Iron in PDB 3mv4: 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: 3mv4
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)
|
30.60 /
1.59
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.311,
140.487,
168.061,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.6 /
16.7
|
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 3mv4). 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: 3mv4:
Jump to Iron binding site number:
1;
2;
3;
Iron binding site 1 out
of 3 in 3mv4
Go back to
Iron Binding Sites List in 3mv4
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:21.9
occ:0.60
|
OH
|
M:TYR408
|
2.0
|
18.1
|
1.0
|
OH
|
M:TYR462
|
2.1
|
21.2
|
1.0
|
O2
|
M:CO3543
|
2.1
|
21.6
|
0.6
|
NE2
|
M:HIS460
|
2.2
|
17.2
|
1.0
|
O1
|
M:CO3543
|
2.3
|
20.8
|
0.6
|
C
|
M:CO3543
|
2.5
|
22.0
|
0.6
|
NE2
|
M:HIS447
|
2.9
|
11.8
|
0.5
|
CE1
|
M:HIS460
|
3.0
|
15.8
|
1.0
|
CZ
|
M:TYR408
|
3.0
|
14.7
|
1.0
|
CZ
|
M:TYR462
|
3.0
|
15.6
|
1.0
|
CE2
|
M:TYR462
|
3.2
|
16.0
|
1.0
|
CD2
|
M:HIS460
|
3.4
|
15.8
|
1.0
|
CE1
|
M:HIS447
|
3.6
|
14.0
|
0.5
|
CE2
|
M:TYR408
|
3.6
|
16.1
|
1.0
|
O3
|
M:CO3543
|
3.8
|
22.9
|
0.6
|
CE1
|
M:TYR408
|
4.0
|
13.7
|
1.0
|
CD2
|
M:HIS447
|
4.1
|
14.4
|
0.5
|
NH1
|
M:ARG457
|
4.1
|
15.6
|
1.0
|
O
|
M:HOH220
|
4.1
|
19.2
|
1.0
|
ND1
|
M:HIS460
|
4.2
|
14.2
|
1.0
|
CE1
|
M:TYR462
|
4.3
|
13.5
|
1.0
|
O
|
M:HOH151
|
4.4
|
15.0
|
1.0
|
CG
|
M:HIS460
|
4.4
|
14.9
|
1.0
|
CD2
|
M:TYR462
|
4.6
|
14.3
|
1.0
|
CG
|
M:ARG457
|
4.7
|
14.4
|
1.0
|
ND1
|
M:HIS447
|
4.8
|
22.6
|
0.5
|
ND1
|
M:HIS447
|
4.8
|
14.0
|
0.5
|
CD2
|
A:TYR16
|
4.9
|
20.7
|
1.0
|
O
|
A:HOH211
|
4.9
|
17.4
|
1.0
|
CD2
|
M:TYR408
|
4.9
|
14.3
|
1.0
|
|
Iron binding site 2 out
of 3 in 3mv4
Go back to
Iron Binding Sites List in 3mv4
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:20.9
occ:0.60
|
OH
|
N:TYR408
|
2.0
|
16.9
|
1.0
|
OH
|
N:TYR462
|
2.1
|
22.6
|
1.0
|
O3
|
N:CO3542
|
2.1
|
23.9
|
0.6
|
O1
|
N:CO3542
|
2.2
|
23.2
|
0.6
|
NE2
|
N:HIS460
|
2.2
|
16.5
|
1.0
|
C
|
N:CO3542
|
2.5
|
24.9
|
0.6
|
CE1
|
N:HIS460
|
2.9
|
16.3
|
1.0
|
NE2
|
N:HIS447
|
2.9
|
22.5
|
0.5
|
CZ
|
N:TYR408
|
3.0
|
14.6
|
1.0
|
CZ
|
N:TYR462
|
3.1
|
16.3
|
1.0
|
CE2
|
N:TYR462
|
3.2
|
15.3
|
1.0
|
CD2
|
N:HIS460
|
3.5
|
17.3
|
1.0
|
CE2
|
N:TYR408
|
3.6
|
14.8
|
1.0
|
CE1
|
N:HIS447
|
3.6
|
23.6
|
0.5
|
O2
|
N:CO3542
|
3.8
|
25.6
|
0.6
|
CE1
|
N:TYR408
|
4.0
|
14.9
|
1.0
|
O
|
N:HOH82
|
4.0
|
18.3
|
1.0
|
CD2
|
N:HIS447
|
4.0
|
23.2
|
0.5
|
NH2
|
N:ARG457
|
4.0
|
14.9
|
1.0
|
ND1
|
N:HIS460
|
4.2
|
14.4
|
1.0
|
CE1
|
N:TYR462
|
4.4
|
13.1
|
1.0
|
O
|
N:HOH207
|
4.4
|
15.3
|
1.0
|
CG
|
N:HIS460
|
4.4
|
13.8
|
1.0
|
CD2
|
N:TYR462
|
4.6
|
13.7
|
1.0
|
CG
|
N:ARG457
|
4.7
|
14.6
|
1.0
|
CD2
|
N:HIS447
|
4.7
|
23.2
|
0.5
|
O
|
N:HOH1555
|
4.8
|
48.4
|
1.0
|
ND1
|
N:HIS447
|
4.9
|
20.2
|
0.5
|
CD2
|
N:TYR408
|
4.9
|
14.8
|
1.0
|
O
|
B:HOH228
|
5.0
|
19.1
|
1.0
|
|
Iron binding site 3 out
of 3 in 3mv4
Go back to
Iron Binding Sites List in 3mv4
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:21.3
occ:0.60
|
OH
|
O:TYR408
|
2.0
|
17.8
|
1.0
|
OH
|
O:TYR462
|
2.1
|
22.9
|
1.0
|
O3
|
O:CO31
|
2.2
|
23.0
|
0.6
|
NE2
|
O:HIS460
|
2.2
|
16.4
|
1.0
|
O2
|
O:CO31
|
2.3
|
22.9
|
0.6
|
C
|
O:CO31
|
2.6
|
23.7
|
0.6
|
CE1
|
O:HIS460
|
2.9
|
15.4
|
1.0
|
NE2
|
O:HIS447
|
3.0
|
12.6
|
0.5
|
CZ
|
O:TYR408
|
3.0
|
15.0
|
1.0
|
CZ
|
O:TYR462
|
3.1
|
16.1
|
1.0
|
CE2
|
O:TYR462
|
3.2
|
15.9
|
1.0
|
CD2
|
O:HIS460
|
3.4
|
16.6
|
1.0
|
CE1
|
O:HIS447
|
3.6
|
14.6
|
0.5
|
CE2
|
O:TYR408
|
3.7
|
15.2
|
1.0
|
O1
|
O:CO31
|
3.9
|
23.9
|
0.6
|
CE1
|
O:TYR408
|
4.0
|
15.5
|
1.0
|
NH1
|
O:ARG457
|
4.1
|
15.2
|
1.0
|
O
|
O:HOH172
|
4.1
|
18.3
|
1.0
|
CD2
|
O:HIS447
|
4.1
|
15.3
|
0.5
|
ND1
|
O:HIS460
|
4.2
|
14.7
|
1.0
|
CE1
|
O:TYR462
|
4.3
|
13.4
|
1.0
|
O
|
O:HOH135
|
4.4
|
15.4
|
1.0
|
CG
|
O:HIS460
|
4.4
|
14.2
|
1.0
|
CD2
|
O:TYR462
|
4.5
|
13.9
|
1.0
|
CG
|
O:ARG457
|
4.7
|
13.8
|
1.0
|
ND1
|
O:HIS447
|
4.8
|
16.3
|
0.5
|
ND1
|
O:HIS447
|
4.9
|
23.0
|
0.5
|
O
|
C:HOH226
|
4.9
|
20.2
|
1.0
|
O
|
O:HOH1563
|
4.9
|
40.4
|
1.0
|
CD2
|
O:TYR408
|
5.0
|
14.9
|
1.0
|
CD2
|
C:TYR16
|
5.0
|
24.1
|
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 15:42:23 2024
|