Iron in PDB 3t67: 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: 3t67
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)
|
30.68 /
1.67
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.009,
140.782,
168.189,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.5 /
18.9
|
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 3t67). 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: 3t67:
Jump to Iron binding site number:
1;
2;
3;
Iron binding site 1 out
of 3 in 3t67
Go back to
Iron Binding Sites List in 3t67
Iron binding site 1 out
of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
![](/pictures/FE/pdb/t6/3t67-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/t6/3t67-FE-sphere_01_stereo.jpg) 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:18.0
occ:0.70
|
OH
|
M:TYR408
|
1.9
|
21.1
|
1.0
|
NE2
|
M:HIS460
|
2.1
|
15.9
|
1.0
|
O4
|
M:CAQ1
|
2.1
|
24.6
|
1.0
|
OH
|
M:TYR447
|
2.2
|
19.0
|
0.5
|
NE2
|
M:HIS462
|
2.2
|
15.3
|
1.0
|
O3
|
M:CAQ1
|
2.5
|
30.3
|
1.0
|
C4
|
M:CAQ1
|
2.9
|
28.2
|
1.0
|
CE1
|
M:HIS460
|
2.9
|
16.5
|
1.0
|
CZ
|
M:TYR408
|
3.0
|
17.7
|
1.0
|
CE1
|
M:HIS462
|
3.1
|
15.8
|
1.0
|
C3
|
M:CAQ1
|
3.1
|
28.1
|
1.0
|
CD2
|
M:HIS460
|
3.2
|
15.8
|
1.0
|
CD2
|
M:HIS462
|
3.2
|
16.0
|
1.0
|
CZ
|
M:TYR447
|
3.4
|
17.6
|
0.5
|
CE2
|
M:TYR408
|
3.7
|
17.7
|
1.0
|
CE2
|
M:TYR447
|
3.8
|
18.0
|
0.5
|
CE1
|
M:TYR408
|
3.9
|
18.0
|
1.0
|
O
|
M:HOH794
|
4.1
|
18.2
|
1.0
|
ND1
|
M:HIS460
|
4.1
|
15.1
|
1.0
|
O
|
M:HOH233
|
4.1
|
16.4
|
1.0
|
NH1
|
M:ARG457
|
4.2
|
16.0
|
1.0
|
C5
|
M:CAQ1
|
4.2
|
29.0
|
1.0
|
ND1
|
M:HIS462
|
4.2
|
14.5
|
1.0
|
CG
|
M:HIS460
|
4.3
|
14.8
|
1.0
|
O
|
A:HOH238
|
4.3
|
18.6
|
1.0
|
CG
|
M:HIS462
|
4.3
|
14.8
|
1.0
|
C2
|
M:CAQ1
|
4.4
|
29.1
|
1.0
|
CE1
|
M:TYR447
|
4.5
|
18.7
|
0.5
|
OE1
|
M:GLN477
|
4.8
|
17.0
|
1.0
|
|
Iron binding site 2 out
of 3 in 3t67
Go back to
Iron Binding Sites List in 3t67
Iron binding site 2 out
of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
![](/pictures/FE/pdb/t6/3t67-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/t6/3t67-FE-sphere_02_stereo.jpg) 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:17.2
occ:0.70
|
OH
|
N:TYR408
|
1.9
|
20.8
|
1.0
|
O4
|
N:CAQ1
|
2.1
|
23.7
|
1.0
|
NE2
|
N:HIS462
|
2.1
|
16.3
|
1.0
|
NE2
|
N:HIS460
|
2.1
|
15.7
|
1.0
|
OH
|
N:TYR447
|
2.2
|
19.4
|
0.5
|
O3
|
N:CAQ1
|
2.3
|
30.6
|
1.0
|
C4
|
N:CAQ1
|
2.8
|
28.0
|
1.0
|
CE1
|
N:HIS460
|
3.0
|
17.3
|
1.0
|
C3
|
N:CAQ1
|
3.0
|
28.5
|
1.0
|
CZ
|
N:TYR408
|
3.0
|
18.8
|
1.0
|
CE1
|
N:HIS462
|
3.0
|
15.9
|
1.0
|
CD2
|
N:HIS462
|
3.2
|
15.3
|
1.0
|
CD2
|
N:HIS460
|
3.3
|
16.8
|
1.0
|
CZ
|
N:TYR447
|
3.4
|
19.1
|
0.5
|
CE2
|
N:TYR408
|
3.8
|
17.7
|
1.0
|
CE1
|
N:TYR408
|
3.8
|
18.9
|
1.0
|
CE1
|
N:TYR447
|
3.9
|
20.0
|
0.5
|
O
|
N:HOH785
|
4.0
|
17.0
|
1.0
|
O
|
N:HOH38
|
4.1
|
15.0
|
1.0
|
C5
|
N:CAQ1
|
4.1
|
28.3
|
1.0
|
ND1
|
N:HIS460
|
4.1
|
16.2
|
1.0
|
ND1
|
N:HIS462
|
4.2
|
16.0
|
1.0
|
NH1
|
N:ARG457
|
4.2
|
17.0
|
1.0
|
O
|
B:HOH209
|
4.2
|
19.1
|
1.0
|
CG
|
N:HIS462
|
4.3
|
15.4
|
1.0
|
C2
|
N:CAQ1
|
4.3
|
29.5
|
1.0
|
CG
|
N:HIS460
|
4.3
|
14.3
|
1.0
|
CE2
|
N:TYR447
|
4.5
|
20.6
|
0.5
|
OE1
|
N:GLN477
|
4.8
|
17.6
|
1.0
|
|
Iron binding site 3 out
of 3 in 3t67
Go back to
Iron Binding Sites List in 3t67
Iron binding site 3 out
of 3 in the Axial Ligand Swapping in Double Mutant Maintains Intradiol-Cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
![](/pictures/FE/pdb/t6/3t67-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/t6/3t67-FE-sphere_03_stereo.jpg) 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:18.9
occ:0.70
|
OH
|
O:TYR408
|
1.9
|
23.3
|
1.0
|
NE2
|
O:HIS460
|
2.1
|
15.3
|
1.0
|
OH
|
O:TYR447
|
2.1
|
17.6
|
0.5
|
NE2
|
O:HIS462
|
2.1
|
17.1
|
1.0
|
O3
|
O:CAQ1
|
2.2
|
24.4
|
1.0
|
O4
|
O:CAQ1
|
2.4
|
31.1
|
1.0
|
CE1
|
O:HIS460
|
2.9
|
16.2
|
1.0
|
C3
|
O:CAQ1
|
3.0
|
28.9
|
1.0
|
CE1
|
O:HIS462
|
3.0
|
17.1
|
1.0
|
CZ
|
O:TYR408
|
3.0
|
22.0
|
1.0
|
C4
|
O:CAQ1
|
3.1
|
28.0
|
1.0
|
CD2
|
O:HIS462
|
3.2
|
17.0
|
1.0
|
CD2
|
O:HIS460
|
3.2
|
17.7
|
1.0
|
CZ
|
O:TYR447
|
3.3
|
17.8
|
0.5
|
CE2
|
O:TYR408
|
3.8
|
20.3
|
1.0
|
CE1
|
O:TYR447
|
3.8
|
17.6
|
0.5
|
CE1
|
O:TYR408
|
3.9
|
22.4
|
1.0
|
O
|
O:HOH787
|
4.0
|
16.9
|
1.0
|
ND1
|
O:HIS460
|
4.1
|
16.0
|
1.0
|
ND1
|
O:HIS462
|
4.2
|
16.6
|
1.0
|
O
|
O:HOH121
|
4.2
|
15.8
|
1.0
|
NH1
|
O:ARG457
|
4.2
|
16.1
|
1.0
|
CG
|
O:HIS460
|
4.3
|
15.3
|
1.0
|
C2
|
O:CAQ1
|
4.3
|
28.3
|
1.0
|
CG
|
O:HIS462
|
4.3
|
15.6
|
1.0
|
O
|
C:HOH207
|
4.3
|
20.5
|
1.0
|
C5
|
O:CAQ1
|
4.4
|
30.2
|
1.0
|
CE2
|
O:TYR447
|
4.4
|
18.6
|
0.5
|
OE1
|
O:GLN477
|
4.8
|
18.1
|
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 20:17:43 2024
|