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Magnesium 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:

Sodium (Na) 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 MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry) (pdb code 7d93). 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 MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry), PDB code: 7d93:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7d93

Go back to Magnesium Binding Sites List in 7d93
Magnesium binding site 1 out of 4 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 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 (P2(1)2(1)2(1) Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:136.5
occ:1.00
 O A:THR371 2.1 139.4 1.0
OD1 A:ASP710 2.1 123.2 1.0
O A:HOH1203 2.2 95.9 1.0
O A:HOH1202 2.2 181.3 1.0
OP3 A:PHD369 2.4 122.8 1.0
OD2 A:PHD369 2.6 122.8 1.0
CG A:ASP710 2.9 113.7 1.0
OD2 A:ASP710 3.0 106.7 1.0
C A:THR371 3.2 133.4 1.0
CG A:PHD369 3.6 117.4 1.0
P A:PHD369 3.6 123.8 1.0
N A:GLY711 3.6 115.1 1.0
OD1 A:PHD369 3.8 113.7 1.0
CB A:THR371 3.9 133.7 1.0
CG2 A:THR371 4.0 131.7 1.0
OD2 A:ASP714 4.1 123.1 1.0
CA A:THR371 4.1 125.4 1.0
O A:SER209 4.1 130.4 1.0
CA A:GLY711 4.1 111.7 1.0
N A:GLY372 4.2 139.4 1.0
OP1 A:PHD369 4.2 110.0 1.0
CB A:ASP710 4.3 110.6 1.0
CA A:GLY372 4.3 142.3 1.0
N A:THR371 4.5 117.3 1.0
C A:ASP710 4.5 107.8 1.0
N A:ASP710 4.5 111.4 1.0
OD1 A:ASN713 4.6 129.4 1.0
CA A:ASP710 4.7 105.9 1.0
OG1 A:THR373 4.7 96.3 1.0
OP2 A:PHD369 4.8 124.5 1.0
CB A:PHD369 4.9 107.2 1.0
C A:GLY372 4.9 124.2 1.0
N A:THR373 4.9 110.3 1.0
ND2 A:ASN713 5.0 150.4 1.0

Magnesium binding site 2 out of 4 in 7d93

Go back to Magnesium Binding Sites List in 7d93
Magnesium binding site 2 out of 4 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 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 (P2(1)2(1)2(1) Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:136.8
occ:1.00
 OD2 A:ASP804 2.1 123.5 1.0
O A:HOH1201 2.2 143.4 1.0
OE2 A:GLU779 2.2 98.9 1.0
OD1 A:ASP804 2.2 117.8 1.0
OE2 A:GLU327 2.3 112.7 1.0
CG A:ASP804 2.3 107.1 1.0
O A:HOH1205 2.4 96.1 1.0
O A:HOH1204 2.5 110.3 1.0
CD A:GLU779 3.0 101.9 1.0
OE1 A:GLU779 3.2 108.6 1.0
CD A:GLU327 3.3 115.7 1.0
OE1 A:GLU327 3.7 110.5 1.0
CB A:ASP804 3.7 85.0 1.0
ND2 A:ASN776 4.2 84.1 1.0
CG A:GLU779 4.3 89.8 1.0
O A:HOH1206 4.4 96.4 1.0
O A:VAL325 4.5 92.7 1.0
CG A:ASN776 4.5 84.2 1.0
OD1 A:ASN776 4.6 90.8 1.0
CG A:GLU327 4.6 125.1 1.0
O A:ALA323 4.7 123.8 1.0
CB A:GLU779 4.8 85.2 1.0
OG A:SER775 4.8 83.1 1.0
N A:GLU327 4.8 107.0 1.0
CG2 A:ILE800 4.8 84.0 1.0
CA A:ASP804 4.9 86.1 1.0
CA A:PRO326 4.9 98.0 1.0

Magnesium binding site 3 out of 4 in 7d93

Go back to Magnesium Binding Sites List in 7d93
Magnesium binding site 3 out of 4 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 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 (P2(1)2(1)2(1) Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:114.6
occ:1.00
 O C:THR371 2.1 102.9 1.0
OD1 C:ASP710 2.1 112.2 1.0
O C:HOH1203 2.1 122.0 1.0
OP3 C:PHD369 2.2 122.9 1.0
O C:HOH1201 2.3 124.2 1.0
OD2 C:PHD369 2.3 95.6 1.0
CG C:ASP710 2.9 110.6 1.0
OD2 C:ASP710 3.1 114.4 1.0
CG C:PHD369 3.3 94.4 1.0
C C:THR371 3.3 100.0 1.0
P C:PHD369 3.4 108.7 1.0
N C:GLY711 3.5 97.3 1.0
OD1 C:PHD369 3.6 98.5 1.0
OD2 C:ASP714 3.8 129.0 1.0
OP1 C:PHD369 4.0 103.9 1.0
CA C:GLY711 4.0 100.0 1.0
CB C:THR371 4.1 131.2 1.0
CA C:THR371 4.1 103.0 1.0
O C:SER209 4.2 99.4 1.0
N C:GLY372 4.3 106.9 1.0
CB C:ASP710 4.3 96.8 1.0
CG2 C:THR371 4.3 137.4 1.0
OD1 C:ASN713 4.4 96.5 1.0
CA C:GLY372 4.4 122.2 1.0
N C:THR371 4.4 97.5 1.0
OG1 C:THR373 4.5 110.5 1.0
C C:ASP710 4.5 95.2 1.0
N C:ASP710 4.5 93.4 1.0
CB C:PHD369 4.6 91.5 1.0
OP2 C:PHD369 4.6 96.3 1.0
CA C:ASP710 4.6 93.4 1.0
ND2 C:ASN713 4.8 118.0 1.0
CG C:ASP714 4.9 126.7 1.0
N C:THR373 4.9 122.4 1.0
C C:GLY372 4.9 130.5 1.0

Magnesium binding site 4 out of 4 in 7d93

Go back to Magnesium Binding Sites List in 7d93
Magnesium binding site 4 out of 4 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 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 MG2+ and Anthroylouabain (P2(1)2(1)2(1) Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:112.3
occ:1.00
 OD2 C:ASP804 2.1 113.8 1.0
OD1 C:ASP804 2.2 103.0 1.0
OE2 C:GLU779 2.2 97.0 1.0
O C:HOH1204 2.3 87.9 1.0
O C:HOH1206 2.3 128.1 1.0
OE2 C:GLU327 2.3 110.2 1.0
CG C:ASP804 2.3 109.4 1.0
O C:HOH1202 2.5 79.0 1.0
CD C:GLU779 3.0 101.3 1.0
OE1 C:GLU779 3.3 102.2 1.0
CD C:GLU327 3.5 100.2 1.0
CB C:ASP804 3.7 112.0 1.0
OE1 C:GLU327 4.0 89.6 1.0
O C:VAL325 4.0 86.2 1.0
CG C:GLU779 4.3 99.5 1.0
ND2 C:ASN776 4.3 79.0 1.0
O C:HOH1205 4.6 83.3 1.0
CG2 C:ILE800 4.7 78.3 1.0
CG C:GLU327 4.7 102.0 1.0
CG C:ASN776 4.7 79.0 1.0
CA C:PRO326 4.7 85.5 1.0
N C:GLU327 4.7 112.6 1.0
OD1 C:ASN776 4.7 79.0 1.0
OG C:SER775 4.8 74.6 1.0
CB C:GLU779 4.8 102.6 1.0
CA C:ASP804 4.9 91.9 1.0
O C:ALA323 4.9 89.0 1.0
C C:VAL325 5.0 84.2 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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