Iron in PDB 3mi5: 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: 3mi5
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)
|
30.62 /
1.78
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
190.543,
167.995,
128.342,
90.00,
132.40,
90.00
|
R / Rfree (%)
|
15.1 /
18.5
|
Other elements in 3mi5:
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 3mi5). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 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: 3mi5:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3mi5
Go back to
Iron Binding Sites List in 3mi5
Iron binding site 1 out
of 6 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:20.9
occ:0.65
|
OH
|
M:TYR462
|
1.9
|
20.6
|
1.0
|
O3
|
M:CAQ539
|
2.0
|
22.0
|
0.7
|
OH
|
M:TYR408
|
2.1
|
19.2
|
1.0
|
O4
|
M:CAQ539
|
2.1
|
20.3
|
0.7
|
NE2
|
M:HIS460
|
2.2
|
16.5
|
1.0
|
CZ
|
M:TYR462
|
2.8
|
17.1
|
1.0
|
C3
|
M:CAQ539
|
2.8
|
22.0
|
0.7
|
C4
|
M:CAQ539
|
2.9
|
20.1
|
0.7
|
CE1
|
M:HIS460
|
3.0
|
16.1
|
1.0
|
CE1
|
M:HIS447
|
3.0
|
21.1
|
0.5
|
CE2
|
M:TYR462
|
3.0
|
17.5
|
1.0
|
CZ
|
M:TYR408
|
3.1
|
14.9
|
1.0
|
CD2
|
M:HIS460
|
3.4
|
16.5
|
1.0
|
NE2
|
M:HIS447
|
3.6
|
22.8
|
0.5
|
CE2
|
M:TYR408
|
3.8
|
16.1
|
1.0
|
NH1
|
M:ARG457
|
3.8
|
13.2
|
1.0
|
O
|
M:HOH861
|
3.9
|
19.2
|
1.0
|
O
|
M:HOH2030
|
3.9
|
29.9
|
1.0
|
CE1
|
M:TYR408
|
4.0
|
13.6
|
1.0
|
ND1
|
M:HIS447
|
4.1
|
21.4
|
0.5
|
CE1
|
M:TYR462
|
4.1
|
16.1
|
1.0
|
C2
|
M:CAQ539
|
4.2
|
21.8
|
0.7
|
ND1
|
M:HIS460
|
4.2
|
14.9
|
1.0
|
C5
|
M:CAQ539
|
4.2
|
22.7
|
0.7
|
CD2
|
M:TYR462
|
4.4
|
15.4
|
1.0
|
CG
|
M:HIS460
|
4.4
|
13.2
|
1.0
|
O
|
M:HOH161
|
4.5
|
17.6
|
1.0
|
OE1
|
M:GLN477
|
4.9
|
16.8
|
1.0
|
CG
|
M:ARG457
|
4.9
|
13.6
|
1.0
|
CD2
|
M:HIS447
|
4.9
|
20.6
|
0.5
|
O
|
A:HOH220
|
4.9
|
20.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 3mi5
Go back to
Iron Binding Sites List in 3mi5
Iron binding site 2 out
of 6 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:21.5
occ:0.65
|
OH
|
N:TYR462
|
2.0
|
24.3
|
1.0
|
O4
|
N:CAQ3
|
2.1
|
28.3
|
0.7
|
OH
|
N:TYR408
|
2.1
|
17.5
|
1.0
|
O3
|
N:CAQ3
|
2.2
|
25.1
|
0.7
|
NE2
|
N:HIS460
|
2.2
|
14.5
|
1.0
|
CZ
|
N:TYR462
|
2.9
|
18.9
|
1.0
|
C4
|
N:CAQ3
|
2.9
|
25.5
|
0.7
|
C3
|
N:CAQ3
|
2.9
|
24.4
|
0.7
|
CE1
|
N:HIS460
|
3.0
|
15.4
|
1.0
|
CE1
|
N:HIS447
|
3.0
|
21.0
|
0.5
|
CE2
|
N:TYR462
|
3.1
|
17.9
|
1.0
|
CZ
|
N:TYR408
|
3.1
|
17.2
|
1.0
|
CD2
|
N:HIS460
|
3.4
|
15.6
|
1.0
|
NE2
|
N:HIS447
|
3.7
|
22.6
|
0.5
|
CE2
|
N:TYR408
|
3.8
|
17.6
|
1.0
|
O
|
N:HOH563
|
3.9
|
18.7
|
1.0
|
NH1
|
N:ARG457
|
3.9
|
15.6
|
1.0
|
O
|
B:HOH2031
|
4.0
|
26.6
|
1.0
|
CE1
|
N:TYR408
|
4.0
|
16.5
|
1.0
|
ND1
|
N:HIS447
|
4.0
|
21.2
|
0.5
|
ND1
|
N:HIS460
|
4.2
|
15.1
|
1.0
|
CE1
|
N:TYR462
|
4.2
|
14.9
|
1.0
|
C5
|
N:CAQ3
|
4.3
|
26.4
|
0.7
|
C2
|
N:CAQ3
|
4.3
|
24.1
|
0.7
|
CD2
|
N:TYR462
|
4.4
|
15.7
|
1.0
|
CG
|
N:HIS460
|
4.4
|
13.3
|
1.0
|
O
|
N:HOH279
|
4.5
|
15.9
|
1.0
|
CG
|
N:ARG457
|
4.8
|
14.1
|
1.0
|
CD2
|
N:HIS447
|
4.9
|
20.9
|
0.5
|
OE1
|
N:GLN477
|
4.9
|
16.9
|
1.0
|
O
|
B:HOH461
|
5.0
|
22.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 3mi5
Go back to
Iron Binding Sites List in 3mi5
Iron binding site 3 out
of 6 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:21.8
occ:0.65
|
OH
|
O:TYR462
|
2.0
|
20.4
|
1.0
|
OH
|
O:TYR408
|
2.0
|
15.1
|
1.0
|
O4
|
O:CAQ4
|
2.1
|
23.2
|
0.7
|
O3
|
O:CAQ4
|
2.1
|
21.1
|
0.7
|
NE2
|
O:HIS460
|
2.3
|
14.5
|
1.0
|
C4
|
O:CAQ4
|
2.9
|
22.3
|
0.7
|
C3
|
O:CAQ4
|
2.9
|
22.2
|
0.7
|
CZ
|
O:TYR462
|
2.9
|
16.3
|
1.0
|
CE1
|
O:HIS460
|
3.0
|
17.2
|
1.0
|
CE1
|
O:HIS447
|
3.0
|
21.9
|
0.5
|
CZ
|
O:TYR408
|
3.1
|
14.1
|
1.0
|
CE2
|
O:TYR462
|
3.1
|
14.9
|
1.0
|
CD2
|
O:HIS460
|
3.5
|
16.3
|
1.0
|
NE2
|
O:HIS447
|
3.6
|
24.0
|
0.5
|
CE2
|
O:TYR408
|
3.8
|
14.3
|
1.0
|
O
|
O:HOH2032
|
3.8
|
27.0
|
1.0
|
O
|
O:HOH698
|
3.9
|
19.4
|
1.0
|
CE1
|
O:TYR408
|
3.9
|
16.6
|
1.0
|
NH1
|
O:ARG457
|
4.0
|
14.5
|
1.0
|
ND1
|
O:HIS447
|
4.1
|
22.1
|
0.5
|
ND1
|
O:HIS460
|
4.2
|
14.3
|
1.0
|
C5
|
O:CAQ4
|
4.2
|
22.1
|
0.7
|
C2
|
O:CAQ4
|
4.2
|
21.1
|
0.7
|
CE1
|
O:TYR462
|
4.2
|
15.2
|
1.0
|
CD2
|
O:TYR462
|
4.5
|
13.3
|
1.0
|
CG
|
O:HIS460
|
4.5
|
14.1
|
1.0
|
O
|
O:HOH120
|
4.5
|
15.2
|
1.0
|
CG
|
O:ARG457
|
4.8
|
14.4
|
1.0
|
CD2
|
O:HIS447
|
4.8
|
20.5
|
0.5
|
O
|
C:HOH599
|
4.9
|
20.6
|
1.0
|
OE1
|
O:GLN477
|
5.0
|
17.6
|
1.0
|
|
Iron binding site 4 out
of 6 in 3mi5
Go back to
Iron Binding Sites List in 3mi5
Iron binding site 4 out
of 6 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 4 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
|
P:Fe600
b:21.1
occ:0.65
|
OH
|
P:TYR462
|
1.9
|
21.3
|
1.0
|
OH
|
P:TYR408
|
2.0
|
17.2
|
1.0
|
O3
|
P:CAQ542
|
2.1
|
19.9
|
0.7
|
O4
|
P:CAQ542
|
2.1
|
23.7
|
0.7
|
NE2
|
P:HIS460
|
2.2
|
15.9
|
1.0
|
CZ
|
P:TYR462
|
2.9
|
16.0
|
1.0
|
C3
|
P:CAQ542
|
2.9
|
21.6
|
0.7
|
C4
|
P:CAQ542
|
2.9
|
23.1
|
0.7
|
CE1
|
P:HIS460
|
3.0
|
15.5
|
1.0
|
CE1
|
P:HIS447
|
3.0
|
21.8
|
0.5
|
CE2
|
P:TYR462
|
3.1
|
16.6
|
1.0
|
CZ
|
P:TYR408
|
3.1
|
16.0
|
1.0
|
CD2
|
P:HIS460
|
3.4
|
15.3
|
1.0
|
NE2
|
P:HIS447
|
3.6
|
23.5
|
0.5
|
CE2
|
P:TYR408
|
3.7
|
15.2
|
1.0
|
O
|
P:HOH815
|
3.8
|
17.8
|
1.0
|
O
|
P:HOH2033
|
3.9
|
28.3
|
1.0
|
NH1
|
P:ARG457
|
3.9
|
13.9
|
1.0
|
CE1
|
P:TYR408
|
4.0
|
13.6
|
1.0
|
ND1
|
P:HIS447
|
4.1
|
21.2
|
0.5
|
CE1
|
P:TYR462
|
4.1
|
16.2
|
1.0
|
ND1
|
P:HIS460
|
4.2
|
15.4
|
1.0
|
C2
|
P:CAQ542
|
4.2
|
23.4
|
0.7
|
C5
|
P:CAQ542
|
4.2
|
22.2
|
0.7
|
CG
|
P:HIS460
|
4.4
|
13.5
|
1.0
|
CD2
|
P:TYR462
|
4.4
|
13.9
|
1.0
|
O
|
P:HOH146
|
4.5
|
17.1
|
1.0
|
CD2
|
P:HIS447
|
4.8
|
20.3
|
0.5
|
O
|
D:HOH305
|
4.9
|
18.8
|
1.0
|
CG
|
P:ARG457
|
4.9
|
13.6
|
1.0
|
OE1
|
P:GLN477
|
5.0
|
16.8
|
1.0
|
|
Iron binding site 5 out
of 6 in 3mi5
Go back to
Iron Binding Sites List in 3mi5
Iron binding site 5 out
of 6 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 5 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
|
Q:Fe600
b:21.6
occ:0.65
|
OH
|
Q:TYR462
|
2.0
|
25.3
|
1.0
|
O3
|
Q:CAQ6
|
2.1
|
25.4
|
0.7
|
O4
|
Q:CAQ6
|
2.2
|
23.0
|
0.7
|
OH
|
Q:TYR408
|
2.2
|
20.5
|
1.0
|
NE2
|
Q:HIS460
|
2.2
|
13.2
|
1.0
|
CZ
|
Q:TYR462
|
2.9
|
19.4
|
1.0
|
C3
|
Q:CAQ6
|
2.9
|
23.5
|
0.7
|
C4
|
Q:CAQ6
|
2.9
|
22.5
|
0.7
|
CE1
|
Q:HIS460
|
3.0
|
15.7
|
1.0
|
CE1
|
Q:HIS447
|
3.0
|
22.5
|
0.5
|
CE2
|
Q:TYR462
|
3.1
|
16.3
|
1.0
|
CZ
|
Q:TYR408
|
3.2
|
19.0
|
1.0
|
CD2
|
Q:HIS460
|
3.4
|
14.6
|
1.0
|
NE2
|
Q:HIS447
|
3.6
|
24.4
|
0.5
|
NH1
|
Q:ARG457
|
3.8
|
16.1
|
1.0
|
O
|
Q:HOH618
|
3.8
|
20.2
|
1.0
|
CE2
|
Q:TYR408
|
3.9
|
17.6
|
1.0
|
O
|
Q:HOH2045
|
3.9
|
26.1
|
1.0
|
CE1
|
Q:TYR408
|
4.0
|
16.2
|
1.0
|
ND1
|
Q:HIS447
|
4.1
|
22.4
|
0.5
|
CE1
|
Q:TYR462
|
4.2
|
15.6
|
1.0
|
ND1
|
Q:HIS460
|
4.2
|
14.7
|
1.0
|
C2
|
Q:CAQ6
|
4.3
|
24.2
|
0.7
|
C5
|
Q:CAQ6
|
4.3
|
23.1
|
0.7
|
CD2
|
Q:TYR462
|
4.4
|
15.6
|
1.0
|
CG
|
Q:HIS460
|
4.4
|
13.8
|
1.0
|
O
|
Q:HOH180
|
4.5
|
15.1
|
1.0
|
CG
|
Q:ARG457
|
4.8
|
15.8
|
1.0
|
OE1
|
Q:GLN477
|
4.8
|
17.7
|
1.0
|
CD2
|
Q:HIS447
|
4.9
|
21.3
|
0.5
|
O
|
E:HOH246
|
5.0
|
23.7
|
1.0
|
|
Iron binding site 6 out
of 6 in 3mi5
Go back to
Iron Binding Sites List in 3mi5
Iron binding site 6 out
of 6 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 6 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
|
R:Fe600
b:22.0
occ:0.65
|
OH
|
R:TYR462
|
1.9
|
22.8
|
1.0
|
OH
|
R:TYR408
|
2.1
|
16.1
|
1.0
|
O4
|
R:CAQ1
|
2.1
|
23.1
|
0.7
|
O3
|
R:CAQ1
|
2.1
|
21.3
|
0.7
|
NE2
|
R:HIS460
|
2.3
|
14.1
|
1.0
|
CZ
|
R:TYR462
|
2.9
|
17.1
|
1.0
|
C4
|
R:CAQ1
|
2.9
|
22.7
|
0.7
|
C3
|
R:CAQ1
|
2.9
|
22.1
|
0.7
|
CE1
|
R:HIS460
|
3.0
|
16.6
|
1.0
|
CE1
|
R:HIS447
|
3.0
|
20.3
|
0.5
|
CE2
|
R:TYR462
|
3.1
|
15.9
|
1.0
|
CZ
|
R:TYR408
|
3.1
|
14.7
|
1.0
|
CD2
|
R:HIS460
|
3.4
|
16.0
|
1.0
|
NE2
|
R:HIS447
|
3.6
|
23.2
|
0.5
|
O
|
R:HOH2037
|
3.8
|
28.0
|
1.0
|
CE2
|
R:TYR408
|
3.8
|
15.0
|
1.0
|
O
|
R:HOH750
|
3.8
|
21.0
|
1.0
|
NH1
|
R:ARG457
|
3.9
|
16.1
|
1.0
|
CE1
|
R:TYR408
|
4.0
|
16.4
|
1.0
|
ND1
|
R:HIS447
|
4.1
|
21.9
|
0.5
|
CE1
|
R:TYR462
|
4.1
|
15.8
|
1.0
|
ND1
|
R:HIS460
|
4.2
|
13.8
|
1.0
|
C5
|
R:CAQ1
|
4.3
|
22.8
|
0.7
|
C2
|
R:CAQ1
|
4.3
|
21.3
|
0.7
|
CD2
|
R:TYR462
|
4.4
|
14.3
|
1.0
|
CG
|
R:HIS460
|
4.5
|
12.7
|
1.0
|
O
|
R:HOH170
|
4.5
|
16.5
|
1.0
|
O
|
F:HOH211
|
4.9
|
21.1
|
1.0
|
CG
|
R:ARG457
|
4.9
|
14.0
|
1.0
|
CD2
|
R:HIS447
|
4.9
|
19.5
|
0.5
|
OE1
|
R: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 14:48:23 2024
|