Magnesium in PDB 1t9d: Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl
Enzymatic activity of Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl
All present enzymatic activity of Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl:
2.2.1.6;
Protein crystallography data
The structure of Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl, PDB code: 1t9d
was solved by
J.A.Mccourt,
S.S.Pang,
L.W.Guddat,
R.G.Duggleby,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.30
|
Space group
|
I 4 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
218.347,
218.347,
361.530,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.4 /
19.5
|
Other elements in 1t9d:
The structure of Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl
(pdb code 1t9d). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl, PDB code: 1t9d:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1t9d
Go back to
Magnesium Binding Sites List in 1t9d
Magnesium binding site 1 out
of 4 in the Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1699
b:19.1
occ:1.00
|
O3B
|
A:P251698
|
2.0
|
21.3
|
1.0
|
OD1
|
A:ASP550
|
2.0
|
23.9
|
1.0
|
O1A
|
A:P251698
|
2.1
|
20.7
|
1.0
|
O
|
A:HOH4061
|
2.1
|
18.7
|
1.0
|
OD1
|
A:ASN577
|
2.2
|
21.1
|
1.0
|
O
|
A:GLU579
|
2.2
|
22.1
|
1.0
|
CG
|
A:ASP550
|
3.1
|
24.8
|
1.0
|
PA
|
A:P251698
|
3.1
|
22.7
|
1.0
|
CG
|
A:ASN577
|
3.1
|
21.2
|
1.0
|
PB
|
A:P251698
|
3.2
|
22.2
|
1.0
|
O3A
|
A:P251698
|
3.3
|
23.0
|
1.0
|
C
|
A:GLU579
|
3.4
|
23.9
|
1.0
|
ND2
|
A:ASN577
|
3.5
|
18.1
|
1.0
|
OD2
|
A:ASP550
|
3.6
|
25.8
|
1.0
|
N
|
A:ASP550
|
3.8
|
21.1
|
1.0
|
O7
|
A:P251698
|
3.8
|
23.3
|
1.0
|
O2B
|
A:P251698
|
3.9
|
19.7
|
1.0
|
N
|
A:GLU579
|
3.9
|
25.9
|
1.0
|
N
|
A:GLY581
|
3.9
|
24.2
|
1.0
|
N
|
A:ALA551
|
4.2
|
19.1
|
1.0
|
CA
|
A:GLU579
|
4.3
|
25.4
|
1.0
|
O2A
|
A:P251698
|
4.3
|
18.7
|
1.0
|
CG
|
A:GLU579
|
4.3
|
24.6
|
1.0
|
CB
|
A:ASP550
|
4.3
|
20.1
|
1.0
|
N
|
A:GLN580
|
4.4
|
25.5
|
1.0
|
O1B
|
A:P251698
|
4.4
|
21.1
|
1.0
|
N
|
A:ASN577
|
4.4
|
22.9
|
1.0
|
CA
|
A:GLN580
|
4.5
|
26.9
|
1.0
|
CA
|
A:ASP550
|
4.5
|
20.5
|
1.0
|
CB
|
A:ASN577
|
4.5
|
22.6
|
1.0
|
O
|
A:LEU575
|
4.5
|
26.9
|
1.0
|
C
|
A:GLY549
|
4.6
|
22.1
|
1.0
|
CA
|
A:GLY549
|
4.6
|
20.4
|
1.0
|
N
|
A:GLU578
|
4.7
|
24.3
|
1.0
|
C
|
A:GLN580
|
4.8
|
24.1
|
1.0
|
CA
|
A:GLY581
|
4.8
|
25.7
|
1.0
|
CB
|
A:ALA551
|
4.8
|
17.9
|
1.0
|
CA
|
A:ASN577
|
4.9
|
23.6
|
1.0
|
C
|
A:ASN577
|
4.9
|
24.0
|
1.0
|
C
|
A:ASP550
|
4.9
|
20.0
|
1.0
|
CB
|
A:GLU579
|
4.9
|
22.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1t9d
Go back to
Magnesium Binding Sites List in 1t9d
Magnesium binding site 2 out
of 4 in the Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg699
b:25.7
occ:1.00
|
O1A
|
B:P25698
|
2.1
|
26.2
|
1.0
|
O3B
|
B:P25698
|
2.1
|
27.5
|
1.0
|
O
|
B:GLU579
|
2.1
|
33.1
|
1.0
|
OD1
|
B:ASN577
|
2.2
|
31.7
|
1.0
|
OD1
|
B:ASP550
|
2.2
|
24.6
|
1.0
|
O
|
B:HOH4287
|
2.3
|
28.4
|
1.0
|
CG
|
B:ASN577
|
3.1
|
30.3
|
1.0
|
PA
|
B:P25698
|
3.1
|
27.7
|
1.0
|
CG
|
B:ASP550
|
3.2
|
25.5
|
1.0
|
O3A
|
B:P25698
|
3.3
|
29.8
|
1.0
|
PB
|
B:P25698
|
3.3
|
31.0
|
1.0
|
C
|
B:GLU579
|
3.4
|
33.4
|
1.0
|
ND2
|
B:ASN577
|
3.4
|
27.1
|
1.0
|
OD2
|
B:ASP550
|
3.8
|
25.9
|
1.0
|
N
|
B:ASP550
|
3.8
|
24.2
|
1.0
|
O7
|
B:P25698
|
3.9
|
29.0
|
1.0
|
O2B
|
B:P25698
|
3.9
|
31.9
|
1.0
|
N
|
B:GLU579
|
4.0
|
32.8
|
1.0
|
N
|
B:GLY581
|
4.0
|
35.8
|
1.0
|
N
|
B:ALA551
|
4.2
|
23.4
|
1.0
|
O2A
|
B:P25698
|
4.2
|
27.0
|
1.0
|
CA
|
B:GLU579
|
4.3
|
34.1
|
1.0
|
N
|
B:GLN580
|
4.3
|
34.0
|
1.0
|
CA
|
B:GLN580
|
4.4
|
34.9
|
1.0
|
N
|
B:ASN577
|
4.4
|
29.8
|
1.0
|
CG
|
B:GLU579
|
4.4
|
32.7
|
1.0
|
CB
|
B:ASP550
|
4.4
|
23.3
|
1.0
|
O
|
B:LEU575
|
4.4
|
31.6
|
1.0
|
O1B
|
B:P25698
|
4.5
|
25.7
|
1.0
|
CB
|
B:ASN577
|
4.5
|
29.6
|
1.0
|
CA
|
B:GLY549
|
4.6
|
26.0
|
1.0
|
CA
|
B:ASP550
|
4.6
|
24.3
|
1.0
|
C
|
B:GLY549
|
4.6
|
24.7
|
1.0
|
C
|
B:GLN580
|
4.8
|
34.1
|
1.0
|
N
|
B:GLU578
|
4.8
|
33.8
|
1.0
|
CA
|
B:GLY581
|
4.8
|
35.9
|
1.0
|
CB
|
B:ALA551
|
4.8
|
20.0
|
1.0
|
CA
|
B:ASN577
|
4.8
|
30.7
|
1.0
|
C
|
B:ASN577
|
4.8
|
31.7
|
1.0
|
C
|
B:ASP550
|
4.9
|
24.1
|
1.0
|
CB
|
B:GLU579
|
5.0
|
32.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1t9d
Go back to
Magnesium Binding Sites List in 1t9d
Magnesium binding site 3 out
of 4 in the Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg3699
b:36.2
occ:1.00
|
O3B
|
C:P223702
|
2.0
|
39.0
|
1.0
|
O
|
C:HOH5774
|
2.1
|
36.4
|
1.0
|
O1A
|
C:P223702
|
2.1
|
40.5
|
1.0
|
OD1
|
C:ASN577
|
2.3
|
47.2
|
1.0
|
OD1
|
C:ASP550
|
2.3
|
30.2
|
1.0
|
O
|
C:GLU579
|
2.3
|
44.0
|
1.0
|
CG
|
C:ASN577
|
3.0
|
46.5
|
1.0
|
ND2
|
C:ASN577
|
3.1
|
44.5
|
1.0
|
PB
|
C:P223702
|
3.1
|
39.0
|
1.0
|
O3A
|
C:P223702
|
3.1
|
40.4
|
1.0
|
PA
|
C:P223702
|
3.1
|
41.3
|
1.0
|
CG
|
C:ASP550
|
3.4
|
30.1
|
1.0
|
C
|
C:GLU579
|
3.5
|
44.8
|
1.0
|
O2B
|
C:P223702
|
3.6
|
40.8
|
1.0
|
N
|
C:ASP550
|
3.9
|
30.1
|
1.0
|
O7
|
C:P223702
|
3.9
|
41.6
|
1.0
|
N
|
C:GLY581
|
4.0
|
49.0
|
1.0
|
OD2
|
C:ASP550
|
4.0
|
28.5
|
1.0
|
N
|
C:GLU579
|
4.1
|
44.3
|
1.0
|
O2A
|
C:P223702
|
4.2
|
38.7
|
1.0
|
CA
|
C:GLY549
|
4.4
|
32.1
|
1.0
|
O1B
|
C:P223702
|
4.4
|
39.1
|
1.0
|
O
|
C:LEU575
|
4.4
|
36.9
|
1.0
|
N
|
C:ALA551
|
4.4
|
29.1
|
1.0
|
CA
|
C:GLU579
|
4.4
|
44.7
|
1.0
|
CB
|
C:ASN577
|
4.4
|
44.2
|
1.0
|
N
|
C:GLN580
|
4.5
|
46.9
|
1.0
|
N
|
C:ASN577
|
4.5
|
41.9
|
1.0
|
C
|
C:GLY549
|
4.5
|
30.8
|
1.0
|
CG
|
C:GLU579
|
4.5
|
43.7
|
1.0
|
CA
|
C:GLN580
|
4.6
|
48.2
|
1.0
|
CB
|
C:ASP550
|
4.6
|
28.7
|
1.0
|
CA
|
C:ASP550
|
4.7
|
30.0
|
1.0
|
CA
|
C:GLY581
|
4.8
|
49.7
|
1.0
|
C
|
C:GLN580
|
4.8
|
48.3
|
1.0
|
N
|
C:GLU578
|
4.8
|
45.4
|
1.0
|
CA
|
C:ASN577
|
4.9
|
44.3
|
1.0
|
C
|
C:ASN577
|
5.0
|
45.1
|
1.0
|
CB
|
C:ALA551
|
5.0
|
25.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1t9d
Go back to
Magnesium Binding Sites List in 1t9d
Magnesium binding site 4 out
of 4 in the Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with A Sulfonylurea Herbicide, Metsulfuron Methyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg2699
b:24.4
occ:1.00
|
O3B
|
D:P222702
|
2.0
|
24.9
|
1.0
|
O
|
D:GLU579
|
2.1
|
28.9
|
1.0
|
O1A
|
D:P222702
|
2.1
|
27.1
|
1.0
|
OD1
|
D:ASN577
|
2.2
|
28.8
|
1.0
|
O
|
D:HOH4819
|
2.2
|
22.8
|
1.0
|
OD1
|
D:ASP550
|
2.2
|
27.2
|
1.0
|
PA
|
D:P222702
|
3.1
|
26.3
|
1.0
|
CG
|
D:ASN577
|
3.2
|
28.4
|
1.0
|
PB
|
D:P222702
|
3.2
|
25.0
|
1.0
|
C
|
D:GLU579
|
3.3
|
29.7
|
1.0
|
O3A
|
D:P222702
|
3.3
|
22.4
|
1.0
|
CG
|
D:ASP550
|
3.3
|
28.3
|
1.0
|
ND2
|
D:ASN577
|
3.4
|
26.1
|
1.0
|
O7
|
D:P222702
|
3.7
|
26.0
|
1.0
|
N
|
D:GLY581
|
3.8
|
28.3
|
1.0
|
OD2
|
D:ASP550
|
3.8
|
27.9
|
1.0
|
O2B
|
D:P222702
|
3.9
|
22.0
|
1.0
|
N
|
D:GLU579
|
3.9
|
29.2
|
1.0
|
N
|
D:ASP550
|
4.1
|
23.6
|
1.0
|
CA
|
D:GLU579
|
4.2
|
29.1
|
1.0
|
CG
|
D:GLU579
|
4.2
|
26.1
|
1.0
|
N
|
D:GLN580
|
4.2
|
31.0
|
1.0
|
O2A
|
D:P222702
|
4.3
|
21.3
|
1.0
|
O1B
|
D:P222702
|
4.4
|
23.1
|
1.0
|
CA
|
D:GLN580
|
4.4
|
30.7
|
1.0
|
N
|
D:ALA551
|
4.4
|
21.1
|
1.0
|
N
|
D:ASN577
|
4.5
|
26.3
|
1.0
|
CB
|
D:ASN577
|
4.6
|
28.4
|
1.0
|
CB
|
D:ASP550
|
4.6
|
25.2
|
1.0
|
CA
|
D:GLY581
|
4.6
|
29.8
|
1.0
|
C
|
D:GLN580
|
4.6
|
27.8
|
1.0
|
O
|
D:LEU575
|
4.7
|
25.5
|
1.0
|
CA
|
D:ASP550
|
4.8
|
23.6
|
1.0
|
N
|
D:GLU578
|
4.8
|
26.4
|
1.0
|
CA
|
D:GLY549
|
4.8
|
23.2
|
1.0
|
CB
|
D:GLU579
|
4.8
|
27.3
|
1.0
|
C
|
D:GLY549
|
4.8
|
25.2
|
1.0
|
CB
|
D:ALA551
|
4.9
|
17.9
|
1.0
|
C
|
D:ASN577
|
4.9
|
26.7
|
1.0
|
CA
|
D:ASN577
|
4.9
|
27.1
|
1.0
|
|
Reference:
J.A.Mccourt,
S.S.Pang,
L.W.Guddat,
R.G.Duggleby.
Elucidating the Specificity of Binding of Sulfonylurea Herbicides to Acetohydroxyacid Synthase. Biochemistry V. 44 2330 2005.
ISSN: ISSN 0006-2960
PubMed: 15709745
DOI: 10.1021/BI047980A
Page generated: Tue Aug 13 14:29:40 2024
|