Iron in PDB 3gob: Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa
Protein crystallography data
The structure of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa, PDB code: 3gob
was solved by
T.J.Rydel,
E.J.Sturman,
F.Moshiri,
G.R.Brown,
Y.Qi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.05
|
Space group
|
P 32
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.010,
81.010,
161.050,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 3gob:
The structure of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa
(pdb code 3gob). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa, PDB code: 3gob:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3gob
Go back to
Iron Binding Sites List in 3gob
Iron binding site 1 out
of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dcsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:29.2
occ:1.00
|
FE1
|
A:FES501
|
0.0
|
29.2
|
1.0
|
S1
|
A:FES501
|
2.2
|
31.5
|
1.0
|
S2
|
A:FES501
|
2.3
|
28.2
|
1.0
|
SG
|
A:CYS68
|
2.3
|
27.0
|
1.0
|
SG
|
A:CYS49
|
2.4
|
25.3
|
1.0
|
FE2
|
A:FES501
|
2.7
|
30.5
|
1.0
|
CB
|
A:CYS49
|
3.1
|
26.1
|
1.0
|
CB
|
A:CYS68
|
3.2
|
27.5
|
1.0
|
CB
|
A:HIS51
|
4.0
|
27.1
|
1.0
|
CB
|
A:TYR70
|
4.2
|
31.8
|
1.0
|
N
|
A:HIS71
|
4.4
|
31.0
|
1.0
|
ND1
|
A:HIS51
|
4.5
|
29.1
|
1.0
|
CA
|
A:CYS49
|
4.6
|
26.0
|
1.0
|
CB
|
A:ALA54
|
4.6
|
28.7
|
1.0
|
CA
|
A:CYS68
|
4.6
|
28.2
|
1.0
|
N
|
A:ARG52
|
4.7
|
29.4
|
1.0
|
ND1
|
A:HIS71
|
4.7
|
33.3
|
1.0
|
CG
|
A:HIS51
|
4.7
|
29.4
|
1.0
|
CD1
|
A:LEU73
|
4.8
|
28.8
|
1.0
|
CG
|
A:LEU73
|
4.9
|
30.1
|
1.0
|
CB
|
A:LEU73
|
4.9
|
28.9
|
1.0
|
N
|
A:HIS51
|
4.9
|
28.1
|
1.0
|
N
|
A:TYR70
|
5.0
|
29.9
|
1.0
|
N
|
A:ALA54
|
5.0
|
28.0
|
1.0
|
CD2
|
A:LEU56
|
5.0
|
23.3
|
1.0
|
|
Iron binding site 2 out
of 6 in 3gob
Go back to
Iron Binding Sites List in 3gob
Iron binding site 2 out
of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dcsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:30.5
occ:1.00
|
FE2
|
A:FES501
|
0.0
|
30.5
|
1.0
|
ND1
|
A:HIS51
|
2.2
|
29.1
|
1.0
|
S2
|
A:FES501
|
2.2
|
28.2
|
1.0
|
S1
|
A:FES501
|
2.3
|
31.5
|
1.0
|
ND1
|
A:HIS71
|
2.3
|
33.3
|
1.0
|
FE1
|
A:FES501
|
2.7
|
29.2
|
1.0
|
CG
|
A:HIS51
|
3.1
|
29.4
|
1.0
|
CG
|
A:HIS71
|
3.2
|
33.4
|
1.0
|
CE1
|
A:HIS51
|
3.2
|
28.8
|
1.0
|
CE1
|
A:HIS71
|
3.3
|
33.6
|
1.0
|
CB
|
A:HIS51
|
3.3
|
27.1
|
1.0
|
CB
|
A:HIS71
|
3.4
|
32.4
|
1.0
|
N
|
A:HIS71
|
3.7
|
31.0
|
1.0
|
CB
|
A:TYR70
|
4.0
|
31.8
|
1.0
|
CA
|
A:HIS71
|
4.1
|
32.8
|
1.0
|
N
|
A:ARG52
|
4.1
|
29.4
|
1.0
|
CD2
|
A:HIS51
|
4.3
|
29.2
|
1.0
|
NE2
|
A:HIS51
|
4.3
|
29.6
|
1.0
|
CD2
|
A:HIS71
|
4.3
|
33.0
|
1.0
|
NE2
|
A:HIS71
|
4.4
|
30.4
|
1.0
|
CG
|
A:TYR70
|
4.4
|
31.9
|
1.0
|
CD1
|
A:TYR70
|
4.4
|
33.7
|
1.0
|
CB
|
A:ARG52
|
4.4
|
30.6
|
1.0
|
SG
|
A:CYS68
|
4.5
|
27.0
|
1.0
|
SG
|
A:CYS49
|
4.5
|
25.3
|
1.0
|
C
|
A:TYR70
|
4.6
|
30.7
|
1.0
|
CA
|
A:HIS51
|
4.7
|
28.9
|
1.0
|
C
|
A:HIS51
|
4.8
|
28.6
|
1.0
|
CA
|
A:ARG52
|
4.9
|
29.7
|
1.0
|
CA
|
A:TYR70
|
4.9
|
31.1
|
1.0
|
C
|
A:HIS71
|
4.9
|
32.3
|
1.0
|
CG
|
A:ARG52
|
4.9
|
32.2
|
1.0
|
|
Iron binding site 3 out
of 6 in 3gob
Go back to
Iron Binding Sites List in 3gob
Iron binding site 3 out
of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dcsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:33.6
occ:1.00
|
FE1
|
B:FES501
|
0.0
|
33.6
|
1.0
|
S1
|
B:FES501
|
2.2
|
37.6
|
1.0
|
S2
|
B:FES501
|
2.3
|
35.5
|
1.0
|
SG
|
B:CYS68
|
2.3
|
30.1
|
1.0
|
SG
|
B:CYS49
|
2.3
|
35.1
|
1.0
|
FE2
|
B:FES501
|
2.7
|
36.0
|
1.0
|
CB
|
B:CYS49
|
3.1
|
34.5
|
1.0
|
CB
|
B:CYS68
|
3.1
|
30.5
|
1.0
|
CB
|
B:HIS51
|
4.1
|
34.4
|
1.0
|
CB
|
B:TYR70
|
4.2
|
33.6
|
1.0
|
N
|
B:HIS71
|
4.3
|
34.3
|
1.0
|
ND1
|
B:HIS51
|
4.4
|
35.1
|
1.0
|
CB
|
B:ALA54
|
4.6
|
33.8
|
1.0
|
CA
|
B:CYS49
|
4.6
|
31.5
|
1.0
|
CA
|
B:CYS68
|
4.6
|
30.3
|
1.0
|
ND1
|
B:HIS71
|
4.6
|
36.3
|
1.0
|
N
|
B:ARG52
|
4.7
|
33.5
|
1.0
|
CG
|
B:HIS51
|
4.8
|
36.0
|
1.0
|
CD1
|
B:LEU73
|
4.9
|
37.8
|
1.0
|
N
|
B:TYR70
|
4.9
|
33.7
|
1.0
|
CG
|
B:LEU73
|
5.0
|
36.1
|
1.0
|
CB
|
B:LEU73
|
5.0
|
35.0
|
1.0
|
N
|
B:ALA54
|
5.0
|
28.8
|
1.0
|
CA
|
B:TYR70
|
5.0
|
33.7
|
1.0
|
N
|
B:HIS51
|
5.0
|
31.7
|
1.0
|
|
Iron binding site 4 out
of 6 in 3gob
Go back to
Iron Binding Sites List in 3gob
Iron binding site 4 out
of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dcsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:36.0
occ:1.00
|
FE2
|
B:FES501
|
0.0
|
36.0
|
1.0
|
ND1
|
B:HIS51
|
2.2
|
35.1
|
1.0
|
S1
|
B:FES501
|
2.2
|
37.6
|
1.0
|
ND1
|
B:HIS71
|
2.2
|
36.3
|
1.0
|
S2
|
B:FES501
|
2.3
|
35.5
|
1.0
|
FE1
|
B:FES501
|
2.7
|
33.6
|
1.0
|
CG
|
B:HIS71
|
3.1
|
33.6
|
1.0
|
CG
|
B:HIS51
|
3.1
|
36.0
|
1.0
|
CE1
|
B:HIS51
|
3.2
|
34.3
|
1.0
|
CE1
|
B:HIS71
|
3.3
|
32.6
|
1.0
|
CB
|
B:HIS71
|
3.3
|
32.8
|
1.0
|
CB
|
B:HIS51
|
3.4
|
34.4
|
1.0
|
N
|
B:HIS71
|
3.7
|
34.3
|
1.0
|
CB
|
B:TYR70
|
4.0
|
33.6
|
1.0
|
CA
|
B:HIS71
|
4.1
|
33.8
|
1.0
|
N
|
B:ARG52
|
4.2
|
33.5
|
1.0
|
NE2
|
B:HIS51
|
4.3
|
34.3
|
1.0
|
CD2
|
B:HIS51
|
4.3
|
35.3
|
1.0
|
CD2
|
B:HIS71
|
4.3
|
31.8
|
1.0
|
NE2
|
B:HIS71
|
4.3
|
32.7
|
1.0
|
CG
|
B:TYR70
|
4.4
|
34.1
|
1.0
|
SG
|
B:CYS49
|
4.4
|
35.1
|
1.0
|
CD1
|
B:TYR70
|
4.4
|
34.0
|
1.0
|
CB
|
B:ARG52
|
4.5
|
35.7
|
1.0
|
SG
|
B:CYS68
|
4.5
|
30.1
|
1.0
|
C
|
B:TYR70
|
4.6
|
33.7
|
1.0
|
CA
|
B:HIS51
|
4.7
|
33.6
|
1.0
|
C
|
B:HIS51
|
4.8
|
34.7
|
1.0
|
C
|
B:HIS71
|
4.9
|
34.0
|
1.0
|
CG
|
B:ARG52
|
4.9
|
38.2
|
1.0
|
CA
|
B:TYR70
|
4.9
|
33.7
|
1.0
|
CA
|
B:ARG52
|
4.9
|
34.3
|
1.0
|
|
Iron binding site 5 out
of 6 in 3gob
Go back to
Iron Binding Sites List in 3gob
Iron binding site 5 out
of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dcsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:29.2
occ:1.00
|
FE1
|
C:FES501
|
0.0
|
29.2
|
1.0
|
S1
|
C:FES501
|
2.2
|
29.0
|
1.0
|
S2
|
C:FES501
|
2.2
|
28.2
|
1.0
|
SG
|
C:CYS68
|
2.3
|
27.2
|
1.0
|
SG
|
C:CYS49
|
2.4
|
27.7
|
1.0
|
FE2
|
C:FES501
|
2.7
|
28.2
|
1.0
|
CB
|
C:CYS49
|
3.1
|
28.2
|
1.0
|
CB
|
C:CYS68
|
3.2
|
24.7
|
1.0
|
CB
|
C:HIS51
|
4.1
|
29.9
|
1.0
|
CB
|
C:TYR70
|
4.2
|
27.5
|
1.0
|
N
|
C:HIS71
|
4.3
|
28.3
|
1.0
|
ND1
|
C:HIS51
|
4.4
|
22.3
|
1.0
|
CA
|
C:CYS49
|
4.6
|
27.9
|
1.0
|
CA
|
C:CYS68
|
4.6
|
27.8
|
1.0
|
CB
|
C:ALA54
|
4.6
|
27.7
|
1.0
|
ND1
|
C:HIS71
|
4.6
|
28.1
|
1.0
|
N
|
C:ARG52
|
4.7
|
32.7
|
1.0
|
CG
|
C:HIS51
|
4.8
|
27.7
|
1.0
|
CD1
|
C:LEU73
|
4.8
|
28.5
|
1.0
|
CG
|
C:LEU73
|
4.9
|
29.8
|
1.0
|
CB
|
C:LEU73
|
4.9
|
26.5
|
1.0
|
N
|
C:TYR70
|
4.9
|
28.6
|
1.0
|
N
|
C:HIS51
|
5.0
|
31.3
|
1.0
|
|
Iron binding site 6 out
of 6 in 3gob
Go back to
Iron Binding Sites List in 3gob
Iron binding site 6 out
of 6 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and 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 with Non-Heme Cobalt and Dcsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:28.2
occ:1.00
|
FE2
|
C:FES501
|
0.0
|
28.2
|
1.0
|
ND1
|
C:HIS71
|
2.2
|
28.1
|
1.0
|
S1
|
C:FES501
|
2.2
|
29.0
|
1.0
|
ND1
|
C:HIS51
|
2.2
|
22.3
|
1.0
|
S2
|
C:FES501
|
2.3
|
28.2
|
1.0
|
FE1
|
C:FES501
|
2.7
|
29.2
|
1.0
|
CG
|
C:HIS71
|
3.1
|
30.8
|
1.0
|
CG
|
C:HIS51
|
3.2
|
27.7
|
1.0
|
CE1
|
C:HIS51
|
3.2
|
30.1
|
1.0
|
CE1
|
C:HIS71
|
3.2
|
28.3
|
1.0
|
CB
|
C:HIS71
|
3.3
|
30.2
|
1.0
|
CB
|
C:HIS51
|
3.4
|
29.9
|
1.0
|
N
|
C:HIS71
|
3.6
|
28.3
|
1.0
|
CB
|
C:TYR70
|
4.0
|
27.5
|
1.0
|
CA
|
C:HIS71
|
4.0
|
29.7
|
1.0
|
N
|
C:ARG52
|
4.2
|
32.7
|
1.0
|
CD2
|
C:HIS71
|
4.2
|
30.3
|
1.0
|
NE2
|
C:HIS71
|
4.3
|
30.4
|
1.0
|
CG
|
C:TYR70
|
4.3
|
27.0
|
1.0
|
NE2
|
C:HIS51
|
4.3
|
30.5
|
1.0
|
CD2
|
C:HIS51
|
4.3
|
26.9
|
1.0
|
CD1
|
C:TYR70
|
4.4
|
26.6
|
1.0
|
SG
|
C:CYS68
|
4.5
|
27.2
|
1.0
|
SG
|
C:CYS49
|
4.5
|
27.7
|
1.0
|
C
|
C:TYR70
|
4.5
|
29.0
|
1.0
|
CB
|
C:ARG52
|
4.5
|
31.5
|
1.0
|
CA
|
C:HIS51
|
4.8
|
29.4
|
1.0
|
C
|
C:HIS71
|
4.8
|
29.4
|
1.0
|
CA
|
C:TYR70
|
4.9
|
28.6
|
1.0
|
C
|
C:HIS51
|
4.9
|
31.6
|
1.0
|
CA
|
C:ARG52
|
5.0
|
30.8
|
1.0
|
CG
|
C:ARG52
|
5.0
|
31.5
|
1.0
|
|
Reference:
R.L.D'ordine,
T.J.Rydel,
M.J.Storek,
E.J.Sturman,
F.Moshiri,
R.K.Bartlett,
G.R.Brown,
R.J.Eilers,
C.Dart,
Y.Qi,
S.Flasinski,
S.J.Franklin.
Dicamba Monooxygenase: Structural Insights Into A Dynamic Rieske Oxygenase That Catalyzes An Exocyclic Monooxygenation. J.Mol.Biol. V. 392 481 2009.
ISSN: ISSN 0022-2836
PubMed: 19616009
DOI: 10.1016/J.JMB.2009.07.022
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