Magnesium in PDB 6kpz: Crystal Structures of Na+,K+-Atpase in Complex with Ouabain

Protein crystallography data

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain, PDB code: 6kpz was solved by H.Ogawa, K.Motoyama, F.Cornelius, B.Vilsen, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.99 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 115.621, 117.810, 493.203, 90.00, 90.00, 90.00
R / Rfree (%) 26.4 / 30.8

Other elements in 6kpz:

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain (pdb code 6kpz). 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 Structures of Na+,K+-Atpase in Complex with Ouabain, PDB code: 6kpz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6kpz

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Magnesium binding site 1 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:43.9
occ:1.00
O A:HOH1202 2.1 43.2 1.0
O A:HOH1201 2.1 63.0 1.0
OD1 A:ASP710 2.2 45.9 1.0
OP3 A:PHD369 2.2 55.9 1.0
O A:THR371 2.2 46.0 1.0
OD2 A:PHD369 2.6 57.7 1.0
CG A:ASP710 2.9 49.0 1.0
OD2 A:ASP710 3.0 52.9 1.0
C A:THR371 3.4 49.6 1.0
P A:PHD369 3.5 47.4 1.0
CG A:PHD369 3.5 51.9 1.0
N A:GLY711 3.5 48.3 1.0
OD1 A:PHD369 3.8 42.1 1.0
OD2 A:ASP714 4.0 48.3 1.0
CB A:THR371 4.0 55.5 1.0
CA A:GLY711 4.0 46.8 1.0
O A:SER209 4.0 57.2 1.0
CA A:THR371 4.2 46.2 1.0
OP1 A:PHD369 4.2 42.7 1.0
CG2 A:THR371 4.3 67.5 1.0
CB A:ASP710 4.3 46.1 1.0
N A:GLY372 4.4 52.0 1.0
OD1 A:ASN713 4.4 56.9 1.0
N A:ASP710 4.5 39.5 1.0
C A:ASP710 4.5 52.7 1.0
CA A:GLY372 4.5 51.3 1.0
N A:THR371 4.5 54.1 1.0
OG1 A:THR373 4.6 43.0 1.0
OP2 A:PHD369 4.6 56.8 1.0
CA A:ASP710 4.7 44.1 1.0
ND2 A:ASN713 4.8 51.6 1.0
CB A:PHD369 4.8 52.7 1.0
CA A:GLY213 4.9 62.8 1.0

Magnesium binding site 2 out of 4 in 6kpz

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Magnesium binding site 2 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:51.2
occ:1.00
OE2 A:GLU779 2.1 47.2 1.0
OD2 A:ASP804 2.1 43.1 1.0
O A:HOH1203 2.2 36.8 1.0
O A:HOH1204 2.2 46.8 1.0
OD1 A:ASP804 2.2 32.5 1.0
CG A:ASP804 2.4 40.2 1.0
O A:HOH1205 2.5 55.3 1.0
CD A:GLU779 2.8 51.9 1.0
OE2 A:GLU327 2.9 67.8 1.0
OE1 A:GLU779 3.0 54.3 1.0
CD A:GLU327 3.9 54.5 1.0
CB A:ASP804 3.9 41.5 1.0
OD1 A:ASN776 4.0 36.2 1.0
OE1 A:GLU327 4.1 52.4 1.0
CG A:GLU779 4.2 39.8 1.0
CG A:ASN776 4.5 38.4 1.0
OG A:SER775 4.6 31.8 1.0
O A:VAL325 4.6 50.0 1.0
O A:ALA323 4.7 46.1 1.0
CB A:GLU779 4.7 36.9 1.0
O A:HOH1206 4.7 45.1 1.0
ND2 A:ASN776 4.8 43.7 1.0
CG2 A:ILE800 4.8 45.9 1.0
CA A:PRO326 4.9 32.9 1.0
CA A:ASP804 4.9 43.9 1.0
CA A:ASN776 5.0 43.1 1.0

Magnesium binding site 3 out of 4 in 6kpz

Go back to Magnesium Binding Sites List in 6kpz
Magnesium binding site 3 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:50.3
occ:1.00
O C:HOH1201 2.0 46.4 1.0
OP3 C:PHD369 2.1 53.3 1.0
O C:HOH1202 2.2 60.3 1.0
OD1 C:ASP710 2.2 43.2 1.0
O C:THR371 2.3 46.7 1.0
OD2 C:PHD369 2.5 49.4 1.0
CG C:ASP710 3.0 44.9 1.0
OD2 C:ASP710 3.2 41.1 1.0
P C:PHD369 3.4 63.6 1.0
CG C:PHD369 3.4 45.1 1.0
C C:THR371 3.4 43.1 1.0
N C:GLY711 3.5 55.7 1.0
OD1 C:PHD369 3.6 48.2 1.0
OD2 C:ASP714 3.9 44.6 1.0
CA C:GLY711 4.0 49.9 1.0
CB C:THR371 4.0 36.4 1.0
O C:SER209 4.0 66.8 1.0
OP1 C:PHD369 4.1 52.9 1.0
CA C:THR371 4.2 41.7 1.0
OD1 C:ASN713 4.2 60.7 1.0
CG2 C:THR371 4.3 33.0 1.0
CB C:ASP710 4.4 36.8 1.0
N C:GLY372 4.4 43.3 1.0
OP2 C:PHD369 4.5 60.6 1.0
N C:THR371 4.5 49.5 1.0
C C:ASP710 4.5 47.9 1.0
N C:ASP710 4.6 38.2 1.0
CA C:GLY372 4.6 45.0 1.0
OG1 C:THR373 4.7 45.4 1.0
ND2 C:ASN713 4.7 47.0 1.0
CB C:PHD369 4.7 44.4 1.0
CA C:ASP710 4.7 37.2 1.0
CA C:GLY213 4.8 49.3 1.0
CG C:ASN713 4.9 57.8 1.0
CG C:ASP714 5.0 41.5 1.0

Magnesium binding site 4 out of 4 in 6kpz

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Magnesium binding site 4 out of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:55.4
occ:1.00
OE2 C:GLU779 2.1 34.8 1.0
OD2 C:ASP804 2.1 42.0 1.0
O C:HOH1203 2.1 40.9 1.0
OD1 C:ASP804 2.3 41.2 1.0
O C:HOH1204 2.3 37.9 1.0
O C:HOH1205 2.3 33.7 1.0
CG C:ASP804 2.4 41.5 1.0
CD C:GLU779 2.8 42.0 1.0
OE2 C:GLU327 2.8 41.7 1.0
OE1 C:GLU779 3.1 36.9 1.0
CD C:GLU327 3.8 52.5 1.0
CB C:ASP804 3.9 42.6 1.0
OE1 C:GLU327 4.1 61.3 1.0
OD1 C:ASN776 4.1 43.8 1.0
CG C:GLU779 4.2 35.7 1.0
O C:VAL325 4.5 50.7 1.0
CG C:ASN776 4.5 42.2 1.0
O C:HOH1206 4.6 25.4 1.0
O C:ALA323 4.6 40.9 1.0
CB C:GLU779 4.7 36.5 1.0
OG C:SER775 4.7 26.1 1.0
CG2 C:ILE800 4.8 42.0 1.0
ND2 C:ASN776 4.9 37.3 1.0
CA C:PRO326 4.9 35.8 1.0
CA C:ASP804 4.9 35.9 1.0
N C:GLU327 5.0 41.0 1.0

Reference:

H.Ogawa, K.Motoyama, F.Cornelius, B.Vilsen, C.Toyoshima. Crystal Structure of the Na,K-Atpase in Complex with Ouabain To Be Published.
Page generated: Mon Jan 25 08:48:54 2021

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