Magnesium in PDB 1q9d: Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State)
Enzymatic activity of Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State)
All present enzymatic activity of Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State):
3.1.3.11;
Protein crystallography data
The structure of Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State), PDB code: 1q9d
was solved by
R.B.Honzatko,
J.Y.Choe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.35
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.860,
166.250,
80.270,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
24.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State)
(pdb code 1q9d). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State), PDB code: 1q9d:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1q9d
Go back to
Magnesium Binding Sites List in 1q9d
Magnesium binding site 1 out
of 4 in the Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:18.2
occ:1.00
|
OE1
|
A:GLU280
|
2.1
|
21.1
|
1.0
|
OD2
|
A:ASP121
|
2.1
|
28.2
|
1.0
|
O1
|
A:PO4403
|
2.1
|
43.6
|
1.0
|
OD2
|
A:ASP118
|
2.2
|
31.4
|
1.0
|
CG
|
A:ASP121
|
3.0
|
27.2
|
1.0
|
CD
|
A:GLU280
|
3.1
|
20.6
|
1.0
|
CG
|
A:ASP118
|
3.2
|
24.3
|
1.0
|
CB
|
A:ASP121
|
3.2
|
24.2
|
1.0
|
P
|
A:PO4403
|
3.2
|
45.9
|
1.0
|
O3
|
A:PO4403
|
3.5
|
42.9
|
1.0
|
O4
|
A:PO4403
|
3.6
|
44.6
|
1.0
|
CG
|
A:GLU280
|
3.6
|
19.9
|
1.0
|
CA
|
A:ASP121
|
3.6
|
21.2
|
1.0
|
OD1
|
A:ASP118
|
3.7
|
22.1
|
1.0
|
OE2
|
A:GLU97
|
3.9
|
35.8
|
1.0
|
C1
|
A:F6P401
|
4.0
|
23.6
|
1.0
|
OE2
|
A:GLU280
|
4.1
|
20.7
|
1.0
|
OD1
|
A:ASP121
|
4.2
|
26.1
|
1.0
|
CB
|
A:ASP118
|
4.3
|
23.4
|
1.0
|
O3
|
A:F6P401
|
4.3
|
19.6
|
1.0
|
MG
|
A:MG405
|
4.5
|
28.6
|
1.0
|
O2
|
A:PO4403
|
4.5
|
44.6
|
1.0
|
CD
|
A:GLU97
|
4.5
|
31.9
|
1.0
|
N
|
A:GLY122
|
4.5
|
19.8
|
1.0
|
OE1
|
A:GLU97
|
4.5
|
32.3
|
1.0
|
O
|
A:HOH634
|
4.5
|
37.9
|
1.0
|
O1
|
A:F6P401
|
4.6
|
22.9
|
1.0
|
C
|
A:ASP121
|
4.6
|
20.7
|
1.0
|
N
|
A:ASP121
|
4.6
|
21.3
|
1.0
|
CD1
|
A:ILE135
|
4.7
|
21.1
|
1.0
|
O
|
A:LEU120
|
4.7
|
21.3
|
1.0
|
C2
|
A:F6P401
|
4.7
|
23.9
|
1.0
|
O2
|
A:F6P401
|
4.7
|
22.2
|
1.0
|
C3
|
A:F6P401
|
4.9
|
23.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1q9d
Go back to
Magnesium Binding Sites List in 1q9d
Magnesium binding site 2 out
of 4 in the Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:28.6
occ:1.00
|
O4
|
A:PO4403
|
2.1
|
44.6
|
1.0
|
OD1
|
A:ASP118
|
2.2
|
22.1
|
1.0
|
OE2
|
A:GLU97
|
2.3
|
35.8
|
1.0
|
O
|
A:LEU120
|
2.4
|
21.3
|
1.0
|
OE1
|
A:GLU98
|
2.8
|
36.0
|
1.0
|
CG
|
A:ASP118
|
3.2
|
24.3
|
1.0
|
C
|
A:LEU120
|
3.3
|
20.2
|
1.0
|
CD
|
A:GLU97
|
3.5
|
31.9
|
1.0
|
P
|
A:PO4403
|
3.5
|
45.9
|
1.0
|
OD2
|
A:ASP118
|
3.6
|
31.4
|
1.0
|
N
|
A:LEU120
|
3.9
|
18.4
|
1.0
|
O1
|
A:PO4403
|
3.9
|
43.6
|
1.0
|
CD
|
A:GLU98
|
4.1
|
33.3
|
1.0
|
CA
|
A:LEU120
|
4.1
|
20.0
|
1.0
|
N
|
A:ASP121
|
4.2
|
21.3
|
1.0
|
O2
|
A:PO4403
|
4.2
|
44.6
|
1.0
|
CB
|
A:GLU97
|
4.2
|
27.2
|
1.0
|
CG
|
A:GLU97
|
4.3
|
29.7
|
1.0
|
OE1
|
A:GLU97
|
4.3
|
32.3
|
1.0
|
CA
|
A:ASP121
|
4.4
|
21.2
|
1.0
|
MG
|
A:MG404
|
4.5
|
18.2
|
1.0
|
O3
|
A:PO4403
|
4.5
|
42.9
|
1.0
|
CB
|
A:ASP118
|
4.5
|
23.4
|
1.0
|
CD
|
A:PRO119
|
4.6
|
18.2
|
1.0
|
OG
|
A:SER123
|
4.6
|
34.7
|
1.0
|
CB
|
A:LEU120
|
4.6
|
21.5
|
1.0
|
CG
|
A:PRO119
|
4.6
|
16.7
|
1.0
|
N
|
A:PRO119
|
4.7
|
20.2
|
1.0
|
CA
|
A:ASP118
|
4.8
|
22.3
|
1.0
|
C
|
A:ASP118
|
4.8
|
21.5
|
1.0
|
OE2
|
A:GLU98
|
4.9
|
34.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1q9d
Go back to
Magnesium Binding Sites List in 1q9d
Magnesium binding site 3 out
of 4 in the Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg414
b:9.7
occ:1.00
|
O4
|
B:PO4413
|
2.0
|
46.3
|
1.0
|
OD2
|
B:ASP118
|
2.1
|
22.9
|
1.0
|
OD2
|
B:ASP121
|
2.2
|
18.5
|
1.0
|
OE1
|
B:GLU280
|
2.3
|
17.5
|
1.0
|
P
|
B:PO4413
|
2.9
|
48.1
|
1.0
|
CG
|
B:ASP121
|
3.0
|
21.0
|
1.0
|
O2
|
B:PO4413
|
3.1
|
46.4
|
1.0
|
CB
|
B:ASP121
|
3.2
|
21.2
|
1.0
|
CD
|
B:GLU280
|
3.2
|
15.9
|
1.0
|
CG
|
B:ASP118
|
3.3
|
19.7
|
1.0
|
O1
|
B:PO4413
|
3.3
|
45.4
|
1.0
|
CA
|
B:ASP121
|
3.5
|
21.1
|
1.0
|
CG
|
B:GLU280
|
3.6
|
16.8
|
1.0
|
C1
|
B:F6P411
|
3.6
|
29.9
|
1.0
|
OE2
|
B:GLU97
|
3.7
|
31.1
|
1.0
|
OD1
|
B:ASP118
|
3.8
|
21.0
|
1.0
|
OD1
|
B:ASP121
|
4.2
|
21.1
|
1.0
|
N
|
B:GLY122
|
4.2
|
22.6
|
1.0
|
O3
|
B:PO4413
|
4.2
|
46.0
|
1.0
|
O1
|
B:F6P411
|
4.3
|
33.3
|
1.0
|
OE2
|
B:GLU280
|
4.3
|
16.0
|
1.0
|
C
|
B:ASP121
|
4.4
|
21.6
|
1.0
|
CB
|
B:ASP118
|
4.5
|
17.3
|
1.0
|
N
|
B:ASP121
|
4.5
|
19.8
|
1.0
|
O3
|
B:F6P411
|
4.5
|
27.4
|
1.0
|
C2
|
B:F6P411
|
4.7
|
27.9
|
1.0
|
O
|
B:LEU120
|
4.7
|
22.9
|
1.0
|
C3
|
B:F6P411
|
4.8
|
27.4
|
1.0
|
CD
|
B:GLU97
|
4.9
|
27.5
|
1.0
|
C
|
B:LEU120
|
5.0
|
21.1
|
1.0
|
O2
|
B:F6P411
|
5.0
|
25.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1q9d
Go back to
Magnesium Binding Sites List in 1q9d
Magnesium binding site 4 out
of 4 in the Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Fructose-1,6-Bisphosphatase Complexed with A New Allosteric Site Inhibitor (I-State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg415
b:31.6
occ:1.00
|
OD1
|
B:ASP118
|
2.4
|
21.0
|
1.0
|
O1
|
B:PO4413
|
2.4
|
45.4
|
1.0
|
OE1
|
B:GLU98
|
2.4
|
33.8
|
1.0
|
O
|
B:LEU120
|
2.6
|
22.9
|
1.0
|
O
|
B:HOH752
|
3.0
|
56.7
|
1.0
|
O
|
B:HOH780
|
3.4
|
43.0
|
1.0
|
C
|
B:LEU120
|
3.5
|
21.1
|
1.0
|
CG
|
B:ASP118
|
3.6
|
19.7
|
1.0
|
CD
|
B:GLU98
|
3.6
|
31.0
|
1.0
|
N
|
B:LEU120
|
3.7
|
21.2
|
1.0
|
OE1
|
B:GLU97
|
3.7
|
27.9
|
1.0
|
CD
|
B:GLU97
|
3.9
|
27.5
|
1.0
|
P
|
B:PO4413
|
3.9
|
48.1
|
1.0
|
CG
|
B:PRO119
|
4.0
|
20.4
|
1.0
|
OE2
|
B:GLU97
|
4.0
|
31.1
|
1.0
|
CA
|
B:LEU120
|
4.1
|
21.4
|
1.0
|
CD
|
B:PRO119
|
4.2
|
19.8
|
1.0
|
OD2
|
B:ASP118
|
4.3
|
22.9
|
1.0
|
CB
|
B:GLU97
|
4.3
|
22.6
|
1.0
|
N
|
B:PRO119
|
4.4
|
19.6
|
1.0
|
CG
|
B:GLU98
|
4.4
|
28.7
|
1.0
|
N
|
B:ASP121
|
4.5
|
19.8
|
1.0
|
C
|
B:ASP118
|
4.5
|
18.0
|
1.0
|
O4
|
B:PO4413
|
4.5
|
46.3
|
1.0
|
OE2
|
B:GLU98
|
4.5
|
30.6
|
1.0
|
O3
|
B:PO4413
|
4.6
|
46.0
|
1.0
|
CA
|
B:ASP118
|
4.6
|
17.6
|
1.0
|
CG
|
B:GLU97
|
4.6
|
28.7
|
1.0
|
CB
|
B:LEU120
|
4.7
|
20.3
|
1.0
|
O2
|
B:PO4413
|
4.7
|
46.4
|
1.0
|
CB
|
B:ASP118
|
4.7
|
17.3
|
1.0
|
C
|
B:PRO119
|
4.8
|
20.8
|
1.0
|
CA
|
B:ASP121
|
4.9
|
21.1
|
1.0
|
CA
|
B:PRO119
|
4.9
|
19.7
|
1.0
|
CB
|
B:PRO119
|
5.0
|
20.2
|
1.0
|
|
Reference:
J.Y.Choe,
S.W.Nelson,
K.L.Arienti,
F.U.Axe,
T.L.Collins,
T.K.Jones,
R.D.Kimmich,
M.J.Newman,
K.Norvell,
W.C.Ripka,
S.J.Romano,
K.M.Short,
D.H.Slee,
H.J.Fromm,
R.B.Honzatko.
Inhibition of Fructose-1,6-Bisphosphatase By A New Class of Allosteric Effectors J.Biol.Chem. V. 278 51176 2003.
ISSN: ISSN 0021-9258
PubMed: 14530289
DOI: 10.1074/JBC.M308396200
Page generated: Tue Aug 13 11:09:29 2024
|