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Magnesium in PDB 5lzq: Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion

Enzymatic activity of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion

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

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion, PDB code: 5lzq 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) 29.75 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.421, 106.763, 161.913, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 27.3

Other elements in 5lzq:

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

Sodium (Na) 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 Imidodiphosphate and Magnesium, and with Bound Sodium Ion (pdb code 5lzq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion, PDB code: 5lzq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5lzq

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Magnesium binding site 1 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


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 Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:0.9
occ:1.00
 OD2 A:ASP206 2.0 1.0 1.0
O5 A:2PN806 2.0 0.8 1.0
OD1 A:ASP202 2.4 0.3 1.0
MG A:MG803 2.7 0.2 1.0
OD2 A:ASP202 2.8 0.1 1.0
CG A:ASP206 2.9 0.5 1.0
CG A:ASP202 2.9 0.9 1.0
OD1 A:ASP206 3.2 0.3 1.0
P2 A:2PN806 3.3 1.0 1.0
O6 A:2PN806 3.6 0.2 1.0
OD2 A:ASP688 3.7 0.5 1.0
OD2 A:ASP692 3.8 0.6 1.0
O4 A:2PN806 4.0 0.5 1.0
CB A:ASP206 4.1 0.6 1.0
O2 A:2PN806 4.3 0.1 1.0
OE2 A:GLU217 4.3 0.9 1.0
CB A:ASP202 4.4 0.3 1.0
O A:ASP202 4.5 0.2 1.0
N1 A:2PN806 4.5 0.0 1.0
CG A:ASP692 4.7 0.2 1.0
OD1 A:ASP692 4.7 0.7 1.0
CG A:ASP688 4.7 0.7 1.0
NZ A:LYS210 4.8 0.5 1.0
C A:ASP202 4.9 0.4 1.0
P1 A:2PN806 5.0 0.5 1.0
OD1 A:ASP660 5.0 0.1 1.0

Magnesium binding site 2 out of 10 in 5lzq

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Magnesium binding site 2 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


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 Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:0.9
occ:1.00
 OD1 A:ASP465 2.2 0.8 1.0
O6 A:2PN806 2.6 0.2 1.0
CG A:ASP465 2.9 0.6 1.0
OD2 A:ASP465 3.0 0.6 1.0
OD2 A:ASP228 3.5 1.0 1.0
O4 A:2PN806 3.6 0.5 1.0
OD1 A:ASP218 3.6 0.1 1.0
P2 A:2PN806 3.7 1.0 1.0
OD2 A:ASP218 3.7 0.0 1.0
OE2 A:GLU217 3.7 0.9 1.0
MG A:MG804 3.8 0.8 1.0
OD2 A:ASP232 4.1 0.8 1.0
CG A:ASP218 4.1 0.8 1.0
O A:ASP465 4.2 0.3 1.0
CB A:ASP465 4.4 0.7 1.0
CG A:ASP228 4.5 0.6 1.0
C A:ASP465 4.7 0.7 1.0
O5 A:2PN806 4.7 0.8 1.0
N1 A:2PN806 4.7 0.0 1.0
CD A:GLU217 4.7 0.1 1.0
OD1 A:ASP228 4.8 0.3 1.0
CA A:ASP465 4.8 0.5 1.0
OD2 A:ASP488 5.0 0.6 1.0

Magnesium binding site 3 out of 10 in 5lzq

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Magnesium binding site 3 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


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 Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:0.2
occ:1.00
 OD2 A:ASP202 2.2 0.1 1.0
OD1 A:ASP692 2.3 0.7 1.0
O2 A:2PN806 2.4 0.1 1.0
OD2 A:ASP692 2.5 0.6 1.0
O5 A:2PN806 2.5 0.8 1.0
CG A:ASP692 2.6 0.2 1.0
MG A:MG801 2.7 0.9 1.0
CG A:ASP202 3.3 0.9 1.0
OD2 A:ASP688 3.5 0.5 1.0
P1 A:2PN806 3.7 0.5 1.0
P2 A:2PN806 3.8 1.0 1.0
OD1 A:ASP688 3.8 0.4 1.0
OD1 A:ASP202 3.8 0.3 1.0
NZ A:LYS199 3.9 0.1 1.0
CG A:ASP688 4.0 0.7 1.0
CB A:ASP692 4.0 0.5 1.0
NZ A:LYS695 4.0 0.7 1.0
N1 A:2PN806 4.1 0.0 1.0
OD2 A:ASP206 4.2 1.0 1.0
OD1 A:ASP660 4.3 0.1 1.0
O1 A:2PN806 4.4 0.8 1.0
O6 A:2PN806 4.4 0.2 1.0
CB A:ASP202 4.6 0.3 1.0
O A:ASP688 4.6 0.4 1.0
O3 A:2PN806 4.8 0.8 1.0
CA A:ASP692 4.8 0.7 1.0
CG A:ASP660 4.9 0.7 1.0
CE A:LYS695 4.9 0.1 1.0
O4 A:2PN806 4.9 0.5 1.0

Magnesium binding site 4 out of 10 in 5lzq

Go back to Magnesium Binding Sites List in 5lzq
Magnesium binding site 4 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


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 Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:0.8
occ:1.00
 OD2 A:ASP465 2.0 0.6 1.0
O1 A:2PN806 2.1 0.8 1.0
OD1 A:ASP232 2.2 0.9 1.0
OD2 A:ASP232 2.3 0.8 1.0
CG A:ASP232 2.5 0.8 1.0
O6 A:2PN806 2.6 0.2 1.0
CG A:ASP465 3.3 0.6 1.0
P1 A:2PN806 3.4 0.5 1.0
N1 A:2PN806 3.7 0.0 1.0
P2 A:2PN806 3.7 1.0 1.0
MG A:MG802 3.8 0.9 1.0
CB A:ASP232 3.8 0.7 1.0
OD1 A:ASP228 3.8 0.3 1.0
OD1 A:ASP465 4.0 0.8 1.0
O2 A:2PN806 4.3 0.1 1.0
CB A:ASP465 4.3 0.7 1.0
O3 A:2PN806 4.5 0.8 1.0
OD2 A:ASP228 4.5 1.0 1.0
OD2 A:ASP236 4.5 0.3 1.0
O5 A:2PN806 4.5 0.8 1.0
CG A:ASP228 4.6 0.6 1.0
CA A:ASP232 4.8 0.9 1.0
O A:ASP228 4.8 0.7 1.0
OD2 A:ASP202 4.8 0.1 1.0
O4 A:2PN806 4.8 0.5 1.0

Magnesium binding site 5 out of 10 in 5lzq

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Magnesium binding site 5 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:0.8
occ:1.00
 N1 A:2PN806 2.1 0.0 1.0
OD1 A:ASN492 2.1 0.6 1.0
OD2 A:ASP660 2.2 0.6 1.0
ND2 A:ASN492 2.2 0.2 1.0
CG A:ASN492 2.4 0.4 1.0
O3 A:2PN806 2.6 0.8 1.0
P1 A:2PN806 2.9 0.5 1.0
CG A:ASP660 3.3 0.7 1.0
P2 A:2PN806 3.6 1.0 1.0
OD1 A:ASP488 3.7 0.6 1.0
O2 A:2PN806 3.8 0.1 1.0
O4 A:2PN806 3.8 0.5 1.0
OD2 A:ASP488 3.8 0.6 1.0
OD1 A:ASP660 3.8 0.1 1.0
CB A:ASN492 3.9 0.6 1.0
O1 A:2PN806 4.1 0.8 1.0
CG A:ASP488 4.1 0.5 1.0
O5 A:2PN806 4.3 0.8 1.0
O A:ASP488 4.4 0.1 1.0
CB A:ASP660 4.5 0.9 1.0
O6 A:2PN806 4.6 0.2 1.0
CA A:ASN492 4.8 0.7 1.0

Magnesium binding site 6 out of 10 in 5lzq

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Magnesium binding site 6 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:0.7
occ:1.00
 O1 B:2PN806 2.1 0.6 1.0
OD1 B:ASP692 2.1 0.9 1.0
OD2 B:ASP202 2.2 0.3 1.0
OD2 B:ASP692 2.4 0.6 1.0
CG B:ASP692 2.5 0.6 1.0
MG B:MG805 2.8 0.0 1.0
CG B:ASP202 3.4 0.2 1.0
P1 B:2PN806 3.5 1.0 1.0
OD2 B:ASP688 3.7 0.9 1.0
O5 B:2PN806 3.7 0.2 1.0
NZ B:LYS199 3.7 0.9 1.0
OD1 B:ASP688 3.8 0.9 1.0
CB B:ASP692 3.9 0.7 1.0
O2 B:2PN806 4.0 0.7 1.0
OD1 B:ASP202 4.0 0.0 1.0
CG B:ASP688 4.0 0.9 1.0
NZ B:LYS695 4.1 0.0 1.0
CE B:LYS695 4.3 0.8 1.0
N1 B:2PN806 4.4 0.3 1.0
O3 B:2PN806 4.4 0.2 1.0
OD1 B:ASP660 4.4 0.6 1.0
P2 B:2PN806 4.4 1.0 1.0
CB B:ASP202 4.5 0.8 1.0
O B:ASP688 4.5 0.1 1.0
OD2 B:ASP206 4.6 0.7 1.0
O6 B:2PN806 4.6 0.3 1.0
CA B:ASP692 4.6 0.8 1.0
CG B:ASP660 5.0 0.3 1.0

Magnesium binding site 7 out of 10 in 5lzq

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Magnesium binding site 7 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:0.2
occ:1.00
 O6 B:2PN806 2.4 0.3 1.0
OD2 B:ASP228 2.5 1.0 1.0
OD1 B:ASP465 3.1 0.6 1.0
O4 B:2PN806 3.2 0.9 1.0
OD1 B:ASP218 3.3 0.0 1.0
P2 B:2PN806 3.3 1.0 1.0
MG B:MG803 3.4 0.1 1.0
CG B:ASP228 3.5 0.8 1.0
OD2 B:ASP465 3.6 0.6 1.0
CG B:ASP465 3.7 0.6 1.0
OE2 B:GLU217 3.8 0.4 1.0
OD1 B:ASP228 3.9 0.2 1.0
OD2 B:ASP218 4.0 0.4 1.0
O5 B:2PN806 4.0 0.2 1.0
OD2 B:ASP232 4.0 0.7 1.0
CG B:ASP218 4.0 0.4 1.0
MG B:MG805 4.5 0.0 1.0
OD1 B:ASP202 4.7 0.0 1.0
N1 B:2PN806 4.8 0.3 1.0
CD B:GLU217 4.8 0.3 1.0
CB B:ASP228 4.9 0.3 1.0
CG B:GLU217 4.9 0.8 1.0
O B:ASP465 5.0 0.9 1.0

Magnesium binding site 8 out of 10 in 5lzq

Go back to Magnesium Binding Sites List in 5lzq
Magnesium binding site 8 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:0.1
occ:1.00
 OD1 B:ASP232 2.2 0.7 1.0
O6 B:2PN806 2.3 0.3 1.0
OD2 B:ASP465 2.4 0.6 1.0
OD2 B:ASP232 2.4 0.7 1.0
CG B:ASP232 2.6 0.4 1.0
O2 B:2PN806 2.9 0.7 1.0
OD1 B:ASP228 3.0 0.2 1.0
MG B:MG802 3.4 0.2 1.0
CG B:ASP465 3.5 0.6 1.0
P2 B:2PN806 3.7 1.0 1.0
CG B:ASP228 3.7 0.8 1.0
OD2 B:ASP228 3.8 1.0 1.0
OD1 B:ASP465 4.0 0.6 1.0
P1 B:2PN806 4.0 1.0 1.0
CB B:ASP232 4.1 0.5 1.0
N1 B:2PN806 4.1 0.3 1.0
O B:ASP228 4.3 0.3 1.0
OD2 B:ASP202 4.3 0.3 1.0
CG B:ASP202 4.5 0.2 1.0
O4 B:2PN806 4.6 0.9 1.0
O5 B:2PN806 4.6 0.2 1.0
O1 B:2PN806 4.6 0.6 1.0
OD1 B:ASP202 4.7 0.0 1.0
CB B:ASP465 4.7 0.6 1.0
MG B:MG805 4.8 0.0 1.0
CA B:ASP232 4.9 0.9 1.0
C B:ASP228 4.9 0.8 1.0
OD2 B:ASP236 5.0 0.5 1.0

Magnesium binding site 9 out of 10 in 5lzq

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Magnesium binding site 9 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:0.1
occ:1.00
 OD1 B:ASN492 2.1 0.7 1.0
OD2 B:ASP660 2.2 0.4 1.0
N1 B:2PN806 2.2 0.3 1.0
O3 B:2PN806 2.2 0.2 1.0
ND2 B:ASN492 2.2 0.6 1.0
CG B:ASN492 2.4 0.6 1.0
P1 B:2PN806 2.7 1.0 1.0
CG B:ASP660 3.3 0.3 1.0
O1 B:2PN806 3.6 0.6 1.0
OD1 B:ASP488 3.7 0.8 1.0
P2 B:2PN806 3.7 1.0 1.0
OD1 B:ASP660 3.9 0.6 1.0
O2 B:2PN806 3.9 0.7 1.0
CB B:ASN492 3.9 0.6 1.0
OD2 B:ASP488 3.9 0.3 1.0
O4 B:2PN806 4.1 0.9 1.0
CG B:ASP488 4.1 0.1 1.0
O5 B:2PN806 4.3 0.2 1.0
CB B:ASP660 4.4 0.5 1.0
O B:ASP488 4.5 0.5 1.0
O6 B:2PN806 4.7 0.3 1.0
CA B:ASN492 4.8 0.6 1.0
CD B:LYS664 5.0 0.6 1.0

Magnesium binding site 10 out of 10 in 5lzq

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Magnesium binding site 10 out of 10 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg805

b:0.0
occ:1.00
 OD1 B:ASP202 2.3 0.0 1.0
O5 B:2PN806 2.3 0.2 1.0
OD2 B:ASP206 2.3 0.7 1.0
OD2 B:ASP202 2.3 0.3 1.0
CG B:ASP202 2.6 0.2 1.0
MG B:MG801 2.8 0.7 1.0
CG B:ASP206 3.2 0.3 1.0
O6 B:2PN806 3.4 0.3 1.0
P2 B:2PN806 3.4 1.0 1.0
OD1 B:ASP206 3.5 0.8 1.0
O1 B:2PN806 3.5 0.6 1.0
OD2 B:ASP688 3.8 0.9 1.0
OD2 B:ASP692 3.9 0.6 1.0
NZ B:LYS663 4.1 0.3 1.0
CB B:ASP202 4.1 0.8 1.0
CB B:ASP206 4.4 0.4 1.0
N1 B:2PN806 4.4 0.3 1.0
P1 B:2PN806 4.4 1.0 1.0
O4 B:2PN806 4.5 0.9 1.0
MG B:MG802 4.5 0.2 1.0
O B:ASP202 4.6 1.0 1.0
CG B:ASP692 4.7 0.6 1.0
OD1 B:ASP692 4.7 0.9 1.0
OE2 B:GLU217 4.7 0.4 1.0
O2 B:2PN806 4.8 0.7 1.0
MG B:MG803 4.8 0.1 1.0
CG B:ASP688 4.9 0.9 1.0
CA B:ASP202 4.9 0.7 1.0
OD1 B:ASP228 4.9 0.2 1.0
C B:ASP202 4.9 0.2 1.0
OD1 B:ASP660 5.0 0.6 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: Sun Sep 29 21:06:49 2024

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