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
Go back to
Magnesium Binding Sites List in 1qez
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 Sites List in 1qez
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
Go back to
Magnesium Binding Sites List in 1qez
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
Go back to
Magnesium Binding Sites List in 1qez
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
Go back to
Magnesium Binding Sites List in 1qez
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
Go back to
Magnesium Binding Sites List in 1qez
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
|