Magnesium in PDB 7d91: Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)

Enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)

All present enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 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+ (P4(3)2(1)2 Symmetry), PDB code: 7d91 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) 14.95 / 3.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.325, 84.325, 646.36, 90, 90, 90
R / Rfree (%) 21.5 / 26

Other elements in 7d91:

The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry) also contains other interesting chemical elements:

Fluorine (F) 3 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 MG2+ (P4(3)2(1)2 Symmetry) (pdb code 7d91). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry), PDB code: 7d91:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7d91

Go back to Magnesium Binding Sites List in 7d91
Magnesium binding site 1 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)


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 MG2+ (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:55.0
occ:1.00
 O A:HOH1201 1.9 68.5 1.0
O A:THR371 2.1 87.1 1.0
OD1 A:ASP710 2.1 70.8 1.0
OD2 A:BFD369 2.1 56.9 1.0
F2 A:BFD369 2.2 87.9 1.0
O A:HOH1204 2.3 111.1 1.0
CG A:ASP710 2.9 71.6 1.0
OD2 A:ASP710 3.2 71.2 1.0
CG A:BFD369 3.2 46.9 1.0
C A:THR371 3.3 65.8 1.0
BE A:BFD369 3.4 76.3 1.0
N A:GLY711 3.7 58.2 1.0
OD2 A:ASP714 3.7 71.9 1.0
OD1 A:BFD369 3.8 48.3 1.0
F3 A:BFD369 4.0 71.2 1.0
N A:GLY372 4.2 56.2 1.0
CA A:GLY372 4.2 57.1 1.0
CA A:THR371 4.2 56.8 1.0
CB A:ASP710 4.3 81.1 1.0
N A:ASP710 4.3 66.5 1.0
OD1 A:ASN713 4.4 57.1 1.0
CB A:THR371 4.4 63.4 1.0
CA A:GLY711 4.4 50.2 1.0
CB A:BFD369 4.4 46.8 1.0
N A:THR371 4.5 57.9 1.0
C A:ASP710 4.6 64.2 1.0
OG1 A:THR373 4.6 71.6 1.0
CA A:ASP710 4.6 74.7 1.0
F1 A:BFD369 4.6 67.1 1.0
N A:THR373 4.6 70.2 1.0
O A:SER209 4.7 67.5 1.0
CG2 A:THR371 4.7 53.6 1.0
CG A:ASP714 4.8 55.7 1.0
C A:GLY372 4.8 62.6 1.0
ND2 A:ASN713 4.9 81.1 1.0

Magnesium binding site 2 out of 3 in 7d91

Go back to Magnesium Binding Sites List in 7d91
Magnesium binding site 2 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)


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 MG2+ (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:38.8
occ:1.00
 O A:HOH1203 2.0 42.6 1.0
OD2 A:ASP740 2.1 54.8 1.0
CG A:ASP740 3.1 56.9 1.0
O A:LYS719 3.1 46.0 1.0
O A:ALA721 3.1 42.0 1.0
OD1 A:ASP740 3.4 55.6 1.0
O A:SER718 3.9 90.5 1.0
C A:LYS719 4.1 46.1 1.0
O A:ASP722 4.1 80.0 1.0
C A:ASP722 4.3 73.7 1.0
C A:ALA721 4.3 42.8 1.0
CB A:ASP740 4.4 62.4 1.0
O A:GLY272 4.4 91.1 1.0
CA A:LYS719 4.5 54.7 1.0
N A:ILE723 4.5 59.4 1.0
CA A:ILE723 4.5 46.0 1.0
N A:GLY724 4.7 49.8 1.0
O A:ALA738 4.8 63.8 1.0
CA A:GLY272 4.9 76.9 1.0
C A:SER718 4.9 74.2 1.0
C A:ILE723 5.0 45.0 1.0

Magnesium binding site 3 out of 3 in 7d91

Go back to Magnesium Binding Sites List in 7d91
Magnesium binding site 3 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)


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 MG2+ (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:71.5
occ:1.00
 OD2 A:ASP804 2.2 89.1 1.0
OE2 A:GLU779 2.3 111.1 1.0
OE2 A:GLU327 2.4 94.4 1.0
O A:HOH1202 2.4 74.8 1.0
OD1 A:ASN776 2.4 62.0 1.0
CG A:ASP804 3.1 69.3 1.0
CD A:GLU779 3.2 92.3 1.0
OE1 A:GLU779 3.4 100.8 1.0
CD A:GLU327 3.6 68.7 1.0
CG A:ASN776 3.7 61.3 1.0
OD1 A:ASP804 3.7 61.6 1.0
CB A:ASP804 4.1 60.7 1.0
O A:ALA323 4.1 50.3 1.0
OE1 A:GLU327 4.1 61.8 1.0
O A:VAL325 4.3 68.5 1.0
ND2 A:ASN776 4.4 86.2 1.0
CG A:GLU779 4.5 61.9 1.0
CG A:GLU327 4.7 44.4 1.0
CB A:ASN776 4.7 37.3 1.0
CA A:PRO326 4.8 58.2 1.0
CA A:ASN776 4.8 37.4 1.0
N A:GLU327 4.9 43.7 1.0
CG2 A:ILE800 4.9 68.8 1.0
CB A:GLU779 5.0 43.7 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: Wed Mar 3 15:02:04 2021

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