Magnesium in PDB 4hyt: Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site

Enzymatic activity of Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site

All present enzymatic activity of Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site:
3.6.3.9;

Protein crystallography data

The structure of Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site, PDB code: 4hyt was solved by M.Laursen, L.Yatime, P.Nissen, N.U.Fedosova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.83 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.470, 118.080, 494.660, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site (pdb code 4hyt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site, PDB code: 4hyt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4hyt

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Magnesium binding site 1 out of 6 in the Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:0.3
occ:1.00
 OP1 A:PHD369 2.0 74.8 1.0
OD2 A:PHD369 2.0 71.8 1.0
OP3 A:PHD369 2.1 74.8 1.0
O A:THR371 2.1 70.7 1.0
P A:PHD369 2.4 74.5 1.0
OD2 A:ASP710 2.4 66.2 1.0
OG1 A:THR371 2.7 68.0 1.0
CG A:ASP710 2.9 64.8 1.0
OD1 A:ASP710 2.9 64.5 1.0
CG A:PHD369 2.9 71.5 1.0
C A:THR371 3.0 71.3 1.0
OD1 A:PHD369 3.1 72.7 1.0
N A:THR371 3.2 71.5 1.0
CA A:THR371 3.4 72.3 1.0
CB A:THR371 3.5 68.1 1.0
OP2 A:PHD369 3.7 75.8 1.0
C A:LYS370 4.1 78.1 1.0
CB A:ASP710 4.2 63.9 1.0
N A:LYS370 4.2 76.8 1.0
CB A:PHD369 4.2 70.1 1.0
N A:GLY372 4.3 89.6 1.0
O A:SER209 4.7 82.6 1.0
CA A:LYS370 4.7 77.7 1.0
OG1 A:THR373 4.7 69.5 1.0
C A:PHD369 4.8 68.1 1.0
O A:LYS370 4.8 77.6 1.0
CG2 A:THR371 4.8 69.7 1.0
CA A:GLY372 4.8 88.9 1.0
N A:THR373 4.8 75.6 1.0
CA A:GLY213 4.8 77.8 1.0
OD2 A:ASP714 4.9 71.2 1.0
ND2 A:ASN713 5.0 67.5 1.0

Magnesium binding site 2 out of 6 in 4hyt

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Magnesium binding site 2 out of 6 in the Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:82.9
occ:1.00
 OD2 A:ASP740 2.1 76.5 1.0
OD1 A:ASP740 2.2 77.6 1.0
CG A:ASP740 2.5 76.7 1.0
O A:LYS719 3.4 65.5 1.0
O A:ALA721 4.0 57.5 1.0
CB A:ASP740 4.0 75.9 1.0
C A:LYS719 4.3 65.5 1.0
O A:SER718 4.3 66.2 1.0
O A:ALA738 4.4 59.1 1.0
O A:GLY272 4.4 0.8 1.0
CA A:GLY272 4.5 0.2 1.0
CA A:LYS719 4.6 65.4 1.0
N A:ASP740 4.8 59.8 1.0
CA A:ASP740 4.9 59.9 1.0
C A:GLY272 4.9 0.3 1.0
CD A:LYS719 5.0 75.3 1.0
N A:GLY724 5.0 61.8 1.0

Magnesium binding site 3 out of 6 in 4hyt

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Magnesium binding site 3 out of 6 in the Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:58.7
occ:1.00
 OE2 A:GLU779 2.0 68.2 1.0
O A:HOH1203 2.1 60.5 1.0
O A:HOH1201 2.1 56.5 1.0
O A:HOH1202 2.1 61.3 1.0
OD1 A:ASP804 2.3 80.5 1.0
OD1 A:ASN776 2.5 0.5 1.0
CG A:ASP804 2.9 82.1 1.0
OD2 A:ASP804 2.9 83.5 1.0
CD A:GLU779 3.1 67.7 1.0
CG A:ASN776 3.3 0.9 1.0
OE1 A:GLU779 3.5 67.2 1.0
ND2 A:ASN776 3.8 0.1 1.0
OG A:SER775 4.1 71.0 1.0
CG A:GLU779 4.3 67.7 1.0
CB A:ASP804 4.4 82.6 1.0
O A:ALA323 4.4 69.3 1.0
OE2 A:GLU327 4.5 85.9 1.0
CA A:ASN776 4.5 79.3 1.0
CB A:ASN776 4.5 0.0 1.0
CB A:GLU779 4.5 68.4 1.0
O A:VAL325 4.6 76.7 1.0
N A:ASN776 4.7 77.7 1.0
C A:SER775 4.9 53.5 1.0
O A:SER775 4.9 54.0 1.0

Magnesium binding site 4 out of 6 in 4hyt

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Magnesium binding site 4 out of 6 in the Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2001

b:0.7
occ:1.00
 OD2 C:ASP710 2.0 0.4 1.0
O C:THR371 2.1 0.7 1.0
OP3 C:PHD369 2.1 0.4 1.0
OD2 C:PHD369 2.2 0.6 1.0
OP1 C:PHD369 2.3 0.5 1.0
CG C:ASP710 2.5 0.9 1.0
OD1 C:ASP710 2.5 0.2 1.0
P C:PHD369 2.6 0.8 1.0
OG1 C:THR371 2.8 0.3 1.0
C C:THR371 3.1 0.6 1.0
CG C:PHD369 3.1 0.9 1.0
OD1 C:PHD369 3.4 0.9 1.0
N C:THR371 3.6 0.5 1.0
CA C:THR371 3.6 0.8 1.0
CB C:THR371 3.7 0.8 1.0
CB C:ASP710 3.9 0.1 1.0
OP2 C:PHD369 4.0 0.1 1.0
N C:GLY372 4.3 0.9 1.0
O C:SER209 4.4 0.7 1.0
C C:LYS370 4.5 0.7 1.0
CB C:PHD369 4.5 0.3 1.0
N C:LYS370 4.7 0.4 1.0
CA C:GLY372 4.7 0.3 1.0
N C:GLY711 4.7 0.7 1.0
OG1 C:THR373 4.8 0.6 1.0
OD2 C:ASP714 4.8 0.1 1.0
N C:THR373 4.9 0.1 1.0
CA C:GLY213 4.9 0.9 1.0
ND2 C:ASN713 4.9 0.0 1.0
OD1 C:ASN713 4.9 0.3 1.0
CA C:ASP710 5.0 1.0 1.0
N C:ASP710 5.0 0.5 1.0

Magnesium binding site 5 out of 6 in 4hyt

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Magnesium binding site 5 out of 6 in the Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:0.9
occ:1.00
 OD1 C:ASP740 2.1 0.8 1.0
OD2 C:ASP740 2.2 0.7 1.0
CG C:ASP740 2.4 0.0 1.0
O C:LYS719 3.6 0.5 1.0
CB C:ASP740 4.0 0.7 1.0
O C:ALA721 4.2 94.6 1.0
O C:ALA738 4.4 0.3 1.0
C C:LYS719 4.5 0.2 1.0
CA C:GLY272 4.5 0.1 1.0
O C:SER718 4.6 0.3 1.0
CA C:LYS719 4.7 0.2 1.0
O C:GLY272 4.8 1.0 1.0
CA C:ASP740 4.8 95.3 1.0
N C:ASP740 4.8 94.0 1.0
CD C:LYS719 5.0 0.8 1.0

Magnesium binding site 6 out of 6 in 4hyt

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Magnesium binding site 6 out of 6 in the Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Na,K-Atpase in the E2P State with Bound Ouabain and MG2+ in the Cation-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:81.1
occ:1.00
 OE2 C:GLU779 2.0 87.1 1.0
O C:HOH2103 2.1 81.0 1.0
O C:HOH2101 2.1 80.5 1.0
O C:HOH2102 2.1 81.8 1.0
OD1 C:ASP804 2.3 0.9 1.0
OD1 C:ASN776 2.5 0.0 1.0
CG C:ASP804 2.9 0.7 1.0
OD2 C:ASP804 2.9 0.2 1.0
CD C:GLU779 3.1 85.8 1.0
CG C:ASN776 3.4 1.0 1.0
OE1 C:GLU779 3.5 83.2 1.0
ND2 C:ASN776 3.8 0.6 1.0
OG C:SER775 4.1 78.6 1.0
CG C:GLU779 4.3 87.3 1.0
CB C:ASP804 4.4 0.8 1.0
O C:ALA323 4.4 88.7 1.0
CA C:ASN776 4.5 90.0 1.0
CB C:ASN776 4.5 0.6 1.0
OE2 C:GLU327 4.5 0.5 1.0
CB C:GLU779 4.5 90.3 1.0
N C:ASN776 4.7 88.3 1.0
O C:VAL325 4.7 96.4 1.0
C C:SER775 4.9 77.1 1.0
O C:SER775 4.9 77.0 1.0

Reference:

M.Laursen, L.Yatime, P.Nissen, N.U.Fedosova. Crystal Structure of the High-Affinity Na+,K+-Atpase-Ouabain Complex with MG2+ Bound in the Cation Binding Site. Proc.Natl.Acad.Sci.Usa V. 110 10958 2013.
ISSN: ISSN 0027-8424
PubMed: 23776223
DOI: 10.1073/PNAS.1222308110
Page generated: Mon Dec 14 18:51:20 2020

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