Iron in PDB 3gl0: Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
Protein crystallography data
The structure of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa), PDB code: 3gl0
was solved by
M.A.Wilson,
R.Dumitru,
W.Z.Jiang,
D.P.Weeks,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.25 /
1.75
|
Space group
|
P 32
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.205,
81.205,
158.557,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.8 /
20.6
|
Other elements in 3gl0:
The structure of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
(pdb code 3gl0). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa), PDB code: 3gl0:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 3gl0
Go back to
Iron Binding Sites List in 3gl0
Iron binding site 1 out
of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:28.6
occ:1.00
|
FE1
|
A:FES500
|
0.0
|
28.6
|
1.0
|
ND1
|
A:HIS51
|
2.1
|
28.5
|
1.0
|
ND1
|
A:HIS71
|
2.1
|
28.0
|
1.0
|
S1
|
A:FES500
|
2.2
|
30.9
|
1.0
|
S2
|
A:FES500
|
2.2
|
28.7
|
1.0
|
FE2
|
A:FES500
|
2.7
|
27.2
|
1.0
|
CE1
|
A:HIS51
|
3.0
|
29.1
|
1.0
|
CG
|
A:HIS51
|
3.1
|
29.6
|
1.0
|
CG
|
A:HIS71
|
3.1
|
32.0
|
1.0
|
CE1
|
A:HIS71
|
3.1
|
28.9
|
1.0
|
CB
|
A:HIS71
|
3.4
|
31.1
|
1.0
|
CB
|
A:HIS51
|
3.4
|
28.6
|
1.0
|
N
|
A:HIS71
|
3.8
|
28.5
|
1.0
|
CB
|
A:TYR70
|
4.1
|
26.3
|
1.0
|
NE2
|
A:HIS51
|
4.1
|
30.6
|
1.0
|
CA
|
A:HIS71
|
4.1
|
28.7
|
1.0
|
N
|
A:ARG52
|
4.2
|
27.1
|
1.0
|
CD2
|
A:HIS51
|
4.2
|
34.2
|
1.0
|
NE2
|
A:HIS71
|
4.2
|
25.9
|
1.0
|
CD2
|
A:HIS71
|
4.2
|
30.7
|
1.0
|
SG
|
A:CYS49
|
4.4
|
26.9
|
1.0
|
CB
|
A:ARG52
|
4.4
|
25.4
|
1.0
|
SG
|
A:CYS68
|
4.4
|
28.2
|
1.0
|
CG
|
A:TYR70
|
4.5
|
25.9
|
1.0
|
CD1
|
A:TYR70
|
4.5
|
22.8
|
1.0
|
C
|
A:TYR70
|
4.6
|
30.1
|
1.0
|
CA
|
A:HIS51
|
4.7
|
28.5
|
1.0
|
C
|
A:HIS71
|
4.8
|
34.7
|
1.0
|
C
|
A:HIS51
|
4.9
|
25.6
|
1.0
|
CA
|
A:ARG52
|
4.9
|
28.2
|
1.0
|
CG
|
A:ARG52
|
4.9
|
27.4
|
1.0
|
CA
|
A:TYR70
|
4.9
|
27.4
|
1.0
|
CD1
|
B:LEU318
|
5.0
|
31.2
|
1.0
|
|
Iron binding site 2 out
of 8 in 3gl0
Go back to
Iron Binding Sites List in 3gl0
Iron binding site 2 out
of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:27.2
occ:1.00
|
FE2
|
A:FES500
|
0.0
|
27.2
|
1.0
|
S1
|
A:FES500
|
2.2
|
30.9
|
1.0
|
S2
|
A:FES500
|
2.2
|
28.7
|
1.0
|
SG
|
A:CYS49
|
2.3
|
26.9
|
1.0
|
SG
|
A:CYS68
|
2.3
|
28.2
|
1.0
|
FE1
|
A:FES500
|
2.7
|
28.6
|
1.0
|
CB
|
A:CYS49
|
3.0
|
24.8
|
1.0
|
CB
|
A:CYS68
|
3.1
|
30.4
|
1.0
|
CB
|
A:HIS51
|
4.0
|
28.6
|
1.0
|
ND1
|
A:HIS51
|
4.3
|
28.5
|
1.0
|
CB
|
A:TYR70
|
4.3
|
26.3
|
1.0
|
N
|
A:HIS71
|
4.5
|
28.5
|
1.0
|
CA
|
A:CYS49
|
4.5
|
23.1
|
1.0
|
CA
|
A:CYS68
|
4.5
|
29.9
|
1.0
|
ND1
|
A:HIS71
|
4.6
|
28.0
|
1.0
|
CB
|
A:ALA54
|
4.6
|
26.9
|
1.0
|
CG
|
A:HIS51
|
4.7
|
29.6
|
1.0
|
N
|
A:ARG52
|
4.7
|
27.1
|
1.0
|
CD1
|
A:LEU73
|
4.8
|
25.6
|
1.0
|
CB
|
A:LEU73
|
4.9
|
33.9
|
1.0
|
N
|
A:TYR70
|
4.9
|
27.2
|
1.0
|
CG
|
A:LEU73
|
4.9
|
34.2
|
1.0
|
CD2
|
A:LEU56
|
5.0
|
28.9
|
1.0
|
C
|
A:CYS49
|
5.0
|
23.1
|
1.0
|
N
|
A:HIS51
|
5.0
|
29.0
|
1.0
|
|
Iron binding site 3 out
of 8 in 3gl0
Go back to
Iron Binding Sites List in 3gl0
Iron binding site 3 out
of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:21.6
occ:1.00
|
NE2
|
A:HIS165
|
2.0
|
23.9
|
1.0
|
OD2
|
A:ASP294
|
2.0
|
28.6
|
1.0
|
NE2
|
A:HIS160
|
2.1
|
25.7
|
1.0
|
O1
|
A:OXY700
|
2.3
|
25.0
|
1.0
|
CG
|
A:ASP294
|
2.7
|
23.1
|
1.0
|
OD1
|
A:ASP294
|
2.8
|
22.9
|
1.0
|
O2
|
A:OXY700
|
2.8
|
36.0
|
1.0
|
CD2
|
A:HIS165
|
3.0
|
23.5
|
1.0
|
CE1
|
A:HIS165
|
3.0
|
26.6
|
1.0
|
CE1
|
A:HIS160
|
3.1
|
26.0
|
1.0
|
CD2
|
A:HIS160
|
3.1
|
25.9
|
1.0
|
OD1
|
A:ASN154
|
3.7
|
24.7
|
1.0
|
O
|
A:HOH384
|
4.0
|
24.9
|
1.0
|
ND1
|
A:HIS165
|
4.1
|
24.4
|
1.0
|
CG
|
A:HIS165
|
4.1
|
21.8
|
1.0
|
CB
|
A:ASP294
|
4.2
|
23.7
|
1.0
|
ND1
|
A:HIS160
|
4.2
|
22.7
|
1.0
|
CG
|
A:HIS160
|
4.3
|
24.1
|
1.0
|
ND2
|
A:ASN154
|
4.4
|
24.3
|
1.0
|
CG
|
A:ASN154
|
4.5
|
22.4
|
1.0
|
CD2
|
A:LEU290
|
4.5
|
26.9
|
1.0
|
O
|
A:ALA289
|
4.7
|
22.0
|
1.0
|
|
Iron binding site 4 out
of 8 in 3gl0
Go back to
Iron Binding Sites List in 3gl0
Iron binding site 4 out
of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:20.0
occ:1.00
|
FE1
|
B:FES500
|
0.0
|
20.0
|
1.0
|
S1
|
B:FES500
|
2.2
|
21.6
|
1.0
|
S2
|
B:FES500
|
2.2
|
22.9
|
1.0
|
SG
|
B:CYS49
|
2.3
|
19.9
|
1.0
|
SG
|
B:CYS68
|
2.4
|
20.0
|
1.0
|
FE2
|
B:FES500
|
2.7
|
21.5
|
1.0
|
CB
|
B:CYS49
|
3.0
|
18.1
|
1.0
|
CB
|
B:CYS68
|
3.2
|
16.4
|
1.0
|
CB
|
B:HIS51
|
4.1
|
18.2
|
1.0
|
CB
|
B:ALA54
|
4.3
|
22.3
|
1.0
|
ND1
|
B:HIS51
|
4.4
|
22.1
|
1.0
|
CB
|
B:TYR70
|
4.4
|
17.9
|
1.0
|
N
|
B:HIS71
|
4.5
|
22.4
|
1.0
|
ND1
|
B:HIS71
|
4.5
|
21.3
|
1.0
|
CA
|
B:CYS49
|
4.5
|
16.8
|
1.0
|
CA
|
B:CYS68
|
4.6
|
17.8
|
1.0
|
CG
|
B:HIS51
|
4.7
|
24.3
|
1.0
|
N
|
B:ARG52
|
4.7
|
22.9
|
1.0
|
CD2
|
B:LEU56
|
4.9
|
21.5
|
1.0
|
N
|
B:HIS51
|
4.9
|
21.1
|
1.0
|
CD1
|
B:LEU73
|
5.0
|
21.7
|
1.0
|
N
|
B:ALA54
|
5.0
|
20.6
|
1.0
|
N
|
B:TYR70
|
5.0
|
21.4
|
1.0
|
CB
|
B:LEU73
|
5.0
|
19.0
|
1.0
|
CG
|
B:LEU73
|
5.0
|
21.2
|
1.0
|
|
Iron binding site 5 out
of 8 in 3gl0
Go back to
Iron Binding Sites List in 3gl0
Iron binding site 5 out
of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:21.5
occ:1.00
|
FE2
|
B:FES500
|
0.0
|
21.5
|
1.0
|
ND1
|
B:HIS71
|
2.1
|
21.3
|
1.0
|
ND1
|
B:HIS51
|
2.1
|
22.1
|
1.0
|
S2
|
B:FES500
|
2.2
|
22.9
|
1.0
|
S1
|
B:FES500
|
2.2
|
21.6
|
1.0
|
FE1
|
B:FES500
|
2.7
|
20.0
|
1.0
|
CE1
|
B:HIS71
|
3.0
|
24.8
|
1.0
|
CE1
|
B:HIS51
|
3.1
|
23.3
|
1.0
|
CG
|
B:HIS51
|
3.1
|
24.3
|
1.0
|
CG
|
B:HIS71
|
3.1
|
23.4
|
1.0
|
CB
|
B:HIS51
|
3.4
|
18.2
|
1.0
|
CB
|
B:HIS71
|
3.5
|
18.6
|
1.0
|
N
|
B:HIS71
|
3.8
|
22.4
|
1.0
|
CA
|
B:HIS71
|
4.2
|
24.0
|
1.0
|
NE2
|
B:HIS71
|
4.2
|
24.6
|
1.0
|
NE2
|
B:HIS51
|
4.2
|
24.4
|
1.0
|
CB
|
B:TYR70
|
4.2
|
17.9
|
1.0
|
CD2
|
B:HIS51
|
4.2
|
25.2
|
1.0
|
N
|
B:ARG52
|
4.2
|
22.9
|
1.0
|
CD2
|
B:HIS71
|
4.3
|
31.7
|
1.0
|
SG
|
B:CYS49
|
4.5
|
19.9
|
1.0
|
SG
|
B:CYS68
|
4.5
|
20.0
|
1.0
|
CD1
|
B:TYR70
|
4.5
|
21.0
|
1.0
|
CB
|
B:ARG52
|
4.5
|
20.0
|
1.0
|
CG
|
B:ARG52
|
4.6
|
30.7
|
1.0
|
CG
|
B:TYR70
|
4.6
|
23.2
|
1.0
|
C
|
B:TYR70
|
4.6
|
20.0
|
1.0
|
CA
|
B:HIS51
|
4.7
|
18.1
|
1.0
|
C
|
B:HIS71
|
4.8
|
24.9
|
1.0
|
C
|
B:HIS51
|
4.9
|
21.5
|
1.0
|
CA
|
B:ARG52
|
5.0
|
18.8
|
1.0
|
CA
|
B:TYR70
|
5.0
|
19.2
|
1.0
|
|
Iron binding site 6 out
of 8 in 3gl0
Go back to
Iron Binding Sites List in 3gl0
Iron binding site 6 out
of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:32.1
occ:1.00
|
OD2
|
B:ASP294
|
2.0
|
34.5
|
1.0
|
NE2
|
B:HIS165
|
2.1
|
35.0
|
1.0
|
NE2
|
B:HIS160
|
2.2
|
39.4
|
1.0
|
O1
|
B:OXY600
|
2.2
|
33.8
|
1.0
|
O2
|
B:OXY600
|
2.5
|
45.5
|
1.0
|
CG
|
B:ASP294
|
2.7
|
34.4
|
1.0
|
OD1
|
B:ASP294
|
2.8
|
32.8
|
1.0
|
CE1
|
B:HIS165
|
3.0
|
37.6
|
1.0
|
CD2
|
B:HIS165
|
3.1
|
36.7
|
1.0
|
CD2
|
B:HIS160
|
3.1
|
40.3
|
1.0
|
CE1
|
B:HIS160
|
3.2
|
40.6
|
1.0
|
OD1
|
B:ASN154
|
3.6
|
31.5
|
1.0
|
O
|
B:HOH437
|
4.0
|
33.3
|
1.0
|
ND1
|
B:HIS165
|
4.2
|
35.9
|
1.0
|
ND2
|
B:ASN154
|
4.2
|
28.1
|
1.0
|
CB
|
B:ASP294
|
4.2
|
31.1
|
1.0
|
CG
|
B:HIS165
|
4.2
|
39.9
|
1.0
|
CG
|
B:ASN154
|
4.3
|
27.5
|
1.0
|
ND1
|
B:HIS160
|
4.3
|
30.4
|
1.0
|
CG
|
B:HIS160
|
4.3
|
31.4
|
1.0
|
CD2
|
B:LEU290
|
4.5
|
41.2
|
1.0
|
O
|
B:ALA289
|
4.7
|
35.6
|
1.0
|
|
Iron binding site 7 out
of 8 in 3gl0
Go back to
Iron Binding Sites List in 3gl0
Iron binding site 7 out
of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:22.3
occ:1.00
|
FE1
|
C:FES500
|
0.0
|
22.3
|
1.0
|
ND1
|
C:HIS71
|
2.1
|
18.6
|
1.0
|
ND1
|
C:HIS51
|
2.2
|
24.6
|
1.0
|
S2
|
C:FES500
|
2.2
|
23.7
|
1.0
|
S1
|
C:FES500
|
2.2
|
22.3
|
1.0
|
FE2
|
C:FES500
|
2.7
|
21.5
|
1.0
|
CE1
|
C:HIS71
|
3.0
|
23.5
|
1.0
|
CG
|
C:HIS71
|
3.1
|
22.0
|
1.0
|
CG
|
C:HIS51
|
3.1
|
24.1
|
1.0
|
CE1
|
C:HIS51
|
3.2
|
25.8
|
1.0
|
CB
|
C:HIS51
|
3.4
|
23.1
|
1.0
|
CB
|
C:HIS71
|
3.5
|
22.2
|
1.0
|
N
|
C:HIS71
|
3.7
|
19.7
|
1.0
|
CB
|
C:TYR70
|
4.1
|
19.7
|
1.0
|
CA
|
C:HIS71
|
4.1
|
22.8
|
1.0
|
NE2
|
C:HIS71
|
4.2
|
21.0
|
1.0
|
N
|
C:ARG52
|
4.2
|
23.1
|
1.0
|
CD2
|
C:HIS71
|
4.2
|
29.3
|
1.0
|
NE2
|
C:HIS51
|
4.3
|
24.6
|
1.0
|
CD2
|
C:HIS51
|
4.3
|
22.5
|
1.0
|
SG
|
C:CYS49
|
4.5
|
21.5
|
1.0
|
CG
|
C:TYR70
|
4.5
|
20.7
|
1.0
|
CB
|
C:ARG52
|
4.5
|
20.2
|
1.0
|
SG
|
C:CYS68
|
4.5
|
22.7
|
1.0
|
CD1
|
C:TYR70
|
4.5
|
24.7
|
1.0
|
C
|
C:TYR70
|
4.5
|
19.6
|
1.0
|
CA
|
C:HIS51
|
4.7
|
21.6
|
1.0
|
CG
|
C:ARG52
|
4.8
|
24.1
|
1.0
|
C
|
C:HIS71
|
4.8
|
23.1
|
1.0
|
C
|
C:HIS51
|
4.8
|
19.3
|
1.0
|
CA
|
C:TYR70
|
4.9
|
21.4
|
1.0
|
CA
|
C:ARG52
|
4.9
|
23.7
|
1.0
|
|
Iron binding site 8 out
of 8 in 3gl0
Go back to
Iron Binding Sites List in 3gl0
Iron binding site 8 out
of 8 in the Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Dicamba Monooxygenase Bound to 3,6 Dichlorosalicylic Acid (Dcsa) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:21.5
occ:1.00
|
FE2
|
C:FES500
|
0.0
|
21.5
|
1.0
|
S2
|
C:FES500
|
2.2
|
23.7
|
1.0
|
S1
|
C:FES500
|
2.2
|
22.3
|
1.0
|
SG
|
C:CYS49
|
2.3
|
21.5
|
1.0
|
SG
|
C:CYS68
|
2.3
|
22.7
|
1.0
|
FE1
|
C:FES500
|
2.7
|
22.3
|
1.0
|
CB
|
C:CYS49
|
3.1
|
22.5
|
1.0
|
CB
|
C:CYS68
|
3.1
|
19.8
|
1.0
|
CB
|
C:HIS51
|
4.0
|
23.1
|
1.0
|
CB
|
C:TYR70
|
4.3
|
19.7
|
1.0
|
N
|
C:HIS71
|
4.4
|
19.7
|
1.0
|
ND1
|
C:HIS51
|
4.4
|
24.6
|
1.0
|
CA
|
C:CYS49
|
4.5
|
19.8
|
1.0
|
ND1
|
C:HIS71
|
4.5
|
18.6
|
1.0
|
CB
|
C:ALA54
|
4.5
|
24.2
|
1.0
|
CA
|
C:CYS68
|
4.6
|
19.5
|
1.0
|
N
|
C:ARG52
|
4.7
|
23.1
|
1.0
|
CG
|
C:HIS51
|
4.8
|
24.1
|
1.0
|
N
|
C:TYR70
|
4.9
|
23.7
|
1.0
|
N
|
C:HIS51
|
4.9
|
23.4
|
1.0
|
CB
|
C:LEU73
|
4.9
|
22.8
|
1.0
|
CD1
|
C:LEU73
|
4.9
|
21.8
|
1.0
|
CG
|
C:LEU73
|
5.0
|
21.3
|
1.0
|
|
Reference:
R.Dumitru,
W.Z.Jiang,
D.P.Weeks,
M.A.Wilson.
Crystal Structure of Dicamba Monooxygenase: A Rieske Nonheme Oxygenase That Catalyzes Oxidative Demethylation. J.Mol.Biol. V. 392 498 2009.
ISSN: ISSN 0022-2836
PubMed: 19616011
DOI: 10.1016/J.JMB.2009.07.021
Page generated: Sun Aug 4 10:45:22 2024
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