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 Mar 3 15:02:13 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy