Manganese in PDB 1e9g: Structure of Inorganic Pyrophosphatase
Enzymatic activity of Structure of Inorganic Pyrophosphatase
All present enzymatic activity of Structure of Inorganic Pyrophosphatase:
3.6.1.1;
Protein crystallography data
The structure of Structure of Inorganic Pyrophosphatase, PDB code: 1e9g
was solved by
P.Heikinheimo,
V.Tuominen,
A.-K.Ahonen,
A.Teplyakov,
B.S.Cooperman,
A.A.Baykov,
R.Lahti,
A.Goldman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
8.00 /
1.15
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.318,
103.087,
116.518,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
n/a /
n/a
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Structure of Inorganic Pyrophosphatase
(pdb code 1e9g). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the
Structure of Inorganic Pyrophosphatase, PDB code: 1e9g:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Manganese binding site 1 out
of 9 in 1e9g
Go back to
Manganese Binding Sites List in 1e9g
Manganese binding site 1 out
of 9 in the Structure of Inorganic Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1001
b:8.6
occ:1.00
|
OD1
|
A:ASP152
|
2.1
|
9.6
|
1.0
|
|
OD2
|
A:ASP120
|
2.1
|
8.4
|
1.0
|
|
O2
|
A:PO43002
|
2.2
|
7.2
|
0.3
|
|
OD2
|
A:ASP115
|
2.2
|
8.8
|
0.6
|
|
O2
|
A:PO43002
|
2.2
|
10.2
|
0.7
|
|
O
|
A:HOH2507
|
2.2
|
8.9
|
1.0
|
|
O
|
A:HOH2523
|
2.2
|
10.7
|
0.7
|
|
OD2
|
A:ASP115
|
2.2
|
7.6
|
0.4
|
|
O4
|
A:PO43002
|
2.4
|
9.4
|
0.3
|
|
P
|
A:PO43002
|
2.8
|
8.8
|
0.3
|
|
CG
|
A:ASP120
|
3.1
|
7.0
|
1.0
|
|
CG
|
A:ASP152
|
3.1
|
9.4
|
1.0
|
|
CG
|
A:ASP115
|
3.2
|
8.3
|
0.4
|
|
CG
|
A:ASP115
|
3.2
|
8.3
|
0.6
|
|
P
|
A:PO43002
|
3.3
|
8.3
|
0.7
|
|
HZ1
|
A:LYS154
|
3.3
|
19.4
|
1.0
|
|
O4
|
A:PO43002
|
3.3
|
9.7
|
0.7
|
|
OD1
|
A:ASP120
|
3.4
|
8.5
|
1.0
|
|
OD2
|
A:ASP152
|
3.5
|
8.7
|
1.0
|
|
O1
|
A:PO43002
|
3.5
|
7.3
|
0.3
|
|
OD1
|
A:ASP115
|
3.6
|
9.6
|
0.6
|
|
OD1
|
A:ASP115
|
3.7
|
11.5
|
0.4
|
|
O
|
A:HOH2519
|
3.7
|
10.0
|
1.0
|
|
HB2
|
A:ASP117
|
3.7
|
10.9
|
0.4
|
|
MN
|
A:MN1002
|
3.7
|
9.1
|
1.0
|
|
MN
|
A:MN1004
|
3.7
|
9.0
|
1.0
|
|
HZ2
|
A:LYS154
|
3.8
|
19.4
|
1.0
|
|
HB2
|
A:ASP117
|
3.8
|
11.5
|
0.6
|
|
O3
|
A:PO43002
|
3.9
|
10.9
|
0.7
|
|
NZ
|
A:LYS154
|
3.9
|
13.0
|
1.0
|
|
HZ3
|
A:LYS154
|
4.0
|
19.4
|
1.0
|
|
O3
|
A:PO43002
|
4.1
|
7.9
|
0.3
|
|
O
|
A:HOH2272
|
4.1
|
10.3
|
1.0
|
|
HH
|
A:TYR93
|
4.1
|
15.0
|
1.0
|
|
HB3
|
A:ASP117
|
4.2
|
10.9
|
0.4
|
|
OD2
|
A:ASP117
|
4.2
|
12.5
|
0.4
|
|
HA
|
A:ASP152
|
4.2
|
9.7
|
1.0
|
|
CB
|
A:ASP117
|
4.4
|
9.1
|
0.4
|
|
HB3
|
A:ASP117
|
4.4
|
11.5
|
0.6
|
|
CB
|
A:ASP115
|
4.4
|
8.4
|
0.4
|
|
CB
|
A:ASP152
|
4.4
|
8.2
|
1.0
|
|
CB
|
A:ASP120
|
4.4
|
7.8
|
1.0
|
|
CB
|
A:ASP115
|
4.5
|
8.6
|
0.6
|
|
O
|
A:HOH2509
|
4.5
|
9.6
|
1.0
|
|
HB2
|
A:ASP115
|
4.5
|
10.1
|
0.4
|
|
HB3
|
A:ASP115
|
4.5
|
10.1
|
0.4
|
|
HB2
|
A:ASP120
|
4.5
|
9.3
|
1.0
|
|
O1
|
A:PO43002
|
4.6
|
9.1
|
0.7
|
|
CB
|
A:ASP117
|
4.6
|
9.6
|
0.6
|
|
O
|
A:PRO118
|
4.6
|
8.1
|
0.4
|
|
OH
|
A:TYR93
|
4.6
|
10.0
|
1.0
|
|
HG3
|
A:GLU101
|
4.6
|
10.6
|
1.0
|
|
O
|
A:PRO118
|
4.6
|
8.7
|
0.6
|
|
OD2
|
A:ASP117
|
4.6
|
13.8
|
0.6
|
|
HB2
|
A:ASP115
|
4.7
|
10.3
|
0.6
|
|
HB3
|
A:ASP115
|
4.7
|
10.3
|
0.6
|
|
CG
|
A:ASP117
|
4.7
|
9.4
|
0.4
|
|
O
|
A:HOH2518
|
4.8
|
9.8
|
1.0
|
|
HB2
|
A:ASP152
|
4.8
|
9.8
|
1.0
|
|
CA
|
A:ASP152
|
4.8
|
8.1
|
1.0
|
|
HB3
|
A:ASP120
|
4.9
|
9.3
|
1.0
|
|
H
|
A:ASP120
|
5.0
|
9.7
|
1.0
|
|
O1
|
A:PO43001
|
5.0
|
5.5
|
0.7
|
|
Manganese binding site 2 out
of 9 in 1e9g
Go back to
Manganese Binding Sites List in 1e9g
Manganese binding site 2 out
of 9 in the Structure of Inorganic Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1002
b:9.1
occ:1.00
|
O1
|
A:PO43002
|
2.1
|
7.3
|
0.3
|
|
O
|
A:HOH2510
|
2.1
|
10.9
|
1.0
|
|
O
|
A:HOH2509
|
2.1
|
9.6
|
1.0
|
|
OD1
|
A:ASP120
|
2.2
|
8.5
|
1.0
|
|
O4
|
A:PO43002
|
2.2
|
9.4
|
0.3
|
|
O4
|
A:PO43002
|
2.2
|
9.7
|
0.7
|
|
O
|
A:HOH2508
|
2.2
|
17.0
|
1.0
|
|
O
|
A:HOH2523
|
2.4
|
10.7
|
0.7
|
|
P
|
A:PO43002
|
2.6
|
8.8
|
0.3
|
|
CG
|
A:ASP120
|
3.2
|
7.0
|
1.0
|
|
HH
|
A:TYR93
|
3.3
|
15.0
|
1.0
|
|
P
|
A:PO43002
|
3.4
|
8.3
|
0.7
|
|
HE2
|
A:TYR93
|
3.6
|
9.2
|
1.0
|
|
O3
|
A:PO43002
|
3.6
|
7.9
|
0.3
|
|
O3
|
A:PO43002
|
3.6
|
10.9
|
0.7
|
|
OD2
|
A:ASP120
|
3.6
|
8.4
|
1.0
|
|
MN
|
A:MN1001
|
3.7
|
8.6
|
1.0
|
|
HB3
|
A:ASP117
|
3.8
|
10.9
|
0.4
|
|
O2
|
A:PO43002
|
3.8
|
7.2
|
0.3
|
|
HB3
|
A:ASP117
|
3.9
|
11.5
|
0.6
|
|
O
|
A:HOH2154
|
3.9
|
10.2
|
1.0
|
|
OH
|
A:TYR93
|
4.0
|
10.0
|
1.0
|
|
O2
|
A:PO43002
|
4.0
|
10.2
|
0.7
|
|
HB2
|
A:ALA95
|
4.1
|
17.1
|
1.0
|
|
OD2
|
A:ASP117
|
4.2
|
12.5
|
0.4
|
|
HZ2
|
A:LYS56
|
4.2
|
32.7
|
1.0
|
|
O
|
A:PRO118
|
4.2
|
8.7
|
0.6
|
|
O
|
A:HOH2507
|
4.2
|
8.9
|
1.0
|
|
HA
|
A:ASP120
|
4.3
|
9.8
|
1.0
|
|
OE1
|
A:GLU48
|
4.3
|
9.5
|
1.0
|
|
CE2
|
A:TYR93
|
4.3
|
7.7
|
1.0
|
|
O
|
A:PRO118
|
4.3
|
8.1
|
0.4
|
|
OD2
|
A:ASP117
|
4.4
|
13.8
|
0.6
|
|
CB
|
A:ASP120
|
4.4
|
7.8
|
1.0
|
|
O
|
A:HOH2180
|
4.4
|
12.3
|
1.0
|
|
HB3
|
A:ASP120
|
4.5
|
9.3
|
1.0
|
|
HZ1
|
A:LYS56
|
4.6
|
32.7
|
1.0
|
|
O1
|
A:PO43002
|
4.6
|
9.1
|
0.7
|
|
CB
|
A:ASP117
|
4.6
|
9.6
|
0.6
|
|
HB2
|
A:ASP117
|
4.6
|
11.5
|
0.6
|
|
CZ
|
A:TYR93
|
4.6
|
8.2
|
1.0
|
|
CB
|
A:ASP117
|
4.6
|
9.1
|
0.4
|
|
OE2
|
A:GLU48
|
4.6
|
10.5
|
1.0
|
|
CG
|
A:ASP117
|
4.6
|
9.2
|
0.6
|
|
O
|
A:HOH2173
|
4.7
|
10.7
|
1.0
|
|
NZ
|
A:LYS56
|
4.7
|
21.8
|
1.0
|
|
O
|
A:GLY94
|
4.7
|
8.2
|
1.0
|
|
HB2
|
A:ASP117
|
4.7
|
10.9
|
0.4
|
|
HD2
|
A:PRO118
|
4.8
|
11.0
|
0.6
|
|
CG
|
A:ASP117
|
4.8
|
9.4
|
0.4
|
|
CA
|
A:ASP120
|
4.8
|
8.2
|
1.0
|
|
HZ3
|
A:LYS56
|
4.8
|
32.7
|
1.0
|
|
HD2
|
A:PRO118
|
4.9
|
10.5
|
0.4
|
|
HB2
|
A:PRO118
|
4.9
|
10.1
|
0.6
|
|
CD
|
A:GLU48
|
4.9
|
8.6
|
1.0
|
|
HB2
|
A:GLU58
|
4.9
|
11.4
|
0.5
|
|
Manganese binding site 3 out
of 9 in 1e9g
Go back to
Manganese Binding Sites List in 1e9g
Manganese binding site 3 out
of 9 in the Structure of Inorganic Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1003
b:11.2
occ:0.70
|
MN
|
A:MN1003
|
0.0
|
11.2
|
0.7
|
|
MN
|
A:MN1003
|
2.0
|
8.7
|
0.3
|
|
O4
|
A:PO43001
|
2.1
|
10.3
|
0.7
|
|
O3
|
A:PO43002
|
2.2
|
7.9
|
0.3
|
|
O
|
A:HOH2511
|
2.2
|
17.9
|
1.0
|
|
O
|
A:HOH2514
|
2.2
|
13.4
|
1.0
|
|
O
|
A:HOH2517
|
2.2
|
13.2
|
0.5
|
|
O3
|
A:PO43002
|
2.3
|
10.9
|
0.7
|
|
OE2
|
A:GLU58
|
2.3
|
9.3
|
0.6
|
|
O4
|
A:PO43001
|
2.7
|
9.9
|
0.3
|
|
HZ3
|
A:LYS56
|
3.0
|
32.7
|
1.0
|
|
O3
|
A:PO43001
|
3.2
|
9.9
|
0.3
|
|
CD
|
A:GLU58
|
3.3
|
8.8
|
0.6
|
|
P
|
A:PO43001
|
3.3
|
11.0
|
0.7
|
|
O1
|
A:PO43001
|
3.3
|
5.5
|
0.7
|
|
O
|
A:HOH2512
|
3.4
|
45.5
|
1.0
|
|
P
|
A:PO43001
|
3.5
|
10.7
|
0.3
|
|
HZ2
|
A:LYS56
|
3.5
|
32.7
|
1.0
|
|
OE1
|
A:GLU58
|
3.5
|
14.9
|
0.5
|
|
HH12
|
A:ARG78
|
3.6
|
15.4
|
1.0
|
|
O
|
A:HOH2513
|
3.6
|
17.9
|
0.5
|
|
OE1
|
A:GLU58
|
3.6
|
10.6
|
0.6
|
|
P
|
A:PO43002
|
3.6
|
8.8
|
0.3
|
|
NZ
|
A:LYS56
|
3.6
|
21.8
|
1.0
|
|
P
|
A:PO43002
|
3.6
|
8.3
|
0.7
|
|
HE3
|
A:LYS56
|
3.8
|
21.7
|
1.0
|
|
OD2
|
A:ASP117
|
3.9
|
12.5
|
0.4
|
|
O1
|
A:PO43001
|
3.9
|
12.9
|
0.3
|
|
O
|
A:HOH2516
|
3.9
|
26.0
|
0.5
|
|
O
|
A:HOH2515
|
4.1
|
24.9
|
0.7
|
|
O1
|
A:PO43002
|
4.1
|
9.1
|
0.7
|
|
O4
|
A:PO43002
|
4.1
|
9.4
|
0.3
|
|
O
|
A:HOH2287
|
4.2
|
18.6
|
1.0
|
|
O2
|
A:PO43002
|
4.2
|
7.2
|
0.3
|
|
O3
|
A:PO43001
|
4.2
|
8.8
|
0.7
|
|
OD2
|
A:ASP117
|
4.2
|
13.8
|
0.6
|
|
CE
|
A:LYS56
|
4.3
|
18.1
|
1.0
|
|
NH1
|
A:ARG78
|
4.3
|
12.8
|
1.0
|
|
O2
|
A:PO43001
|
4.3
|
11.4
|
0.7
|
|
O
|
A:HOH2523
|
4.3
|
10.7
|
0.7
|
|
O2
|
A:PO43002
|
4.4
|
10.2
|
0.7
|
|
HH11
|
A:ARG78
|
4.4
|
15.4
|
1.0
|
|
CD
|
A:GLU58
|
4.4
|
9.3
|
0.5
|
|
HZ1
|
A:LYS56
|
4.4
|
32.7
|
1.0
|
|
OD2
|
A:ASP71
|
4.4
|
13.0
|
1.0
|
|
CG
|
A:GLU58
|
4.6
|
10.2
|
0.6
|
|
O
|
A:HOH2508
|
4.6
|
17.0
|
1.0
|
|
OE2
|
A:GLU58
|
4.6
|
14.5
|
0.5
|
|
O
|
A:HOH2175
|
4.6
|
35.8
|
1.0
|
|
HG2
|
A:GLU58
|
4.6
|
12.3
|
0.6
|
|
O1
|
A:PO43002
|
4.7
|
7.3
|
0.3
|
|
O4
|
A:PO43002
|
4.7
|
9.7
|
0.7
|
|
HD2
|
A:LYS56
|
4.7
|
14.6
|
1.0
|
|
O2
|
A:PO43001
|
4.8
|
15.3
|
0.3
|
|
O
|
A:HOH2519
|
5.0
|
10.0
|
1.0
|
|
MN
|
A:MN1004
|
5.0
|
9.0
|
1.0
|
|
O
|
A:HOH2185
|
5.0
|
19.0
|
1.0
|
|
Manganese binding site 4 out
of 9 in 1e9g
Go back to
Manganese Binding Sites List in 1e9g
Manganese binding site 4 out
of 9 in the Structure of Inorganic Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1003
b:8.7
occ:0.29
|
MN
|
A:MN1003
|
0.0
|
8.7
|
0.3
|
|
O
|
A:HOH2517
|
1.5
|
13.2
|
0.5
|
|
MN
|
A:MN1003
|
2.0
|
11.2
|
0.7
|
|
O
|
A:HOH2514
|
2.1
|
13.4
|
1.0
|
|
O
|
A:HOH2513
|
2.1
|
17.9
|
0.5
|
|
O
|
A:HOH2516
|
2.2
|
26.0
|
0.5
|
|
O4
|
A:PO43001
|
2.2
|
9.9
|
0.3
|
|
O
|
A:HOH2515
|
2.3
|
24.9
|
0.7
|
|
O
|
A:HOH2512
|
2.4
|
45.5
|
1.0
|
|
O4
|
A:PO43001
|
2.5
|
10.3
|
0.7
|
|
O
|
A:HOH2511
|
3.1
|
17.9
|
1.0
|
|
HH12
|
A:ARG78
|
3.3
|
15.4
|
1.0
|
|
P
|
A:PO43001
|
3.4
|
11.0
|
0.7
|
|
P
|
A:PO43001
|
3.5
|
10.7
|
0.3
|
|
O1
|
A:PO43001
|
3.6
|
5.5
|
0.7
|
|
O
|
A:HOH2001
|
3.7
|
14.5
|
0.3
|
|
O2
|
A:PO43001
|
3.8
|
11.4
|
0.7
|
|
OE2
|
A:GLU58
|
3.8
|
9.3
|
0.6
|
|
O1
|
A:PO43001
|
4.0
|
12.9
|
0.3
|
|
O3
|
A:PO43002
|
4.0
|
7.9
|
0.3
|
|
O3
|
A:PO43002
|
4.0
|
10.9
|
0.7
|
|
NH1
|
A:ARG78
|
4.0
|
12.8
|
1.0
|
|
OD2
|
A:ASP71
|
4.1
|
13.0
|
1.0
|
|
O3
|
A:PO43001
|
4.1
|
9.9
|
0.3
|
|
HZ2
|
A:LYS73
|
4.1
|
40.1
|
1.0
|
|
O
|
A:HOH2287
|
4.1
|
18.6
|
1.0
|
|
HH11
|
A:ARG78
|
4.1
|
15.4
|
1.0
|
|
O
|
A:HOH2164
|
4.1
|
42.1
|
1.0
|
|
O
|
A:HOH2521
|
4.2
|
26.4
|
1.0
|
|
O
|
A:HOH2175
|
4.2
|
35.8
|
1.0
|
|
O
|
A:HOH2520
|
4.3
|
14.8
|
1.0
|
|
O
|
A:HOH2185
|
4.5
|
19.0
|
1.0
|
|
OE1
|
A:GLU58
|
4.6
|
10.6
|
0.6
|
|
CD
|
A:GLU58
|
4.6
|
8.8
|
0.6
|
|
OE1
|
A:GLU58
|
4.6
|
14.9
|
0.5
|
|
O
|
A:HOH2087
|
4.6
|
32.9
|
1.0
|
|
HZ1
|
A:LYS73
|
4.7
|
40.1
|
1.0
|
|
O2
|
A:PO43001
|
4.7
|
15.3
|
0.3
|
|
O
|
A:HOH2213
|
4.7
|
35.7
|
1.0
|
|
HZ3
|
A:LYS56
|
4.7
|
32.7
|
1.0
|
|
O3
|
A:PO43001
|
4.8
|
8.8
|
0.7
|
|
NZ
|
A:LYS73
|
4.8
|
26.7
|
1.0
|
|
HE3
|
A:LYS56
|
4.9
|
21.7
|
1.0
|
|
OD2
|
A:ASP117
|
4.9
|
12.5
|
0.4
|
|
CG
|
A:ASP71
|
5.0
|
13.2
|
1.0
|
|
Manganese binding site 5 out
of 9 in 1e9g
Go back to
Manganese Binding Sites List in 1e9g
Manganese binding site 5 out
of 9 in the Structure of Inorganic Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1004
b:9.0
occ:1.00
|
O1
|
A:PO43001
|
2.0
|
12.9
|
0.3
|
|
OD2
|
A:ASP147
|
2.1
|
9.9
|
1.0
|
|
O2
|
A:PO43002
|
2.1
|
10.2
|
0.7
|
|
O
|
A:HOH2519
|
2.2
|
10.0
|
1.0
|
|
OD2
|
A:ASP152
|
2.2
|
8.7
|
1.0
|
|
O1
|
A:PO43001
|
2.2
|
5.5
|
0.7
|
|
O
|
A:HOH2518
|
2.3
|
9.8
|
1.0
|
|
O2
|
A:PO43002
|
2.3
|
7.2
|
0.3
|
|
HZ2
|
A:LYS154
|
3.1
|
19.4
|
1.0
|
|
CG
|
A:ASP152
|
3.2
|
9.4
|
1.0
|
|
P
|
A:PO43002
|
3.2
|
8.3
|
0.7
|
|
CG
|
A:ASP147
|
3.2
|
9.0
|
1.0
|
|
P
|
A:PO43001
|
3.3
|
10.7
|
0.3
|
|
O1
|
A:PO43002
|
3.4
|
9.1
|
0.7
|
|
O3
|
A:PO43001
|
3.5
|
9.9
|
0.3
|
|
HB3
|
A:ASP147
|
3.5
|
11.0
|
1.0
|
|
P
|
A:PO43001
|
3.5
|
11.0
|
0.7
|
|
OD1
|
A:ASP152
|
3.7
|
9.6
|
1.0
|
|
MN
|
A:MN1001
|
3.7
|
8.6
|
1.0
|
|
P
|
A:PO43002
|
3.7
|
8.8
|
0.3
|
|
HB2
|
A:ASP147
|
3.7
|
11.0
|
1.0
|
|
CB
|
A:ASP147
|
3.7
|
9.1
|
1.0
|
|
O3
|
A:PO43001
|
3.8
|
8.8
|
0.7
|
|
HH
|
A:TYR192
|
3.9
|
15.8
|
1.0
|
|
O3
|
A:PO43002
|
3.9
|
10.9
|
0.7
|
|
OD2
|
A:ASP115
|
3.9
|
8.8
|
0.6
|
|
NZ
|
A:LYS154
|
3.9
|
13.0
|
1.0
|
|
OH
|
A:TYR192
|
4.0
|
10.5
|
1.0
|
|
O
|
A:HOH2520
|
4.1
|
14.8
|
1.0
|
|
HZ1
|
A:LYS154
|
4.1
|
19.4
|
1.0
|
|
O3
|
A:PO43002
|
4.1
|
7.9
|
0.3
|
|
O
|
A:HOH2514
|
4.1
|
13.4
|
1.0
|
|
OD2
|
A:ASP115
|
4.1
|
7.6
|
0.4
|
|
O2
|
A:PO43001
|
4.1
|
15.3
|
0.3
|
|
HZ2
|
A:LYS193
|
4.2
|
18.4
|
1.0
|
|
HZ3
|
A:LYS154
|
4.3
|
19.4
|
1.0
|
|
OD1
|
A:ASP147
|
4.3
|
9.8
|
1.0
|
|
O
|
A:HOH2322
|
4.4
|
10.5
|
1.0
|
|
CB
|
A:ASP152
|
4.4
|
8.2
|
1.0
|
|
O2
|
A:PO43001
|
4.4
|
11.4
|
0.7
|
|
O4
|
A:PO43001
|
4.4
|
9.9
|
0.3
|
|
HB2
|
A:ASP152
|
4.4
|
9.8
|
1.0
|
|
O4
|
A:PO43002
|
4.4
|
9.7
|
0.7
|
|
HD21
|
A:LEU145
|
4.5
|
17.6
|
1.0
|
|
O4
|
A:PO43001
|
4.5
|
10.3
|
0.7
|
|
HB3
|
A:ASP152
|
4.6
|
9.8
|
1.0
|
|
O4
|
A:PO43002
|
4.6
|
9.4
|
0.3
|
|
HZ3
|
A:LYS193
|
4.6
|
18.4
|
1.0
|
|
O1
|
A:PO43002
|
4.7
|
7.3
|
0.3
|
|
OD2
|
A:ASP120
|
4.7
|
8.4
|
1.0
|
|
O
|
A:HOH2523
|
4.8
|
10.7
|
0.7
|
|
HD22
|
A:LEU145
|
4.9
|
17.6
|
1.0
|
|
HB2
|
A:ASP115
|
4.9
|
10.1
|
0.4
|
|
NZ
|
A:LYS193
|
4.9
|
12.3
|
1.0
|
|
HH
|
A:TYR93
|
4.9
|
15.0
|
1.0
|
|
HE2
|
A:LYS154
|
4.9
|
14.4
|
1.0
|
|
CE
|
A:LYS154
|
5.0
|
12.0
|
1.0
|
|
MN
|
A:MN1003
|
5.0
|
11.2
|
0.7
|
|
Manganese binding site 6 out
of 9 in 1e9g
Go back to
Manganese Binding Sites List in 1e9g
Manganese binding site 6 out
of 9 in the Structure of Inorganic Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1005
b:7.7
occ:1.00
|
OD1
|
B:ASP152
|
2.1
|
8.8
|
1.0
|
|
OD2
|
B:ASP120
|
2.1
|
8.0
|
1.0
|
|
O4
|
B:PO43002
|
2.2
|
7.5
|
1.0
|
|
OD2
|
B:ASP115
|
2.2
|
8.4
|
1.0
|
|
O
|
B:HOH2488
|
2.2
|
8.4
|
1.0
|
|
O
|
B:HOH2489
|
2.3
|
7.9
|
1.0
|
|
CG
|
B:ASP152
|
3.1
|
8.1
|
1.0
|
|
CG
|
B:ASP120
|
3.1
|
7.4
|
1.0
|
|
CG
|
B:ASP115
|
3.2
|
8.4
|
1.0
|
|
P
|
B:PO43002
|
3.3
|
8.5
|
1.0
|
|
O1
|
B:PO43002
|
3.3
|
7.4
|
1.0
|
|
OD1
|
B:ASP120
|
3.3
|
7.5
|
1.0
|
|
OD2
|
B:ASP152
|
3.5
|
7.4
|
1.0
|
|
HZ3
|
B:LYS154
|
3.5
|
21.0
|
1.0
|
|
OD1
|
B:ASP115
|
3.6
|
8.9
|
1.0
|
|
MN
|
B:MN1006
|
3.6
|
7.6
|
1.0
|
|
O
|
B:HOH2496
|
3.7
|
9.1
|
1.0
|
|
MN
|
B:MN1008
|
3.7
|
8.2
|
1.0
|
|
HB3
|
B:ASP117
|
3.8
|
8.3
|
0.4
|
|
HZ1
|
B:LYS154
|
3.8
|
21.0
|
1.0
|
|
HZ2
|
B:LYS154
|
3.8
|
21.0
|
1.0
|
|
O3
|
B:PO43002
|
3.9
|
8.0
|
1.0
|
|
NZ
|
B:LYS154
|
3.9
|
14.0
|
1.0
|
|
HH
|
B:TYR93
|
4.0
|
12.7
|
1.0
|
|
O
|
B:HOH2246
|
4.1
|
9.0
|
1.0
|
|
HA
|
B:ASP152
|
4.3
|
9.4
|
1.0
|
|
CB
|
B:ASP152
|
4.4
|
8.0
|
1.0
|
|
CB
|
B:ASP120
|
4.5
|
7.0
|
1.0
|
|
CB
|
B:ASP115
|
4.5
|
9.1
|
1.0
|
|
OD2
|
B:ASP117
|
4.5
|
10.3
|
1.0
|
|
O
|
B:HOH2491
|
4.5
|
8.8
|
1.0
|
|
O2
|
B:PO43002
|
4.5
|
8.7
|
1.0
|
|
OH
|
B:TYR93
|
4.5
|
8.5
|
1.0
|
|
CB
|
B:ASP117
|
4.6
|
8.8
|
1.0
|
|
HB2
|
B:ASP120
|
4.6
|
8.4
|
1.0
|
|
HB3
|
B:ASP115
|
4.6
|
10.9
|
1.0
|
|
HB2
|
B:ASP115
|
4.6
|
10.9
|
1.0
|
|
O
|
B:PRO118
|
4.7
|
8.0
|
1.0
|
|
HG3
|
B:GLU101
|
4.7
|
9.9
|
1.0
|
|
O
|
B:HOH2497
|
4.7
|
8.6
|
1.0
|
|
HB2
|
B:ASP152
|
4.8
|
9.5
|
1.0
|
|
HB2
|
B:ASP117
|
4.8
|
22.7
|
0.6
|
|
CA
|
B:ASP152
|
4.8
|
7.8
|
1.0
|
|
HB3
|
B:ASP120
|
5.0
|
8.4
|
1.0
|
|
Manganese binding site 7 out
of 9 in 1e9g
Go back to
Manganese Binding Sites List in 1e9g
Manganese binding site 7 out
of 9 in the Structure of Inorganic Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1006
b:7.6
occ:1.00
|
O1
|
B:PO43002
|
2.1
|
7.4
|
1.0
|
|
O
|
B:HOH2490
|
2.1
|
8.2
|
1.0
|
|
OD1
|
B:ASP120
|
2.2
|
7.5
|
1.0
|
|
O
|
B:HOH2491
|
2.2
|
8.8
|
1.0
|
|
O
|
B:HOH2492
|
2.2
|
12.8
|
1.0
|
|
O
|
B:HOH2489
|
2.3
|
7.9
|
1.0
|
|
CG
|
B:ASP120
|
3.2
|
7.4
|
1.0
|
|
HH
|
B:TYR93
|
3.2
|
12.7
|
1.0
|
|
P
|
B:PO43002
|
3.3
|
8.5
|
1.0
|
|
O3
|
B:PO43002
|
3.6
|
8.0
|
1.0
|
|
OD2
|
B:ASP120
|
3.6
|
8.0
|
1.0
|
|
HE2
|
B:TYR93
|
3.6
|
10.1
|
1.0
|
|
MN
|
B:MN1005
|
3.6
|
7.7
|
1.0
|
|
O
|
B:HOH2132
|
3.9
|
9.5
|
1.0
|
|
O4
|
B:PO43002
|
3.9
|
7.5
|
1.0
|
|
OH
|
B:TYR93
|
4.0
|
8.5
|
1.0
|
|
HB3
|
B:ALA95
|
4.1
|
14.6
|
1.0
|
|
O
|
B:HOH2488
|
4.2
|
8.4
|
1.0
|
|
O
|
B:PRO118
|
4.2
|
8.0
|
1.0
|
|
OE1
|
B:GLU48
|
4.3
|
8.3
|
1.0
|
|
HA
|
B:ASP120
|
4.3
|
8.1
|
1.0
|
|
CE2
|
B:TYR93
|
4.3
|
8.4
|
1.0
|
|
CB
|
B:ASP120
|
4.4
|
7.0
|
1.0
|
|
OD2
|
B:ASP117
|
4.4
|
10.3
|
1.0
|
|
O
|
B:HOH2155
|
4.4
|
12.6
|
1.0
|
|
HB3
|
B:ASP120
|
4.5
|
8.4
|
1.0
|
|
HB3
|
B:ASP117
|
4.5
|
18.8
|
0.4
|
|
HB2
|
B:ASP117
|
4.5
|
22.7
|
0.6
|
|
O2
|
B:PO43002
|
4.5
|
8.7
|
1.0
|
|
CZ
|
B:TYR93
|
4.6
|
8.1
|
1.0
|
|
HZ3
|
B:LYS56
|
4.6
|
15.2
|
1.0
|
|
OE2
|
B:GLU48
|
4.6
|
9.5
|
1.0
|
|
CB
|
B:ASP117
|
4.6
|
8.8
|
1.0
|
|
HB3
|
B:ASP117
|
4.6
|
8.3
|
0.4
|
|
CG
|
B:ASP117
|
4.7
|
10.2
|
1.0
|
|
O
|
B:GLY94
|
4.7
|
7.3
|
1.0
|
|
HD2
|
B:PRO118
|
4.8
|
10.1
|
1.0
|
|
CA
|
B:ASP120
|
4.8
|
6.8
|
1.0
|
|
HG2
|
B:GLU58
|
4.9
|
7.9
|
0.6
|
|
O
|
B:HOH2147
|
4.9
|
10.0
|
1.0
|
|
HZ2
|
B:LYS56
|
4.9
|
15.2
|
1.0
|
|
CD
|
B:GLU48
|
4.9
|
8.0
|
1.0
|
|
HZ1
|
B:LYS56
|
4.9
|
15.2
|
1.0
|
|
HZ3
|
B:LYS154
|
5.0
|
21.0
|
1.0
|
|
Manganese binding site 8 out
of 9 in 1e9g
Go back to
Manganese Binding Sites List in 1e9g
Manganese binding site 8 out
of 9 in the Structure of Inorganic Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1007
b:9.6
occ:1.00
|
OE2
|
B:GLU58
|
2.1
|
5.8
|
0.6
|
|
O3
|
B:PO43001
|
2.1
|
10.1
|
1.0
|
|
O3
|
B:PO43002
|
2.1
|
8.0
|
1.0
|
|
O
|
B:HOH2495
|
2.2
|
9.5
|
1.0
|
|
O
|
B:HOH2494
|
2.2
|
13.0
|
1.0
|
|
O
|
B:HOH2493
|
2.2
|
13.3
|
1.0
|
|
OE2
|
B:GLU58
|
2.5
|
11.1
|
0.4
|
|
CD
|
B:GLU58
|
3.1
|
8.6
|
0.6
|
|
HZ1
|
B:LYS56
|
3.1
|
15.2
|
1.0
|
|
P
|
B:PO43001
|
3.3
|
9.3
|
1.0
|
|
O4
|
B:PO43001
|
3.4
|
9.2
|
1.0
|
|
CD
|
B:GLU58
|
3.4
|
9.0
|
0.4
|
|
OE1
|
B:GLU58
|
3.4
|
10.7
|
0.6
|
|
P
|
B:PO43002
|
3.6
|
8.5
|
1.0
|
|
OE1
|
B:GLU58
|
3.6
|
16.9
|
0.4
|
|
HH12
|
B:ARG78
|
3.7
|
11.2
|
1.0
|
|
HZ3
|
B:LYS56
|
3.8
|
15.2
|
1.0
|
|
NZ
|
B:LYS56
|
3.8
|
10.1
|
1.0
|
|
O2
|
B:PO43002
|
4.0
|
8.7
|
1.0
|
|
HE3
|
B:LYS56
|
4.1
|
11.6
|
1.0
|
|
O1
|
B:PO43001
|
4.2
|
8.2
|
1.0
|
|
O
|
B:HOH2095
|
4.2
|
26.0
|
1.0
|
|
O
|
B:HOH2096
|
4.3
|
32.6
|
1.0
|
|
O
|
B:HOH2261
|
4.3
|
11.7
|
1.0
|
|
O
|
B:HOH2489
|
4.3
|
7.9
|
1.0
|
|
O4
|
B:PO43002
|
4.3
|
7.5
|
1.0
|
|
OD2
|
B:ASP117
|
4.3
|
10.3
|
1.0
|
|
OD2
|
B:ASP71
|
4.4
|
9.2
|
0.4
|
|
NH1
|
B:ARG78
|
4.4
|
9.3
|
1.0
|
|
O2
|
B:PO43001
|
4.4
|
10.0
|
1.0
|
|
CG
|
B:GLU58
|
4.4
|
6.6
|
0.6
|
|
O
|
B:HOH2492
|
4.4
|
12.8
|
1.0
|
|
HH11
|
B:ARG78
|
4.5
|
11.2
|
1.0
|
|
CE
|
B:LYS56
|
4.5
|
9.7
|
1.0
|
|
HG2
|
B:GLU58
|
4.5
|
7.9
|
0.6
|
|
HZ2
|
B:LYS56
|
4.5
|
15.2
|
1.0
|
|
HD2
|
B:LYS56
|
4.6
|
10.7
|
1.0
|
|
O1
|
B:PO43002
|
4.6
|
7.4
|
1.0
|
|
HG3
|
B:GLU58
|
4.8
|
7.9
|
0.6
|
|
CG
|
B:GLU58
|
4.8
|
7.7
|
0.4
|
|
O
|
B:HOH2496
|
4.9
|
9.1
|
1.0
|
|
HG2
|
B:GLU58
|
4.9
|
9.2
|
0.4
|
|
MN
|
B:MN1008
|
4.9
|
8.2
|
1.0
|
|
OD2
|
B:ASP71
|
4.9
|
16.0
|
0.6
|
|
Manganese binding site 9 out
of 9 in 1e9g
Go back to
Manganese Binding Sites List in 1e9g
Manganese binding site 9 out
of 9 in the Structure of Inorganic Pyrophosphatase
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of Structure of Inorganic Pyrophosphatase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1008
b:8.2
occ:1.00
|
OD2
|
B:ASP147
|
2.1
|
8.3
|
1.0
|
|
O4
|
B:PO43001
|
2.2
|
9.2
|
1.0
|
|
O
|
B:HOH2496
|
2.2
|
9.1
|
1.0
|
|
O4
|
B:PO43002
|
2.2
|
7.5
|
1.0
|
|
OD2
|
B:ASP152
|
2.2
|
7.4
|
1.0
|
|
O
|
B:HOH2497
|
2.3
|
8.6
|
1.0
|
|
CG
|
B:ASP147
|
3.2
|
7.5
|
1.0
|
|
CG
|
B:ASP152
|
3.2
|
8.1
|
1.0
|
|
HZ2
|
B:LYS154
|
3.3
|
21.0
|
1.0
|
|
P
|
B:PO43002
|
3.3
|
8.5
|
1.0
|
|
O2
|
B:PO43002
|
3.4
|
8.7
|
1.0
|
|
P
|
B:PO43001
|
3.5
|
9.3
|
1.0
|
|
HB3
|
B:ASP147
|
3.5
|
9.5
|
1.0
|
|
MN
|
B:MN1005
|
3.7
|
7.7
|
1.0
|
|
OD1
|
B:ASP152
|
3.7
|
8.8
|
1.0
|
|
O1
|
B:PO43001
|
3.7
|
8.2
|
1.0
|
|
HB2
|
B:ASP147
|
3.7
|
9.5
|
1.0
|
|
CB
|
B:ASP147
|
3.8
|
7.9
|
1.0
|
|
HH
|
B:TYR192
|
3.9
|
13.8
|
1.0
|
|
O3
|
B:PO43002
|
3.9
|
8.0
|
1.0
|
|
OD2
|
B:ASP115
|
4.0
|
8.4
|
1.0
|
|
OH
|
B:TYR192
|
4.0
|
9.2
|
1.0
|
|
O
|
B:HOH2499
|
4.0
|
13.1
|
1.0
|
|
NZ
|
B:LYS154
|
4.1
|
14.0
|
1.0
|
|
O
|
B:HOH2495
|
4.1
|
9.5
|
1.0
|
|
HZ1
|
B:LYS193
|
4.1
|
14.0
|
1.0
|
|
O
|
B:HOH2297
|
4.3
|
10.3
|
1.0
|
|
HZ3
|
B:LYS154
|
4.3
|
21.0
|
1.0
|
|
OD1
|
B:ASP147
|
4.3
|
8.9
|
1.0
|
|
HZ1
|
B:LYS154
|
4.3
|
21.0
|
1.0
|
|
CB
|
B:ASP152
|
4.4
|
8.0
|
1.0
|
|
O2
|
B:PO43001
|
4.4
|
10.0
|
1.0
|
|
HB2
|
B:ASP152
|
4.4
|
9.5
|
1.0
|
|
HZ2
|
B:LYS193
|
4.5
|
14.0
|
1.0
|
|
O3
|
B:PO43001
|
4.5
|
10.1
|
1.0
|
|
HD21
|
B:LEU145
|
4.5
|
15.4
|
1.0
|
|
O1
|
B:PO43002
|
4.6
|
7.4
|
1.0
|
|
HB3
|
B:ASP152
|
4.6
|
9.5
|
1.0
|
|
OD2
|
B:ASP120
|
4.7
|
8.0
|
1.0
|
|
NZ
|
B:LYS193
|
4.7
|
9.3
|
1.0
|
|
O
|
B:HOH2489
|
4.8
|
7.9
|
1.0
|
|
HD22
|
B:LEU145
|
4.8
|
15.4
|
1.0
|
|
MN
|
B:MN1007
|
4.9
|
9.6
|
1.0
|
|
Reference:
P.Heikinheimo,
V.Tuominen,
A.-K.Ahonen,
A.Teplyakov,
B.S.Cooperman,
A.A.Baykov,
R.Lahti,
A.Goldman.
Toward A Quantum-Mechanical Description of Metal-Assisted Phosphoryl Transfer in Pyrophosphatase Proc.Natl.Acad.Sci.Usa V. 98 3121 2001.
ISSN: ISSN 0027-8424
PubMed: 11248042
DOI: 10.1073/PNAS.061612498
Page generated: Sat Oct 5 10:09:21 2024
|
