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Magnesium in PDB 1qez: Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase.

Enzymatic activity of Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase.

All present enzymatic activity of Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase.:
3.6.1.1;

Protein crystallography data

The structure of Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase., PDB code: 1qez was solved by V.-M.Leppanen, H.Nummelin, T.Hansen, R.Lahti, G.Schafer, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.120, 98.730, 107.250, 90.00, 78.01, 90.00
R / Rfree (%) 19.7 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase. (pdb code 1qez). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase., PDB code: 1qez:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1qez

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Magnesium binding site 1 out of 6 in the Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1201

b:44.4
occ:1.00
 OD2 A:ASP1062 2.3 59.1 1.0
OD1 A:ASP1099 2.4 59.4 1.0
O A:HOH7070 2.6 37.7 1.0
O A:HOH7044 2.7 31.8 1.0
OD2 A:ASP1099 2.8 59.4 1.0
CG A:ASP1099 2.8 59.4 1.0
O A:HOH7014 2.9 36.5 1.0
CG A:ASP1062 3.5 59.1 1.0
OD2 A:ASP1067 4.0 55.8 1.0
OD1 A:ASP1062 4.1 59.1 1.0
CB A:ASP1099 4.1 59.4 1.0
O A:HOH7004 4.3 58.4 1.0
NZ A:LYS1101 4.5 36.8 1.0
CB A:ASP1062 4.6 59.1 1.0
CA A:ASP1099 4.7 36.8 1.0
O A:ALA1100 4.7 41.3 1.0
N A:ALA1100 4.9 41.5 1.0
CG A:ASP1067 5.0 55.8 1.0

Magnesium binding site 2 out of 6 in 1qez

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Magnesium binding site 2 out of 6 in the Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2201

b:22.8
occ:1.00
 OD1 B:ASP2099 2.2 24.9 1.0
O B:HOH7046 2.4 19.8 1.0
O B:HOH7038 2.4 21.8 1.0
OD2 B:ASP2062 2.4 32.6 1.0
O B:HOH7049 2.4 28.3 1.0
O B:HOH7048 2.5 33.5 1.0
CG B:ASP2099 2.7 24.9 1.0
OD2 B:ASP2099 2.8 24.9 1.0
CG B:ASP2062 3.6 32.6 1.0
OD2 B:ASP2067 3.9 32.4 1.0
CB B:ASP2099 4.1 24.9 1.0
OD1 B:ASP2062 4.1 32.6 1.0
O B:ALA2100 4.3 11.8 1.0
NZ B:LYS2101 4.5 11.5 1.0
CA B:ASP2099 4.6 35.0 1.0
N B:ALA2100 4.6 14.6 1.0
O B:HOH7071 4.7 38.8 1.0
CB B:ASP2062 4.8 32.6 1.0
CG B:ASP2067 4.9 32.4 1.0

Magnesium binding site 3 out of 6 in 1qez

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Magnesium binding site 3 out of 6 in the Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3201

b:28.7
occ:1.00
 OD1 C:ASP3099 2.1 45.7 1.0
OD2 C:ASP3062 2.3 53.9 1.0
O C:HOH7040 2.3 35.2 1.0
O C:HOH7037 2.4 48.1 1.0
O C:HOH7032 2.5 41.2 1.0
CG C:ASP3099 2.9 45.7 1.0
OD2 C:ASP3099 3.3 45.7 1.0
CG C:ASP3062 3.4 53.9 1.0
OD1 C:ASP3062 3.9 53.9 1.0
O C:ALA3100 4.0 28.7 1.0
CB C:ASP3099 4.1 45.7 1.0
N C:ALA3100 4.2 20.9 1.0
CA C:ASP3099 4.3 37.8 1.0
OD2 C:ASP3067 4.4 43.6 1.0
CG C:GLU3060 4.6 42.4 1.0
CB C:ASP3062 4.6 53.9 1.0
CB C:GLU3060 4.6 42.4 1.0
OE1 C:GLU3060 4.7 42.4 1.0
C C:ASP3099 4.8 37.8 1.0
C C:ALA3100 4.9 20.9 1.0

Magnesium binding site 4 out of 6 in 1qez

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Magnesium binding site 4 out of 6 in the Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4201

b:39.4
occ:1.00
 O D:HOH7074 2.1 68.6 1.0
O D:HOH7013 2.3 43.9 1.0
O D:HOH7033 2.3 36.6 1.0
OD1 D:ASP4099 2.3 50.4 1.0
OD2 D:ASP4062 2.4 73.4 1.0
O D:HOH7050 2.4 46.6 1.0
CG D:ASP4099 3.1 50.4 1.0
OD2 D:ASP4099 3.2 50.4 1.0
CG D:ASP4062 3.5 73.4 1.0
OD2 D:ASP4067 3.9 62.9 1.0
OD1 D:ASP4062 3.9 73.4 1.0
O D:HOH7072 4.2 60.9 1.0
O D:ALA4100 4.2 53.1 1.0
CB D:ASP4099 4.4 50.4 1.0
N D:ALA4100 4.6 35.0 1.0
NZ D:LYS4101 4.7 44.4 1.0
CB D:ASP4062 4.7 73.4 1.0
O D:PRO4065 4.7 45.3 1.0
CA D:ASP4099 4.8 52.2 1.0
CG D:ASP4067 4.8 62.9 1.0
CG D:GLU4060 4.8 56.3 1.0
CB D:GLU4060 4.9 56.3 1.0

Magnesium binding site 5 out of 6 in 1qez

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Magnesium binding site 5 out of 6 in the Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg5201

b:19.9
occ:1.00
 OD1 E:ASP5099 2.3 27.8 1.0
O E:HOH7047 2.3 54.3 1.0
O E:HOH7034 2.3 28.0 1.0
O E:HOH7035 2.3 22.5 1.0
OD2 E:ASP5062 2.5 39.7 1.0
CG E:ASP5099 3.0 27.8 1.0
OD2 E:ASP5099 3.1 27.8 1.0
CG E:ASP5062 3.6 39.7 1.0
OD2 E:ASP5067 3.8 37.2 1.0
OD1 E:ASP5062 4.0 39.7 1.0
O E:ALA5100 4.1 25.1 1.0
CB E:ASP5099 4.3 27.8 1.0
N E:ALA5100 4.6 26.6 1.0
NZ E:LYS5101 4.6 27.6 1.0
CA E:ASP5099 4.7 36.7 1.0
CG E:ASP5067 4.7 37.2 1.0
O E:PRO5065 4.8 30.1 1.0
O E:HOH7069 4.9 50.6 1.0
CB E:ASP5062 4.9 39.7 1.0
CG E:GLU5060 4.9 27.3 1.0
CB E:GLU5060 5.0 27.3 1.0

Magnesium binding site 6 out of 6 in 1qez

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Magnesium binding site 6 out of 6 in the Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg6201

b:38.2
occ:1.00
 OD1 F:ASP6099 2.1 47.5 1.0
O F:HOH7012 2.1 32.5 1.0
O F:HOH7051 2.2 39.2 1.0
O F:HOH7030 2.3 18.9 1.0
OD2 F:ASP6062 2.4 43.4 1.0
O F:HOH7015 2.5 19.3 1.0
CG F:ASP6099 3.0 47.5 1.0
CG F:ASP6062 3.5 43.4 1.0
OD2 F:ASP6099 3.6 47.5 1.0
O F:ALA6100 3.7 38.2 1.0
OD1 F:ASP6062 4.0 43.4 1.0
N F:ALA6100 4.0 31.7 1.0
CB F:ASP6099 4.2 47.5 1.0
CA F:ASP6099 4.3 33.5 1.0
CG F:GLU6060 4.3 40.1 1.0
OE1 F:GLU6060 4.3 40.1 1.0
CB F:GLU6060 4.4 40.1 1.0
OD2 F:ASP6067 4.6 47.5 1.0
C F:ASP6099 4.7 33.5 1.0
C F:ALA6100 4.7 31.7 1.0
CB F:ASP6062 4.7 43.4 1.0
CD F:GLU6060 4.9 40.1 1.0
CA F:ALA6100 4.9 31.7 1.0

Reference:

V.M.Leppanen, H.Nummelin, T.Hansen, R.Lahti, G.Schafer, A.Goldman. Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: Structure, Thermostability, and Effect of Metal Ion in An Archael Pyrophosphatase. Protein Sci. V. 8 1218 1999.
ISSN: ISSN 0961-8368
PubMed: 10386872
Page generated: Tue Aug 13 11:49:34 2024

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