Magnesium in PDB 6ll8: Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Protein crystallography data
The structure of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form, PDB code: 6ll8
was solved by
M.Horitani,
K.Kusubayashi,
K.Oshima,
A.Yato,
H.Sugimoto,
K.Watanabe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.57 /
1.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.490,
78.980,
75.300,
90.00,
98.59,
90.00
|
R / Rfree (%)
|
9.7 /
12.2
|
Other elements in 6ll8:
The structure of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
(pdb code 6ll8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form, PDB code: 6ll8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 6ll8
Go back to
Magnesium Binding Sites List in 6ll8
Magnesium binding site 1 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:6.6
occ:1.00
|
O1
|
A:2PN407
|
2.0
|
8.0
|
1.0
|
F
|
A:F411
|
2.0
|
7.4
|
1.0
|
OD2
|
A:ASP72
|
2.0
|
7.3
|
1.0
|
OD2
|
A:ASP12
|
2.1
|
7.9
|
1.0
|
NE2
|
A:HIS8
|
2.2
|
7.1
|
1.0
|
OD1
|
A:ASP12
|
2.4
|
7.8
|
1.0
|
CG
|
A:ASP12
|
2.6
|
7.5
|
1.0
|
CG
|
A:ASP72
|
3.0
|
7.5
|
1.0
|
P1
|
A:2PN407
|
3.1
|
7.6
|
1.0
|
CD2
|
A:HIS8
|
3.2
|
6.8
|
1.0
|
CE1
|
A:HIS8
|
3.3
|
7.5
|
1.0
|
MG
|
A:MG404
|
3.3
|
10.4
|
1.0
|
OD1
|
A:ASP72
|
3.3
|
8.1
|
1.0
|
MG
|
A:MG402
|
3.5
|
7.3
|
1.0
|
O2
|
A:2PN407
|
3.6
|
7.9
|
1.0
|
O3
|
A:2PN407
|
3.6
|
8.0
|
1.0
|
OG
|
A:SER15
|
4.0
|
8.2
|
1.0
|
CB
|
A:ASP12
|
4.1
|
7.7
|
1.0
|
O
|
A:HOH596
|
4.1
|
9.1
|
1.0
|
NZ
|
A:LYS203
|
4.2
|
9.0
|
1.0
|
CB
|
A:ASP14
|
4.2
|
7.3
|
1.0
|
CB
|
A:ASP72
|
4.3
|
7.5
|
1.0
|
CG
|
A:HIS8
|
4.3
|
7.3
|
1.0
|
ND1
|
A:HIS8
|
4.4
|
7.6
|
1.0
|
N1
|
A:2PN407
|
4.5
|
7.3
|
1.0
|
N
|
A:SER15
|
4.5
|
7.6
|
1.0
|
O
|
A:ASP72
|
4.6
|
7.7
|
1.0
|
OD2
|
A:ASP14
|
4.6
|
8.3
|
1.0
|
CE
|
A:LYS203
|
4.6
|
9.5
|
1.0
|
O
|
A:HOH574
|
4.6
|
11.3
|
1.0
|
CB
|
A:SER15
|
4.8
|
8.5
|
1.0
|
CE1
|
A:HIS95
|
4.8
|
8.0
|
1.0
|
OD1
|
A:ASP146
|
4.8
|
11.5
|
1.0
|
N
|
A:ASP12
|
4.8
|
7.7
|
1.0
|
OD2
|
A:ASP146
|
4.9
|
8.7
|
1.0
|
CG
|
A:ASP14
|
4.9
|
8.9
|
1.0
|
CA
|
A:ASP12
|
4.9
|
7.6
|
1.0
|
MG
|
A:MG403
|
5.0
|
8.2
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 6ll8
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Magnesium Binding Sites List in 6ll8
Magnesium binding site 2 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:7.3
occ:1.00
|
F
|
A:F411
|
2.0
|
7.4
|
1.0
|
O3
|
A:2PN407
|
2.0
|
8.0
|
1.0
|
OD2
|
A:ASP14
|
2.1
|
8.3
|
1.0
|
OD2
|
A:ASP146
|
2.1
|
8.7
|
1.0
|
OD1
|
A:ASP72
|
2.2
|
8.1
|
1.0
|
NE2
|
A:HIS94
|
2.2
|
7.1
|
1.0
|
CE1
|
A:HIS94
|
3.1
|
6.8
|
1.0
|
CG
|
A:ASP72
|
3.1
|
7.5
|
1.0
|
CG
|
A:ASP14
|
3.1
|
8.9
|
1.0
|
P1
|
A:2PN407
|
3.2
|
7.6
|
1.0
|
CG
|
A:ASP146
|
3.2
|
9.8
|
1.0
|
CD2
|
A:HIS94
|
3.4
|
6.9
|
1.0
|
OD2
|
A:ASP72
|
3.5
|
7.3
|
1.0
|
CB
|
A:ASP14
|
3.5
|
7.3
|
1.0
|
O1
|
A:2PN407
|
3.5
|
8.0
|
1.0
|
MG
|
A:MG401
|
3.5
|
6.6
|
1.0
|
OD1
|
A:ASP146
|
3.6
|
11.5
|
1.0
|
MG
|
A:MG404
|
3.7
|
10.4
|
1.0
|
O2
|
A:2PN407
|
3.8
|
7.9
|
1.0
|
OG
|
A:SER116
|
4.1
|
9.0
|
1.0
|
CE1
|
A:HIS95
|
4.2
|
8.0
|
1.0
|
N
|
A:SER116
|
4.3
|
7.6
|
1.0
|
OD1
|
A:ASP14
|
4.3
|
10.4
|
1.0
|
O
|
A:HOH800
|
4.3
|
10.4
|
1.0
|
ND1
|
A:HIS94
|
4.3
|
7.7
|
1.0
|
CB
|
A:ASP72
|
4.4
|
7.5
|
1.0
|
NZ
|
A:LYS294
|
4.5
|
9.2
|
1.0
|
CG
|
A:HIS94
|
4.5
|
6.8
|
1.0
|
N1
|
A:2PN407
|
4.5
|
7.3
|
1.0
|
CB
|
A:ASP146
|
4.5
|
9.4
|
1.0
|
OD2
|
A:ASP12
|
4.7
|
7.9
|
1.0
|
CA
|
A:CYS115
|
4.8
|
7.6
|
1.0
|
CB
|
A:SER116
|
4.8
|
8.7
|
1.0
|
CA
|
A:ASP14
|
4.9
|
7.7
|
1.0
|
NE2
|
A:HIS95
|
5.0
|
8.7
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 6ll8
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Magnesium Binding Sites List in 6ll8
Magnesium binding site 3 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:8.2
occ:1.00
|
O2
|
A:2PN407
|
2.0
|
7.9
|
1.0
|
O5
|
A:2PN407
|
2.0
|
8.3
|
1.0
|
O
|
A:HOH540
|
2.1
|
9.8
|
1.0
|
O
|
A:HOH596
|
2.1
|
9.1
|
1.0
|
O
|
A:HOH803
|
2.1
|
10.2
|
1.0
|
O
|
A:HOH735
|
2.2
|
10.8
|
1.0
|
P1
|
A:2PN407
|
3.3
|
7.6
|
1.0
|
P2
|
A:2PN407
|
3.3
|
8.4
|
1.0
|
MG
|
A:MG404
|
3.3
|
10.4
|
1.0
|
N1
|
A:2PN407
|
3.5
|
7.3
|
1.0
|
O
|
A:HOH595
|
3.7
|
9.0
|
1.0
|
NH2
|
A:ARG293
|
3.8
|
8.8
|
1.0
|
O
|
A:HOH800
|
3.8
|
10.4
|
1.0
|
O
|
A:HOH549
|
3.9
|
13.1
|
1.0
|
OD2
|
A:ASP12
|
4.0
|
7.9
|
1.0
|
O1
|
A:2PN407
|
4.0
|
8.0
|
1.0
|
O
|
A:HOH798
|
4.1
|
15.7
|
1.0
|
OD2
|
A:ASP201
|
4.2
|
12.9
|
1.0
|
O6
|
A:2PN407
|
4.2
|
9.0
|
1.0
|
OD1
|
A:ASP201
|
4.3
|
10.9
|
1.0
|
OE1
|
A:GLN216
|
4.4
|
11.8
|
1.0
|
O4
|
A:2PN407
|
4.4
|
9.4
|
1.0
|
O3
|
A:2PN407
|
4.4
|
8.0
|
1.0
|
CG
|
A:ASP201
|
4.7
|
10.8
|
1.0
|
OD1
|
A:ASP146
|
4.8
|
11.5
|
1.0
|
F
|
A:F411
|
4.8
|
7.4
|
1.0
|
CZ
|
A:ARG293
|
4.9
|
8.2
|
1.0
|
MG
|
A:MG401
|
5.0
|
6.6
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 6ll8
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Magnesium Binding Sites List in 6ll8
Magnesium binding site 4 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:10.4
occ:1.00
|
OD1
|
A:ASP146
|
2.2
|
11.5
|
1.0
|
F
|
A:F411
|
2.2
|
7.4
|
1.0
|
O2
|
A:2PN407
|
2.3
|
7.9
|
1.0
|
O
|
A:HOH735
|
2.4
|
10.8
|
1.0
|
O
|
A:HOH574
|
2.4
|
11.3
|
1.0
|
OD2
|
A:ASP12
|
2.4
|
7.9
|
1.0
|
CG
|
A:ASP12
|
3.1
|
7.5
|
1.0
|
CG
|
A:ASP146
|
3.1
|
9.8
|
1.0
|
P1
|
A:2PN407
|
3.2
|
7.6
|
1.0
|
MG
|
A:MG401
|
3.3
|
6.6
|
1.0
|
MG
|
A:MG403
|
3.3
|
8.2
|
1.0
|
OD2
|
A:ASP146
|
3.5
|
8.7
|
1.0
|
O
|
A:HOH596
|
3.6
|
9.1
|
1.0
|
O1
|
A:2PN407
|
3.6
|
8.0
|
1.0
|
O3
|
A:2PN407
|
3.7
|
8.0
|
1.0
|
OD1
|
A:ASP12
|
3.7
|
7.8
|
1.0
|
MG
|
A:MG402
|
3.7
|
7.3
|
1.0
|
CB
|
A:ASP12
|
3.9
|
7.7
|
1.0
|
O
|
A:HOH800
|
4.0
|
10.4
|
1.0
|
CB
|
A:ASP14
|
4.1
|
7.3
|
1.0
|
O
|
A:HOH803
|
4.2
|
10.2
|
1.0
|
CB
|
A:ASP146
|
4.4
|
9.4
|
1.0
|
O
|
A:HOH798
|
4.4
|
15.7
|
1.0
|
CA
|
A:ASP146
|
4.5
|
9.1
|
1.0
|
O
|
A:HOH510
|
4.6
|
29.3
|
1.0
|
O
|
A:HOH549
|
4.6
|
13.1
|
1.0
|
N
|
A:ASP14
|
4.7
|
7.7
|
1.0
|
N1
|
A:2PN407
|
4.7
|
7.3
|
1.0
|
OD2
|
A:ASP72
|
4.8
|
7.3
|
1.0
|
OD2
|
A:ASP14
|
4.9
|
8.3
|
1.0
|
O5
|
A:2PN407
|
4.9
|
8.3
|
1.0
|
O
|
A:HOH540
|
5.0
|
9.8
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 6ll8
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Magnesium Binding Sites List in 6ll8
Magnesium binding site 5 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:14.4
occ:1.00
|
O
|
A:HOH909
|
2.9
|
21.8
|
1.0
|
N
|
A:GLU44
|
3.3
|
9.5
|
1.0
|
O
|
A:HOH533
|
3.3
|
21.3
|
1.0
|
CD
|
A:PRO43
|
3.5
|
11.7
|
1.0
|
CB
|
A:GLU44
|
3.7
|
10.7
|
1.0
|
CG
|
A:LYS186
|
3.8
|
13.0
|
1.0
|
N
|
A:PRO43
|
3.8
|
9.8
|
1.0
|
CB
|
A:PRO43
|
3.8
|
12.2
|
1.0
|
CA
|
A:LYS186
|
3.9
|
10.0
|
1.0
|
CD
|
A:ARG200
|
3.9
|
13.9
|
1.0
|
O
|
A:HOH561
|
3.9
|
25.8
|
1.0
|
CB
|
A:SER42
|
4.0
|
11.5
|
1.0
|
CG
|
A:PRO43
|
4.0
|
14.1
|
1.0
|
CA
|
A:GLU44
|
4.1
|
9.5
|
1.0
|
CA
|
A:PRO43
|
4.1
|
10.2
|
1.0
|
C
|
A:PRO43
|
4.1
|
9.6
|
1.0
|
OG
|
A:SER42
|
4.2
|
12.6
|
1.0
|
CB
|
A:LYS186
|
4.3
|
10.6
|
1.0
|
O
|
A:HOH918
|
4.4
|
25.1
|
1.0
|
NH1
|
A:ARG200
|
4.4
|
17.4
|
1.0
|
N
|
A:LYS186
|
4.5
|
9.6
|
1.0
|
NE
|
A:ARG200
|
4.5
|
14.8
|
1.0
|
C
|
A:SER42
|
4.5
|
10.2
|
1.0
|
O
|
A:VAL185
|
4.7
|
10.5
|
1.0
|
CZ
|
A:ARG200
|
4.7
|
15.0
|
1.0
|
CA
|
A:SER42
|
4.7
|
10.8
|
1.0
|
CG
|
A:ARG200
|
4.8
|
12.2
|
1.0
|
C
|
A:VAL185
|
4.8
|
10.0
|
1.0
|
CG1
|
A:VAL185
|
4.8
|
11.0
|
1.0
|
O
|
A:LYS186
|
4.8
|
11.8
|
1.0
|
C
|
A:LYS186
|
4.9
|
10.4
|
1.0
|
CD
|
A:LYS186
|
4.9
|
14.9
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 6ll8
Go back to
Magnesium Binding Sites List in 6ll8
Magnesium binding site 6 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:7.1
occ:1.00
|
F
|
B:F410
|
2.0
|
8.1
|
1.0
|
OD2
|
B:ASP72
|
2.0
|
8.1
|
1.0
|
O2
|
B:2PN406
|
2.0
|
8.4
|
1.0
|
OD2
|
B:ASP12
|
2.1
|
8.6
|
1.0
|
NE2
|
B:HIS8
|
2.2
|
8.1
|
1.0
|
OD1
|
B:ASP12
|
2.4
|
8.2
|
1.0
|
CG
|
B:ASP12
|
2.6
|
8.0
|
1.0
|
CG
|
B:ASP72
|
3.0
|
7.8
|
1.0
|
P1
|
B:2PN406
|
3.1
|
8.1
|
1.0
|
CD2
|
B:HIS8
|
3.2
|
7.5
|
1.0
|
MG
|
B:MG404
|
3.3
|
10.7
|
1.0
|
CE1
|
B:HIS8
|
3.3
|
8.0
|
1.0
|
OD1
|
B:ASP72
|
3.3
|
8.5
|
1.0
|
MG
|
B:MG402
|
3.5
|
7.9
|
1.0
|
O1
|
B:2PN406
|
3.6
|
8.3
|
1.0
|
O3
|
B:2PN406
|
3.6
|
8.7
|
1.0
|
OG
|
B:SER15
|
4.0
|
8.8
|
1.0
|
CB
|
B:ASP12
|
4.1
|
8.0
|
1.0
|
O
|
B:HOH584
|
4.1
|
9.5
|
1.0
|
NZ
|
B:LYS203
|
4.2
|
9.6
|
1.0
|
CB
|
B:ASP14
|
4.2
|
8.7
|
1.0
|
CB
|
B:ASP72
|
4.3
|
7.9
|
1.0
|
CG
|
B:HIS8
|
4.3
|
7.7
|
1.0
|
ND1
|
B:HIS8
|
4.4
|
7.8
|
1.0
|
N1
|
B:2PN406
|
4.5
|
7.6
|
1.0
|
N
|
B:SER15
|
4.5
|
8.2
|
1.0
|
O
|
B:ASP72
|
4.6
|
8.1
|
1.0
|
OD2
|
B:ASP14
|
4.6
|
8.6
|
1.0
|
CE
|
B:LYS203
|
4.6
|
9.8
|
1.0
|
O
|
B:HOH561
|
4.7
|
11.8
|
1.0
|
CB
|
B:SER15
|
4.7
|
8.4
|
1.0
|
CE1
|
B:HIS95
|
4.8
|
8.9
|
1.0
|
OD1
|
B:ASP146
|
4.8
|
12.3
|
1.0
|
N
|
B:ASP12
|
4.9
|
8.1
|
1.0
|
OD2
|
B:ASP146
|
4.9
|
9.3
|
1.0
|
CG
|
B:ASP14
|
4.9
|
8.9
|
1.0
|
CA
|
B:ASP12
|
5.0
|
8.1
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 6ll8
Go back to
Magnesium Binding Sites List in 6ll8
Magnesium binding site 7 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:7.9
occ:1.00
|
F
|
B:F410
|
2.0
|
8.1
|
1.0
|
O3
|
B:2PN406
|
2.1
|
8.7
|
1.0
|
OD2
|
B:ASP14
|
2.1
|
8.6
|
1.0
|
OD2
|
B:ASP146
|
2.1
|
9.3
|
1.0
|
OD1
|
B:ASP72
|
2.2
|
8.5
|
1.0
|
NE2
|
B:HIS94
|
2.2
|
7.2
|
1.0
|
CE1
|
B:HIS94
|
3.1
|
7.4
|
1.0
|
CG
|
B:ASP14
|
3.1
|
8.9
|
1.0
|
CG
|
B:ASP72
|
3.1
|
7.8
|
1.0
|
P1
|
B:2PN406
|
3.2
|
8.1
|
1.0
|
CG
|
B:ASP146
|
3.2
|
9.7
|
1.0
|
CD2
|
B:HIS94
|
3.4
|
7.4
|
1.0
|
CB
|
B:ASP14
|
3.4
|
8.7
|
1.0
|
OD2
|
B:ASP72
|
3.5
|
8.1
|
1.0
|
MG
|
B:MG401
|
3.5
|
7.1
|
1.0
|
O2
|
B:2PN406
|
3.5
|
8.4
|
1.0
|
OD1
|
B:ASP146
|
3.6
|
12.3
|
1.0
|
MG
|
B:MG404
|
3.7
|
10.7
|
1.0
|
O1
|
B:2PN406
|
3.8
|
8.3
|
1.0
|
OG
|
B:SER116
|
4.1
|
9.4
|
1.0
|
CE1
|
B:HIS95
|
4.2
|
8.9
|
1.0
|
OD1
|
B:ASP14
|
4.2
|
10.6
|
1.0
|
N
|
B:SER116
|
4.2
|
7.8
|
1.0
|
O
|
B:HOH790
|
4.3
|
11.2
|
1.0
|
ND1
|
B:HIS94
|
4.3
|
7.7
|
1.0
|
CB
|
B:ASP72
|
4.4
|
7.9
|
1.0
|
CG
|
B:HIS94
|
4.5
|
6.9
|
1.0
|
NZ
|
B:LYS294
|
4.5
|
9.1
|
1.0
|
CB
|
B:ASP146
|
4.5
|
9.5
|
1.0
|
N1
|
B:2PN406
|
4.5
|
7.6
|
1.0
|
CA
|
B:CYS115
|
4.8
|
8.4
|
1.0
|
OD2
|
B:ASP12
|
4.8
|
8.6
|
1.0
|
CB
|
B:SER116
|
4.8
|
8.8
|
1.0
|
CA
|
B:ASP14
|
4.9
|
8.5
|
1.0
|
NE2
|
B:HIS95
|
5.0
|
9.3
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 6ll8
Go back to
Magnesium Binding Sites List in 6ll8
Magnesium binding site 8 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg403
b:8.8
occ:1.00
|
O1
|
B:2PN406
|
2.0
|
8.3
|
1.0
|
O4
|
B:2PN406
|
2.0
|
8.9
|
1.0
|
O
|
B:HOH535
|
2.1
|
10.6
|
1.0
|
O
|
B:HOH584
|
2.1
|
9.5
|
1.0
|
O
|
B:HOH791
|
2.1
|
10.7
|
1.0
|
O
|
B:HOH714
|
2.1
|
11.2
|
1.0
|
P1
|
B:2PN406
|
3.3
|
8.1
|
1.0
|
P2
|
B:2PN406
|
3.3
|
8.9
|
1.0
|
MG
|
B:MG404
|
3.3
|
10.7
|
1.0
|
N1
|
B:2PN406
|
3.5
|
7.6
|
1.0
|
O
|
B:HOH568
|
3.7
|
9.7
|
1.0
|
NH1
|
B:ARG293
|
3.8
|
9.5
|
1.0
|
O
|
B:HOH790
|
3.9
|
11.2
|
1.0
|
O
|
B:HOH537
|
3.9
|
13.9
|
1.0
|
OD2
|
B:ASP12
|
4.0
|
8.6
|
1.0
|
O2
|
B:2PN406
|
4.0
|
8.4
|
1.0
|
O
|
B:HOH807
|
4.1
|
16.5
|
1.0
|
OD2
|
B:ASP201
|
4.1
|
13.9
|
1.0
|
O5
|
B:2PN406
|
4.2
|
9.8
|
1.0
|
OD1
|
B:ASP201
|
4.3
|
11.5
|
1.0
|
OE1
|
B:GLN216
|
4.3
|
11.5
|
1.0
|
O6
|
B:2PN406
|
4.4
|
9.4
|
1.0
|
O3
|
B:2PN406
|
4.4
|
8.7
|
1.0
|
CG
|
B:ASP201
|
4.6
|
11.7
|
1.0
|
OD1
|
B:ASP146
|
4.8
|
12.3
|
1.0
|
F
|
B:F410
|
4.8
|
8.1
|
1.0
|
CZ
|
B:ARG293
|
4.9
|
9.6
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 6ll8
Go back to
Magnesium Binding Sites List in 6ll8
Magnesium binding site 9 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg404
b:10.7
occ:1.00
|
OD1
|
B:ASP146
|
2.2
|
12.3
|
1.0
|
F
|
B:F410
|
2.2
|
8.1
|
1.0
|
O1
|
B:2PN406
|
2.3
|
8.3
|
1.0
|
O
|
B:HOH714
|
2.4
|
11.2
|
1.0
|
OD2
|
B:ASP12
|
2.4
|
8.6
|
1.0
|
O
|
B:HOH561
|
2.4
|
11.8
|
1.0
|
CG
|
B:ASP12
|
3.1
|
8.0
|
1.0
|
CG
|
B:ASP146
|
3.1
|
9.7
|
1.0
|
P1
|
B:2PN406
|
3.2
|
8.1
|
1.0
|
MG
|
B:MG401
|
3.3
|
7.1
|
1.0
|
MG
|
B:MG403
|
3.3
|
8.8
|
1.0
|
OD2
|
B:ASP146
|
3.5
|
9.3
|
1.0
|
O
|
B:HOH584
|
3.6
|
9.5
|
1.0
|
O2
|
B:2PN406
|
3.6
|
8.4
|
1.0
|
O3
|
B:2PN406
|
3.6
|
8.7
|
1.0
|
OD1
|
B:ASP12
|
3.7
|
8.2
|
1.0
|
MG
|
B:MG402
|
3.7
|
7.9
|
1.0
|
O
|
B:HOH790
|
3.9
|
11.2
|
1.0
|
CB
|
B:ASP12
|
3.9
|
8.0
|
1.0
|
CB
|
B:ASP14
|
4.1
|
8.7
|
1.0
|
O
|
B:HOH791
|
4.2
|
10.7
|
1.0
|
CB
|
B:ASP146
|
4.4
|
9.5
|
1.0
|
O
|
B:HOH807
|
4.4
|
16.5
|
1.0
|
CA
|
B:ASP146
|
4.5
|
9.9
|
1.0
|
O
|
B:HOH537
|
4.6
|
13.9
|
1.0
|
O
|
B:HOH585
|
4.7
|
22.0
|
1.0
|
N1
|
B:2PN406
|
4.7
|
7.6
|
1.0
|
N
|
B:ASP14
|
4.7
|
8.3
|
1.0
|
OD2
|
B:ASP72
|
4.8
|
8.1
|
1.0
|
OD2
|
B:ASP14
|
4.9
|
8.6
|
1.0
|
O4
|
B:2PN406
|
4.9
|
8.9
|
1.0
|
O
|
B:HOH535
|
5.0
|
10.6
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 6ll8
Go back to
Magnesium Binding Sites List in 6ll8
Magnesium binding site 10 out
of 10 in the Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Type II Inorganic Pyrophosphatase (Ppase) From the Psychrophilic Bacterium Shewanella Sp. As-11, Mg-Pnp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg405
b:15.0
occ:1.00
|
O
|
B:HOH903
|
2.9
|
17.2
|
0.5
|
N
|
B:GLU44
|
3.3
|
10.3
|
1.0
|
O
|
B:HOH543
|
3.3
|
20.7
|
1.0
|
NZ
|
B:LYS186
|
3.4
|
17.1
|
0.4
|
CD
|
B:PRO43
|
3.5
|
12.8
|
1.0
|
CG
|
B:LYS186
|
3.8
|
13.5
|
0.4
|
O
|
B:HOH587
|
3.8
|
28.0
|
1.0
|
CB
|
B:GLU44
|
3.8
|
11.1
|
1.0
|
CG
|
B:LYS186
|
3.8
|
14.2
|
0.6
|
CB
|
B:PRO43
|
3.8
|
13.0
|
1.0
|
N
|
B:PRO43
|
3.8
|
11.3
|
1.0
|
CA
|
B:LYS186
|
3.8
|
11.4
|
0.6
|
CA
|
B:LYS186
|
3.8
|
11.3
|
0.4
|
CD
|
B:ARG200
|
3.9
|
13.7
|
1.0
|
CB
|
B:SER42
|
4.0
|
12.8
|
1.0
|
CG
|
B:PRO43
|
4.0
|
13.7
|
1.0
|
CA
|
B:GLU44
|
4.1
|
10.4
|
1.0
|
C
|
B:PRO43
|
4.2
|
10.7
|
1.0
|
CA
|
B:PRO43
|
4.2
|
10.8
|
1.0
|
OG
|
B:SER42
|
4.2
|
13.1
|
1.0
|
CB
|
B:LYS186
|
4.2
|
12.1
|
0.6
|
CB
|
B:LYS186
|
4.2
|
11.9
|
0.4
|
NE
|
B:ARG200
|
4.4
|
14.5
|
1.0
|
NH1
|
B:ARG200
|
4.4
|
16.6
|
1.0
|
N
|
B:LYS186
|
4.5
|
10.7
|
1.0
|
C
|
B:SER42
|
4.5
|
11.3
|
1.0
|
CE
|
B:LYS186
|
4.6
|
19.1
|
0.4
|
CZ
|
B:ARG200
|
4.6
|
15.9
|
1.0
|
O
|
B:VAL185
|
4.7
|
11.2
|
1.0
|
CA
|
B:SER42
|
4.7
|
11.2
|
1.0
|
CD
|
B:LYS186
|
4.8
|
14.3
|
0.4
|
CG
|
B:ARG200
|
4.8
|
12.3
|
1.0
|
O
|
B:LYS186
|
4.8
|
12.5
|
1.0
|
C
|
B:VAL185
|
4.8
|
10.9
|
1.0
|
C
|
B:LYS186
|
4.9
|
11.1
|
1.0
|
CG1
|
B:VAL185
|
4.9
|
11.5
|
1.0
|
CD
|
B:LYS186
|
5.0
|
14.1
|
0.6
|
|
Reference:
M.Horitani,
K.Kusubayashi,
K.Oshima,
A.Yato,
H.Sugimoto,
K.Watanabe.
X-Ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase. Sci Rep V. 10 4368 2020.
ISSN: ESSN 2045-2322
PubMed: 32152422
DOI: 10.1038/S41598-020-61217-6
Page generated: Tue Oct 1 10:29:58 2024
|