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Magnesium in PDB 5lzr: Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium

Enzymatic activity of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium

All present enzymatic activity of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium, PDB code: 5lzr was solved by C.Wilkinson, J.Kellosalo, T.Kajander, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.46 / 4.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.720, 108.870, 105.810, 90.00, 108.79, 90.00
R / Rfree (%) 23.2 / 27.9

Other elements in 5lzr:

The structure of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium also contains other interesting chemical elements:

Tungsten (W) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium (pdb code 5lzr). 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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium, PDB code: 5lzr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5lzr

Go back to Magnesium Binding Sites List in 5lzr
Magnesium binding site 1 out of 4 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:0.1
occ:1.00
 O2 A:WO4801 2.5 0.7 0.8
OD1 A:ASP692 3.3 0.1 1.0
OD2 A:ASP660 3.5 0.8 1.0
MG A:MG803 3.6 0.9 1.0
OD2 A:ASP692 3.7 0.1 1.0
OD2 A:ASP202 3.8 0.8 1.0
CG A:ASP692 3.8 0.1 1.0
OD2 A:ASP688 4.1 0.1 1.0
W A:WO4801 4.1 0.7 0.8
OD1 A:ASP660 4.1 0.8 1.0
CG A:ASP660 4.2 0.8 1.0
O4 A:WO4801 4.6 0.7 0.8
OD1 A:ASP688 4.6 0.1 1.0
CG A:ASP202 4.7 0.8 1.0
CG A:ASP688 4.8 0.1 1.0
OD1 A:ASP202 4.8 0.8 1.0
O1 A:WO4801 4.9 0.7 0.8

Magnesium binding site 2 out of 4 in 5lzr

Go back to Magnesium Binding Sites List in 5lzr
Magnesium binding site 2 out of 4 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:0.9
occ:1.00
 O4 A:WO4801 2.8 0.7 0.8
OD2 A:ASP202 3.3 0.8 1.0
OD1 A:ASP232 3.5 0.3 1.0
MG A:MG802 3.6 0.1 1.0
OD2 A:ASP232 3.9 0.3 1.0
OD2 A:ASP228 4.0 0.4 1.0
O2 A:WO4801 4.1 0.7 0.8
CG A:ASP232 4.1 0.3 1.0
W A:WO4801 4.1 0.7 0.8
CG A:ASP202 4.2 0.8 1.0
OD1 A:ASP202 4.5 0.8 1.0
OD1 A:ASP228 4.5 0.4 1.0
CG A:ASP228 4.7 0.4 1.0

Magnesium binding site 3 out of 4 in 5lzr

Go back to Magnesium Binding Sites List in 5lzr
Magnesium binding site 3 out of 4 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:1.0
occ:1.00
 O2 B:WO4801 2.2 0.2 0.5
OD2 B:ASP465 2.4 0.1 1.0
OD1 B:ASN492 3.0 0.2 1.0
ND2 B:ASN492 3.3 0.2 1.0
CG B:ASP465 3.5 0.1 1.0
CG B:ASN492 3.5 0.2 1.0
W B:WO4801 3.7 0.2 0.5
OD1 B:ASP465 4.1 0.1 1.0
O4 B:WO4801 4.1 0.2 0.5
OD1 B:ASP488 4.2 0.1 1.0
OD2 B:ASP488 4.4 0.1 1.0
O3 B:WO4801 4.5 0.2 0.5
CB B:ASP465 4.5 0.1 1.0
CG B:ASP488 4.8 0.1 1.0

Magnesium binding site 4 out of 4 in 5lzr

Go back to Magnesium Binding Sites List in 5lzr
Magnesium binding site 4 out of 4 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Tungstate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:0.6
occ:1.00
 O4 B:WO4801 2.5 0.2 0.5
OD2 B:ASP688 3.4 0.5 1.0
OD2 B:ASP692 3.5 0.1 1.0
O3 B:WO4801 3.5 0.2 0.5
W B:WO4801 3.6 0.2 0.5
OD1 B:ASP660 3.8 0.2 1.0
CG B:ASP692 4.4 0.1 1.0
CG B:ASP688 4.4 0.5 1.0
OD2 B:ASP660 4.4 0.2 1.0
O1 B:WO4801 4.4 0.2 0.5
CG B:ASP660 4.5 0.2 1.0
OD2 B:ASP202 4.5 0.4 1.0
OD1 B:ASP692 4.5 0.1 1.0
NZ B:LYS663 4.6 0.4 1.0
OD1 B:ASP688 4.7 0.5 1.0
CE B:LYS663 4.9 0.4 1.0

Reference:

K.M.Li, C.Wilkinson, J.Kellosalo, J.Y.Tsai, T.Kajander, L.J.Jeuken, Y.J.Sun, A.Goldman. Membrane Pyrophosphatases From Thermotoga Maritima and Vigna Radiata Suggest A Conserved Coupling Mechanism. Nat Commun V. 7 13596 2016.
ISSN: ESSN 2041-1723
PubMed: 27922000
DOI: 10.1038/NCOMMS13596
Page generated: Mon Dec 14 20:49:49 2020

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