Iron in PDB 3mfl: Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Enzymatic activity of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
All present enzymatic activity of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase:
1.13.11.3;
Protein crystallography data
The structure of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase, PDB code: 3mfl
was solved by
V.M.Purpero,
J.D.Lipscomb,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
23.87 /
1.78
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.319,
140.769,
168.183,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.7 /
18.5
|
Other elements in 3mfl:
The structure of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
(pdb code 3mfl). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the
Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase, PDB code: 3mfl:
Jump to Iron binding site number:
1;
2;
3;
Iron binding site 1 out
of 3 in 3mfl
Go back to
Iron Binding Sites List in 3mfl
Iron binding site 1 out
of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe600
b:25.1
occ:0.70
|
O4
|
M:DHY539
|
2.0
|
18.2
|
0.1
|
OH
|
M:TYR462
|
2.0
|
22.7
|
1.0
|
O3
|
M:DHY539
|
2.1
|
22.2
|
0.6
|
OH
|
M:TYR408
|
2.1
|
17.8
|
1.0
|
O4
|
M:DHY539
|
2.1
|
22.4
|
0.6
|
O3
|
M:DHY539
|
2.2
|
18.5
|
0.1
|
NE2
|
M:HIS460
|
2.2
|
14.2
|
1.0
|
C4
|
M:DHY539
|
2.7
|
18.4
|
0.1
|
C3
|
M:DHY539
|
2.8
|
18.2
|
0.1
|
C3
|
M:DHY539
|
2.8
|
22.4
|
0.6
|
C4
|
M:DHY539
|
2.8
|
23.4
|
0.6
|
CZ
|
M:TYR462
|
2.9
|
17.5
|
1.0
|
CE1
|
M:HIS460
|
3.0
|
14.6
|
1.0
|
NE2
|
M:HIS447
|
3.0
|
21.4
|
0.5
|
CE2
|
M:TYR462
|
3.0
|
16.7
|
1.0
|
CZ
|
M:TYR408
|
3.2
|
16.0
|
1.0
|
CD2
|
M:HIS460
|
3.4
|
14.2
|
1.0
|
CE1
|
M:HIS447
|
3.7
|
22.1
|
0.5
|
CE2
|
M:TYR408
|
3.8
|
16.7
|
1.0
|
O
|
A:HOH232
|
3.9
|
21.1
|
0.5
|
NH1
|
M:ARG457
|
3.9
|
14.6
|
1.0
|
O
|
M:HOH808
|
3.9
|
17.9
|
1.0
|
CE1
|
M:TYR408
|
4.1
|
14.9
|
1.0
|
C5
|
M:DHY539
|
4.1
|
18.2
|
0.1
|
CD2
|
M:HIS447
|
4.1
|
20.0
|
0.5
|
CE1
|
M:TYR462
|
4.2
|
17.0
|
1.0
|
C2
|
M:DHY539
|
4.2
|
23.8
|
0.6
|
C2
|
M:DHY539
|
4.2
|
18.3
|
0.1
|
C5
|
M:DHY539
|
4.2
|
23.3
|
0.6
|
ND1
|
M:HIS460
|
4.2
|
13.5
|
1.0
|
CD2
|
M:TYR462
|
4.4
|
16.0
|
1.0
|
CG
|
M:HIS460
|
4.4
|
11.8
|
1.0
|
O
|
M:HOH227
|
4.5
|
16.9
|
1.0
|
CG
|
M:ARG457
|
4.8
|
13.4
|
1.0
|
OE1
|
M:GLN477
|
4.9
|
15.9
|
1.0
|
O
|
A:HOH232
|
4.9
|
9.0
|
0.5
|
ND1
|
M:HIS447
|
4.9
|
21.6
|
0.5
|
|
Iron binding site 2 out
of 3 in 3mfl
Go back to
Iron Binding Sites List in 3mfl
Iron binding site 2 out
of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe600
b:24.4
occ:0.70
|
O4
|
N:DHY539
|
2.0
|
21.4
|
0.3
|
OH
|
N:TYR408
|
2.1
|
16.8
|
1.0
|
OH
|
N:TYR462
|
2.1
|
22.3
|
1.0
|
O3
|
N:DHY539
|
2.2
|
23.1
|
0.3
|
O3
|
N:DHY539
|
2.2
|
22.3
|
0.3
|
O4
|
N:DHY539
|
2.2
|
22.5
|
0.3
|
NE2
|
N:HIS460
|
2.3
|
13.4
|
1.0
|
C4
|
N:DHY539
|
2.9
|
23.0
|
0.3
|
C3
|
N:DHY539
|
2.9
|
22.2
|
0.3
|
CZ
|
N:TYR462
|
3.0
|
16.0
|
1.0
|
C3
|
N:DHY539
|
3.0
|
23.5
|
0.3
|
CE1
|
N:HIS460
|
3.0
|
16.2
|
1.0
|
NE2
|
N:HIS447
|
3.0
|
21.3
|
0.5
|
C4
|
N:DHY539
|
3.0
|
24.4
|
0.3
|
CZ
|
N:TYR408
|
3.1
|
14.6
|
1.0
|
CE2
|
N:TYR462
|
3.1
|
15.9
|
1.0
|
CD2
|
N:HIS460
|
3.4
|
15.5
|
1.0
|
CE2
|
N:TYR408
|
3.8
|
14.5
|
1.0
|
CE1
|
N:HIS447
|
3.8
|
21.6
|
0.5
|
O
|
N:HOH756
|
3.8
|
16.4
|
1.0
|
O
|
B:HOH894
|
3.9
|
18.1
|
0.5
|
NH2
|
N:ARG457
|
3.9
|
13.4
|
1.0
|
CD2
|
N:HIS447
|
4.0
|
20.6
|
0.5
|
CE1
|
N:TYR408
|
4.0
|
14.7
|
1.0
|
C5
|
N:DHY539
|
4.2
|
22.9
|
0.3
|
ND1
|
N:HIS460
|
4.2
|
14.3
|
1.0
|
CE1
|
N:TYR462
|
4.3
|
14.8
|
1.0
|
C2
|
N:DHY539
|
4.3
|
22.7
|
0.3
|
C2
|
N:DHY539
|
4.3
|
24.2
|
0.3
|
C5
|
N:DHY539
|
4.3
|
24.4
|
0.3
|
CD2
|
N:TYR462
|
4.4
|
13.3
|
1.0
|
CG
|
N:HIS460
|
4.5
|
11.8
|
1.0
|
O
|
N:HOH37
|
4.5
|
14.6
|
1.0
|
CG
|
N:ARG457
|
4.8
|
13.4
|
1.0
|
O
|
B:HOH894
|
4.9
|
8.9
|
0.5
|
OE1
|
N:GLN477
|
4.9
|
15.7
|
1.0
|
ND1
|
N:HIS447
|
5.0
|
20.5
|
0.5
|
|
Iron binding site 3 out
of 3 in 3mfl
Go back to
Iron Binding Sites List in 3mfl
Iron binding site 3 out
of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe600
b:24.0
occ:0.65
|
O4
|
O:DHY540
|
1.8
|
15.8
|
0.1
|
O3
|
O:DHY540
|
2.1
|
20.6
|
0.6
|
OH
|
O:TYR462
|
2.1
|
25.5
|
1.0
|
OH
|
O:TYR408
|
2.1
|
21.1
|
1.0
|
O4
|
O:DHY540
|
2.2
|
21.9
|
0.6
|
NE2
|
O:HIS460
|
2.2
|
13.5
|
1.0
|
O3
|
O:DHY540
|
2.4
|
17.4
|
0.1
|
C4
|
O:DHY540
|
2.7
|
16.8
|
0.1
|
C3
|
O:DHY540
|
2.8
|
21.6
|
0.6
|
C4
|
O:DHY540
|
2.9
|
22.0
|
0.6
|
CE1
|
O:HIS460
|
2.9
|
15.4
|
1.0
|
C3
|
O:DHY540
|
2.9
|
16.9
|
0.1
|
NE2
|
O:HIS447
|
3.0
|
21.9
|
0.5
|
CZ
|
O:TYR462
|
3.0
|
20.2
|
1.0
|
CZ
|
O:TYR408
|
3.2
|
18.8
|
1.0
|
CE2
|
O:TYR462
|
3.2
|
19.7
|
1.0
|
CD2
|
O:HIS460
|
3.4
|
16.3
|
1.0
|
CE1
|
O:HIS447
|
3.7
|
22.7
|
0.5
|
NH1
|
O:ARG457
|
3.8
|
15.3
|
1.0
|
CE2
|
O:TYR408
|
3.8
|
19.4
|
1.0
|
O
|
O:HOH770
|
3.8
|
19.6
|
1.0
|
O
|
O:HOH768
|
3.9
|
28.8
|
1.0
|
C5
|
O:DHY540
|
4.0
|
16.9
|
0.1
|
CD2
|
O:HIS447
|
4.0
|
20.6
|
0.5
|
CE1
|
O:TYR408
|
4.1
|
18.1
|
1.0
|
C2
|
O:DHY540
|
4.1
|
21.8
|
0.6
|
ND1
|
O:HIS460
|
4.2
|
14.9
|
1.0
|
C5
|
O:DHY540
|
4.2
|
22.4
|
0.6
|
CE1
|
O:TYR462
|
4.3
|
17.0
|
1.0
|
C2
|
O:DHY540
|
4.3
|
17.0
|
0.1
|
CG
|
O:HIS460
|
4.4
|
13.2
|
1.0
|
CD2
|
O:TYR462
|
4.5
|
16.7
|
1.0
|
O
|
O:HOH827
|
4.6
|
15.8
|
1.0
|
CG
|
O:ARG457
|
4.7
|
13.5
|
1.0
|
ND1
|
O:HIS447
|
4.9
|
21.5
|
0.5
|
OE1
|
O:GLN477
|
4.9
|
17.9
|
1.0
|
|
Reference:
V.M.Purpero,
J.D.Lipscomb.
Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase To Be Published.
Page generated: Sun Aug 4 14:46:54 2024
|