A:THR373 4.6 102.8 1.0
CA A:ASP710 4.6 57.5 1.0
ND2 A:ASN713 4.7 100.8 1.0
CG A:ASP714 4.9 83.4 1.0
CG A:ASN713 5.0 75.3 1.0

Magnesium binding site 2 out of 4 in 7d94

Go back to Magnesium Binding Sites List in 7d94
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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
A:Mg1103

b:50.8
occ:1.00
 O A:HOH1202 2.0 45.3 1.0
OE1 A:GLU327 2.1 63.6 1.0
O A:ALA323 2.9 57.3 1.0
OD1 A:ASN776 3.0 125.0 1.0
O A:VAL325 3.1 63.3 1.0
OD1 A:ASP804 3.1 100.2 1.0
CD A:GLU327 3.3 63.2 1.0
OE2 A:GLU779 3.8 107.1 1.0
CG A:ASP804 3.8 77.4 1.0
RB A:RB1104 3.9 101.8 1.0
CG A:ASN776 4.0 92.7 1.0
C A:VAL325 4.0 43.2 1.0
C A:ALA323 4.0 87.2 1.0
CG A:GLU327 4.0 52.0 1.0
OD2 A:ASP804 4.2 67.0 1.0
OE2 A:GLU327 4.2 78.9 1.0
ND2 A:ASN776 4.3 92.1 1.0
O24 A:BUF1121 4.3 69.6 1.0
N A:VAL325 4.3 66.0 1.0
N A:GLU327 4.5 74.5 1.0
CA A:PRO326 4.6 54.8 1.0
N A:PRO326 4.7 36.5 1.0
CA A:ALA323 4.7 86.5 1.0
CD A:GLU779 4.8 94.0 1.0
CA A:VAL325 4.8 56.0 1.0
CB A:ASP804 4.9 66.6 1.0
O A:VAL322 4.9 72.2 1.0
N A:ASN324 5.0 80.0 1.0

Magnesium binding site 3 out of 4 in 7d94

Go back to Magnesium Binding Sites List in 7d94
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg1101

b:63.1
occ:1.00
 O C:HOH1201 2.0 63.3 1.0
O C:THR371 2.1 70.2 1.0
OD1 C:ASP710 2.1 56.0 1.0
OP3 C:PHD369 2.1 87.7 1.0
O C:HOH1203 2.2 68.5 1.0
OD2 C:PHD369 2.4 70.1 1.0
CG C:ASP710 2.9 60.1 1.0
OD2 C:ASP710 3.0 59.6 1.0
C C:THR371 3.3 65.8 1.0
CG C:PHD369 3.3 70.1 1.0
P C:PHD369 3.4 81.1 1.0
N C:GLY711 3.5 62.6 1.0
OD1 C:PHD369 3.6 62.3 1.0
OD2 C:ASP714 3.9 61.7 1.0
OP1 C:PHD369 4.0 61.1 1.0
CB C:THR371 4.0 95.2 1.0
CA C:GLY711 4.1 58.1 1.0
CA C:THR371 4.1 63.1 1.0
O C:SER209 4.2 80.3 1.0
N C:GLY372 4.3 84.4 1.0
CB C:ASP710 4.3 52.1 1.0
CG2 C:THR371 4.4 57.9 1.0
N C:THR371 4.4 72.6 1.0
OD1 C:ASN713 4.4 97.8 1.0
CA C:GLY372 4.4 73.8 1.0
OG1 C:THR373 4.5 64.6 1.0
C C:ASP710 4.5 63.2 1.0
N C:ASP710 4.5 56.9 1.0
CB C:PHD369 4.5 53.5 1.0
OP2 C:PHD369 4.5 109.1 1.0
CA C:ASP710 4.6 51.5 1.0
ND2 C:ASN713 4.9 113.4 1.0
N C:THR373 4.9 87.9 1.0
CG C:ASP714 5.0 53.3 1.0
C C:GLY372 5.0 60.3 1.0
CA C:GLY213 5.0 79.7 1.0

Magnesium binding site 4 out of 4 in 7d94

Go back to Magnesium Binding Sites List in 7d94
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg1103

b:28.3
occ:1.00
 OE2 C:GLU327 2.0 43.5 1.0
O C:HOH1202 2.2 44.2 1.0
OD2 C:ASP804 2.8 52.9 1.0
O C:ALA323 3.1 57.1 1.0
OD1 C:ASN776 3.1 98.4 1.0
CD C:GLU327 3.2 52.9 1.0
O C:VAL325 3.2 63.1 1.0
OE1 C:GLU779 3.4 112.6 1.0
CG C:ASP804 3.7 55.4 1.0
RB C:RB1104 3.7 99.7 1.0
OE1 C:GLU327 4.1 58.0 1.0
C C:VAL325 4.1 50.7 1.0
CG C:GLU327 4.1 49.8 1.0
CG C:ASN776 4.1 53.8 1.0
C C:ALA323 4.2 62.9 1.0
OD1 C:ASP804 4.2 50.7 1.0
CD C:GLU779 4.4 84.9 1.0
O24 C:BUF1121 4.5 49.2 1.0
N C:GLU327 4.5 42.1 1.0
N C:VAL325 4.5 42.6 1.0
CA C:PRO326 4.6 76.7 1.0
ND2 C:ASN776 4.6 47.4 1.0
CB C:ASP804 4.7 104.2 1.0
N C:PRO326 4.7 56.7 1.0
OE2 C:GLU779 4.9 105.6 1.0
CA C:ALA323 4.9 71.3 1.0
CG2 C:ILE800 4.9 51.8 1.0
CA C:VAL325 5.0 45.3 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 15:42:27 2024

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