Iron in PDB 3gke: Crystal Structure of Dicamba Monooxygenase
Protein crystallography data
The structure of Crystal Structure of Dicamba Monooxygenase, PDB code: 3gke
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)
|
42.15 /
1.75
|
Space group
|
P 32
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.026,
81.026,
158.154,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.3 /
19.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Dicamba Monooxygenase
(pdb code 3gke). 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, PDB code: 3gke:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 3gke
Go back to
Iron Binding Sites List in 3gke
Iron binding site 1 out
of 8 in the Crystal Structure of Dicamba Monooxygenase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:27.0
occ:1.00
|
FE1
|
A:FES500
|
0.0
|
27.0
|
1.0
|
ND1
|
A:HIS51
|
2.1
|
29.8
|
1.0
|
ND1
|
A:HIS71
|
2.2
|
26.3
|
1.0
|
S1
|
A:FES500
|
2.2
|
28.2
|
1.0
|
S2
|
A:FES500
|
2.2
|
24.8
|
1.0
|
FE2
|
A:FES500
|
2.7
|
26.5
|
1.0
|
CE1
|
A:HIS51
|
3.1
|
30.7
|
1.0
|
CG
|
A:HIS51
|
3.1
|
28.2
|
1.0
|
CE1
|
A:HIS71
|
3.1
|
26.4
|
1.0
|
CG
|
A:HIS71
|
3.1
|
27.2
|
1.0
|
CB
|
A:HIS51
|
3.4
|
26.6
|
1.0
|
CB
|
A:HIS71
|
3.4
|
26.3
|
1.0
|
N
|
A:HIS71
|
3.8
|
26.1
|
1.0
|
CB
|
A:TYR70
|
4.0
|
26.4
|
1.0
|
CA
|
A:HIS71
|
4.2
|
25.8
|
1.0
|
NE2
|
A:HIS51
|
4.2
|
29.8
|
1.0
|
NE2
|
A:HIS71
|
4.2
|
26.3
|
1.0
|
N
|
A:ARG52
|
4.2
|
26.3
|
1.0
|
CD2
|
A:HIS51
|
4.2
|
31.8
|
1.0
|
CD2
|
A:HIS71
|
4.2
|
31.6
|
1.0
|
SG
|
A:CYS49
|
4.4
|
26.4
|
1.0
|
CG
|
A:TYR70
|
4.4
|
25.9
|
1.0
|
SG
|
A:CYS68
|
4.4
|
26.6
|
1.0
|
CB
|
A:ARG52
|
4.5
|
23.6
|
1.0
|
CD1
|
A:TYR70
|
4.5
|
23.9
|
1.0
|
C
|
A:TYR70
|
4.6
|
29.1
|
1.0
|
CA
|
A:HIS51
|
4.7
|
28.5
|
1.0
|
C
|
A:HIS71
|
4.8
|
31.7
|
1.0
|
C
|
A:HIS51
|
4.9
|
28.8
|
1.0
|
CA
|
A:TYR70
|
4.9
|
25.5
|
1.0
|
CA
|
A:ARG52
|
4.9
|
25.8
|
1.0
|
CG
|
A:ARG52
|
5.0
|
30.3
|
1.0
|
|
Iron binding site 2 out
of 8 in 3gke
Go back to
Iron Binding Sites List in 3gke
Iron binding site 2 out
of 8 in the Crystal Structure of Dicamba Monooxygenase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:26.5
occ:1.00
|
FE2
|
A:FES500
|
0.0
|
26.5
|
1.0
|
S1
|
A:FES500
|
2.2
|
28.2
|
1.0
|
S2
|
A:FES500
|
2.2
|
24.8
|
1.0
|
SG
|
A:CYS68
|
2.3
|
26.6
|
1.0
|
SG
|
A:CYS49
|
2.3
|
26.4
|
1.0
|
FE1
|
A:FES500
|
2.7
|
27.0
|
1.0
|
CB
|
A:CYS49
|
3.1
|
23.9
|
1.0
|
CB
|
A:CYS68
|
3.1
|
24.7
|
1.0
|
CB
|
A:HIS51
|
4.1
|
26.6
|
1.0
|
CB
|
A:TYR70
|
4.3
|
26.4
|
1.0
|
ND1
|
A:HIS51
|
4.3
|
29.8
|
1.0
|
N
|
A:HIS71
|
4.5
|
26.1
|
1.0
|
ND1
|
A:HIS71
|
4.5
|
26.3
|
1.0
|
CA
|
A:CYS49
|
4.5
|
22.3
|
1.0
|
CB
|
A:ALA54
|
4.6
|
26.7
|
1.0
|
CA
|
A:CYS68
|
4.6
|
28.1
|
1.0
|
CG
|
A:HIS51
|
4.7
|
28.2
|
1.0
|
N
|
A:ARG52
|
4.7
|
26.3
|
1.0
|
CD1
|
A:LEU73
|
4.8
|
27.4
|
1.0
|
N
|
A:TYR70
|
4.9
|
26.1
|
1.0
|
CG
|
A:LEU73
|
4.9
|
29.9
|
1.0
|
CB
|
A:LEU73
|
5.0
|
28.2
|
1.0
|
N
|
A:HIS51
|
5.0
|
28.5
|
1.0
|
|
Iron binding site 3 out
of 8 in 3gke
Go back to
Iron Binding Sites List in 3gke
Iron binding site 3 out
of 8 in the Crystal Structure of Dicamba Monooxygenase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:21.1
occ:1.00
|
NE2
|
A:HIS165
|
2.0
|
25.8
|
1.0
|
OD2
|
A:ASP294
|
2.0
|
24.5
|
1.0
|
OXT
|
A:ACT354
|
2.1
|
26.7
|
1.0
|
NE2
|
A:HIS160
|
2.1
|
25.6
|
1.0
|
CG
|
A:ASP294
|
2.7
|
24.9
|
1.0
|
OD1
|
A:ASP294
|
2.8
|
25.6
|
1.0
|
C
|
A:ACT354
|
2.9
|
31.7
|
1.0
|
CE1
|
A:HIS165
|
3.0
|
22.4
|
1.0
|
O
|
A:ACT354
|
3.0
|
27.7
|
1.0
|
CE1
|
A:HIS160
|
3.1
|
26.5
|
1.0
|
CD2
|
A:HIS165
|
3.1
|
21.8
|
1.0
|
CD2
|
A:HIS160
|
3.1
|
26.9
|
1.0
|
OD1
|
A:ASN154
|
3.7
|
23.8
|
1.0
|
O
|
A:HOH385
|
4.0
|
20.5
|
1.0
|
ND1
|
A:HIS165
|
4.1
|
22.4
|
1.0
|
CG
|
A:HIS165
|
4.2
|
22.5
|
1.0
|
ND1
|
A:HIS160
|
4.2
|
23.4
|
1.0
|
CB
|
A:ASP294
|
4.2
|
26.6
|
1.0
|
CG
|
A:HIS160
|
4.2
|
27.0
|
1.0
|
ND2
|
A:ASN154
|
4.3
|
21.9
|
1.0
|
CH3
|
A:ACT354
|
4.3
|
31.6
|
1.0
|
CG
|
A:ASN154
|
4.4
|
23.8
|
1.0
|
CD2
|
A:LEU290
|
4.5
|
29.4
|
1.0
|
O
|
A:ALA289
|
4.7
|
22.6
|
1.0
|
|
Iron binding site 4 out
of 8 in 3gke
Go back to
Iron Binding Sites List in 3gke
Iron binding site 4 out
of 8 in the Crystal Structure of Dicamba Monooxygenase
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 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
|
21.7
|
1.0
|
S2
|
B:FES500
|
2.2
|
22.6
|
1.0
|
SG
|
B:CYS49
|
2.3
|
20.1
|
1.0
|
SG
|
B:CYS68
|
2.3
|
19.5
|
1.0
|
FE2
|
B:FES500
|
2.7
|
21.4
|
1.0
|
CB
|
B:CYS49
|
3.1
|
19.1
|
1.0
|
CB
|
B:CYS68
|
3.2
|
14.4
|
1.0
|
CB
|
B:HIS51
|
4.1
|
18.5
|
1.0
|
CB
|
B:ALA54
|
4.3
|
17.8
|
1.0
|
ND1
|
B:HIS51
|
4.3
|
21.6
|
1.0
|
CB
|
B:TYR70
|
4.4
|
20.8
|
1.0
|
ND1
|
B:HIS71
|
4.5
|
22.5
|
1.0
|
N
|
B:HIS71
|
4.5
|
22.3
|
1.0
|
CA
|
B:CYS49
|
4.5
|
19.4
|
1.0
|
CA
|
B:CYS68
|
4.6
|
18.2
|
1.0
|
CG
|
B:HIS51
|
4.7
|
24.1
|
1.0
|
N
|
B:ARG52
|
4.7
|
20.2
|
1.0
|
CD1
|
B:LEU73
|
4.9
|
21.9
|
1.0
|
CD2
|
B:LEU56
|
4.9
|
19.1
|
1.0
|
N
|
B:HIS51
|
4.9
|
18.1
|
1.0
|
CG
|
B:LEU73
|
5.0
|
20.6
|
1.0
|
N
|
B:ALA54
|
5.0
|
20.8
|
1.0
|
CB
|
B:LEU73
|
5.0
|
19.3
|
1.0
|
N
|
B:TYR70
|
5.0
|
20.2
|
1.0
|
|
Iron binding site 5 out
of 8 in 3gke
Go back to
Iron Binding Sites List in 3gke
Iron binding site 5 out
of 8 in the Crystal Structure of Dicamba Monooxygenase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:21.4
occ:1.00
|
FE2
|
B:FES500
|
0.0
|
21.4
|
1.0
|
ND1
|
B:HIS51
|
2.1
|
21.6
|
1.0
|
ND1
|
B:HIS71
|
2.1
|
22.5
|
1.0
|
S2
|
B:FES500
|
2.2
|
22.6
|
1.0
|
S1
|
B:FES500
|
2.2
|
21.7
|
1.0
|
FE1
|
B:FES500
|
2.7
|
20.0
|
1.0
|
CE1
|
B:HIS71
|
3.0
|
24.5
|
1.0
|
CE1
|
B:HIS51
|
3.1
|
24.1
|
1.0
|
CG
|
B:HIS51
|
3.1
|
24.1
|
1.0
|
CG
|
B:HIS71
|
3.2
|
24.7
|
1.0
|
CB
|
B:HIS51
|
3.4
|
18.5
|
1.0
|
CB
|
B:HIS71
|
3.6
|
19.4
|
1.0
|
N
|
B:HIS71
|
3.8
|
22.3
|
1.0
|
NE2
|
B:HIS71
|
4.2
|
25.9
|
1.0
|
NE2
|
B:HIS51
|
4.2
|
23.4
|
1.0
|
CB
|
B:TYR70
|
4.2
|
20.8
|
1.0
|
CA
|
B:HIS71
|
4.2
|
22.9
|
1.0
|
N
|
B:ARG52
|
4.2
|
20.2
|
1.0
|
CD2
|
B:HIS51
|
4.2
|
22.7
|
1.0
|
CD2
|
B:HIS71
|
4.3
|
30.0
|
1.0
|
SG
|
B:CYS49
|
4.4
|
20.1
|
1.0
|
SG
|
B:CYS68
|
4.5
|
19.5
|
1.0
|
CD1
|
B:TYR70
|
4.5
|
20.5
|
1.0
|
CB
|
B:ARG52
|
4.5
|
21.7
|
1.0
|
CG
|
B:ARG52
|
4.5
|
32.0
|
1.0
|
CG
|
B:TYR70
|
4.6
|
22.1
|
1.0
|
C
|
B:TYR70
|
4.7
|
22.4
|
1.0
|
CA
|
B:HIS51
|
4.7
|
19.7
|
1.0
|
C
|
B:HIS71
|
4.9
|
21.4
|
1.0
|
C
|
B:HIS51
|
4.9
|
21.1
|
1.0
|
CA
|
B:ARG52
|
5.0
|
18.7
|
1.0
|
|
Iron binding site 6 out
of 8 in 3gke
Go back to
Iron Binding Sites List in 3gke
Iron binding site 6 out
of 8 in the Crystal Structure of Dicamba Monooxygenase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:30.1
occ:1.00
|
OD2
|
B:ASP294
|
1.9
|
35.5
|
1.0
|
NE2
|
B:HIS165
|
2.0
|
34.8
|
1.0
|
O1
|
B:OXY600
|
2.1
|
42.5
|
1.0
|
NE2
|
B:HIS160
|
2.2
|
32.3
|
1.0
|
O2
|
B:OXY600
|
2.6
|
41.5
|
1.0
|
CG
|
B:ASP294
|
2.6
|
36.7
|
1.0
|
OD1
|
B:ASP294
|
2.7
|
33.0
|
1.0
|
CE1
|
B:HIS165
|
2.9
|
37.2
|
1.0
|
CD2
|
B:HIS165
|
3.1
|
39.5
|
1.0
|
CD2
|
B:HIS160
|
3.1
|
35.2
|
1.0
|
CE1
|
B:HIS160
|
3.1
|
31.9
|
1.0
|
OD1
|
B:ASN154
|
3.6
|
28.4
|
1.0
|
ND1
|
B:HIS165
|
4.1
|
37.3
|
1.0
|
O
|
B:HOH466
|
4.1
|
24.8
|
1.0
|
CB
|
B:ASP294
|
4.1
|
33.0
|
1.0
|
CG
|
B:HIS165
|
4.2
|
39.9
|
1.0
|
ND2
|
B:ASN154
|
4.2
|
26.7
|
1.0
|
ND1
|
B:HIS160
|
4.3
|
30.7
|
1.0
|
CG
|
B:HIS160
|
4.3
|
29.8
|
1.0
|
CG
|
B:ASN154
|
4.3
|
29.8
|
1.0
|
CD2
|
B:LEU290
|
4.7
|
42.2
|
1.0
|
O
|
B:ALA289
|
4.9
|
32.9
|
1.0
|
|
Iron binding site 7 out
of 8 in 3gke
Go back to
Iron Binding Sites List in 3gke
Iron binding site 7 out
of 8 in the Crystal Structure of Dicamba Monooxygenase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:22.0
occ:1.00
|
FE1
|
C:FES500
|
0.0
|
22.0
|
1.0
|
ND1
|
C:HIS71
|
2.1
|
18.8
|
1.0
|
ND1
|
C:HIS51
|
2.1
|
22.8
|
1.0
|
S2
|
C:FES500
|
2.2
|
23.0
|
1.0
|
S1
|
C:FES500
|
2.2
|
21.8
|
1.0
|
FE2
|
C:FES500
|
2.7
|
21.1
|
1.0
|
CE1
|
C:HIS71
|
3.0
|
23.4
|
1.0
|
CG
|
C:HIS51
|
3.1
|
25.4
|
1.0
|
CG
|
C:HIS71
|
3.1
|
22.0
|
1.0
|
CE1
|
C:HIS51
|
3.1
|
23.6
|
1.0
|
CB
|
C:HIS51
|
3.4
|
22.4
|
1.0
|
CB
|
C:HIS71
|
3.4
|
20.3
|
1.0
|
N
|
C:HIS71
|
3.7
|
22.0
|
1.0
|
CB
|
C:TYR70
|
4.0
|
21.5
|
1.0
|
CA
|
C:HIS71
|
4.1
|
23.0
|
1.0
|
NE2
|
C:HIS71
|
4.2
|
21.3
|
1.0
|
N
|
C:ARG52
|
4.2
|
22.4
|
1.0
|
CD2
|
C:HIS71
|
4.2
|
27.2
|
1.0
|
NE2
|
C:HIS51
|
4.2
|
25.6
|
1.0
|
CD2
|
C:HIS51
|
4.2
|
20.9
|
1.0
|
CG
|
C:TYR70
|
4.4
|
18.4
|
1.0
|
SG
|
C:CYS49
|
4.5
|
20.6
|
1.0
|
SG
|
C:CYS68
|
4.5
|
20.9
|
1.0
|
CB
|
C:ARG52
|
4.5
|
22.4
|
1.0
|
CD1
|
C:TYR70
|
4.5
|
21.1
|
1.0
|
C
|
C:TYR70
|
4.5
|
21.3
|
1.0
|
CA
|
C:HIS51
|
4.6
|
21.6
|
1.0
|
C
|
C:HIS51
|
4.8
|
21.8
|
1.0
|
CG
|
C:ARG52
|
4.8
|
24.0
|
1.0
|
C
|
C:HIS71
|
4.8
|
26.0
|
1.0
|
CA
|
C:TYR70
|
4.9
|
21.2
|
1.0
|
CA
|
C:ARG52
|
4.9
|
23.8
|
1.0
|
|
Iron binding site 8 out
of 8 in 3gke
Go back to
Iron Binding Sites List in 3gke
Iron binding site 8 out
of 8 in the Crystal Structure of Dicamba Monooxygenase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:21.1
occ:1.00
|
FE2
|
C:FES500
|
0.0
|
21.1
|
1.0
|
S2
|
C:FES500
|
2.2
|
23.0
|
1.0
|
S1
|
C:FES500
|
2.2
|
21.8
|
1.0
|
SG
|
C:CYS49
|
2.3
|
20.6
|
1.0
|
SG
|
C:CYS68
|
2.3
|
20.9
|
1.0
|
FE1
|
C:FES500
|
2.7
|
22.0
|
1.0
|
CB
|
C:CYS49
|
3.1
|
21.4
|
1.0
|
CB
|
C:CYS68
|
3.2
|
18.1
|
1.0
|
CB
|
C:HIS51
|
4.0
|
22.4
|
1.0
|
CB
|
C:TYR70
|
4.3
|
21.5
|
1.0
|
N
|
C:HIS71
|
4.4
|
22.0
|
1.0
|
ND1
|
C:HIS51
|
4.4
|
22.8
|
1.0
|
CB
|
C:ALA54
|
4.5
|
23.8
|
1.0
|
ND1
|
C:HIS71
|
4.5
|
18.8
|
1.0
|
CA
|
C:CYS49
|
4.5
|
19.0
|
1.0
|
CA
|
C:CYS68
|
4.6
|
18.6
|
1.0
|
N
|
C:ARG52
|
4.7
|
22.4
|
1.0
|
CG
|
C:HIS51
|
4.7
|
25.4
|
1.0
|
N
|
C:TYR70
|
4.9
|
22.4
|
1.0
|
CD1
|
C:LEU73
|
4.9
|
24.4
|
1.0
|
N
|
C:HIS51
|
4.9
|
22.8
|
1.0
|
CB
|
C:LEU73
|
4.9
|
21.5
|
1.0
|
CG
|
C:LEU73
|
4.9
|
23.9
|
1.0
|
CD2
|
C:LEU56
|
5.0
|
21.1
|
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 10:43:25 2024
|