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Magnesium in PDB 7d92: Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry)

Enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry), PDB code: 7d92 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) 14.94 / 3.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.234, 84.234, 646.262, 90, 90, 90
R / Rfree (%) 20.9 / 25.7

Other elements in 7d92:

The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry) (pdb code 7d92). 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+ and Anthroylouabain (P4(3)2(1)2 Symmetry), PDB code: 7d92:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7d92

Go back to Magnesium Binding Sites List in 7d92
Magnesium binding site 1 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:121.8
occ:1.00
OD2 A:BFD369 2.0 210.2 1.0
O A:THR371 2.0 214.0 1.0
O A:HOH1201 2.0 140.2 1.0
OD1 A:ASP710 2.1 206.1 1.0
O A:HOH1202 2.2 149.1 1.0
F2 A:BFD369 2.3 161.5 1.0
CG A:ASP710 2.7 191.5 1.0
OD2 A:ASP710 2.9 195.2 1.0
CG A:BFD369 3.2 179.4 1.0
C A:THR371 3.3 185.1 1.0
N A:GLY711 3.6 135.6 1.0
BE A:BFD369 3.6 168.9 1.0
OD2 A:ASP714 3.7 139.9 1.0
OD1 A:BFD369 3.9 171.7 1.0
CB A:ASP710 4.1 164.8 1.0
N A:ASP710 4.1 129.5 1.0
N A:GLY372 4.2 150.7 1.0
CA A:GLY372 4.2 121.7 1.0
OG1 A:THR373 4.2 108.2 1.0
CA A:THR371 4.2 170.0 1.0
F3 A:BFD369 4.3 162.2 1.0
CB A:BFD369 4.3 141.9 1.0
CA A:GLY711 4.3 131.9 1.0
OD1 A:ASN713 4.4 177.6 1.0
CB A:THR371 4.4 179.6 1.0
C A:ASP710 4.4 139.4 1.0
CA A:ASP710 4.4 145.4 1.0
N A:THR373 4.5 103.5 1.0
N A:THR371 4.5 158.2 1.0
O A:SER209 4.6 122.4 1.0
CG2 A:THR371 4.8 178.9 1.0
F1 A:BFD369 4.8 165.0 1.0
C A:GLY372 4.8 104.5 1.0
ND2 A:ASN713 4.8 177.1 1.0
CG A:ASP714 4.9 136.1 1.0

Magnesium binding site 2 out of 3 in 7d92

Go back to Magnesium Binding Sites List in 7d92
Magnesium binding site 2 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:102.5
occ:1.00
OD2 A:ASP740 2.1 186.2 1.0
O A:HOH1204 2.1 103.3 1.0
CG A:ASP740 3.0 172.2 1.0
O A:ALA721 3.1 161.2 1.0
O A:LYS719 3.2 144.9 1.0
OD1 A:ASP740 3.3 174.0 1.0
O A:SER718 3.9 124.4 1.0
C A:LYS719 4.1 141.8 1.0
O A:ASP722 4.1 166.8 1.0
C A:ALA721 4.3 156.8 1.0
C A:ASP722 4.3 160.5 1.0
CB A:ASP740 4.4 150.8 1.0
O A:GLY272 4.4 146.0 1.0
CA A:LYS719 4.4 139.9 1.0
N A:ILE723 4.6 145.2 1.0
CA A:ILE723 4.6 132.0 1.0
N A:GLY724 4.7 118.6 1.0
O A:ALA738 4.8 119.8 1.0
C A:SER718 4.9 131.3 1.0
CA A:GLY272 4.9 147.6 1.0
C A:ILE723 5.0 121.3 1.0

Magnesium binding site 3 out of 3 in 7d92

Go back to Magnesium Binding Sites List in 7d92
Magnesium binding site 3 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:105.0
occ:1.00
OD2 A:ASP804 2.1 189.0 1.0
O A:HOH1203 2.1 114.9 1.0
OE2 A:GLU779 2.2 98.3 1.0
CG A:ASP804 2.2 172.0 1.0
OD1 A:ASP804 2.2 178.7 1.0
OE2 A:GLU327 2.3 136.4 1.0
O A:HOH1205 2.3 116.2 1.0
O A:HOH1207 2.5 149.1 1.0
CD A:GLU779 3.2 97.7 1.0
CD A:GLU327 3.4 133.2 1.0
OE1 A:GLU779 3.5 95.8 1.0
CB A:ASP804 3.5 135.1 1.0
OE1 A:GLU327 3.8 139.2 1.0
O A:VAL325 4.3 122.0 1.0
CG2 A:ILE800 4.4 101.6 1.0
ND2 A:ASN776 4.4 107.5 1.0
CG A:GLU779 4.5 97.3 1.0
OD1 A:ASN776 4.6 107.1 1.0
O A:HOH1206 4.6 162.4 1.0
CG A:ASN776 4.6 106.4 1.0
O A:ALA323 4.7 116.4 1.0
CG A:GLU327 4.7 127.2 1.0
CA A:PRO326 4.7 123.2 1.0
CA A:ASP804 4.7 111.5 1.0
N A:GLU327 4.8 118.5 1.0
CB A:GLU779 5.0 95.8 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 15:41:53 2024

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