Iron in PDB 4who: Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5
Enzymatic activity of Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5
All present enzymatic activity of Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5:
1.13.11.3;
Protein crystallography data
The structure of Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5, PDB code: 4who
was solved by
C.J.Knoot,
J.D.Lipscomb,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.45 /
1.83
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.092,
140.636,
168.660,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18 /
21.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5
(pdb code 4who). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the
Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5, PDB code: 4who:
Jump to Iron binding site number:
1;
2;
3;
Iron binding site 1 out
of 3 in 4who
Go back to
Iron Binding Sites List in 4who
Iron binding site 1 out
of 3 in the Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe601
b:17.4
occ:0.75
|
OH
|
B:TYR408
|
1.9
|
18.1
|
1.0
|
OH
|
B:TYR447
|
2.2
|
20.2
|
1.0
|
NE2
|
B:HIS462
|
2.2
|
15.3
|
1.0
|
O
|
B:HOH868
|
2.2
|
15.1
|
0.8
|
NE2
|
B:HIS460
|
2.2
|
16.3
|
1.0
|
CZ
|
B:TYR408
|
3.0
|
16.0
|
1.0
|
CE1
|
B:HIS460
|
3.1
|
16.2
|
1.0
|
CE1
|
B:HIS462
|
3.1
|
15.8
|
1.0
|
O
|
B:HOH869
|
3.3
|
24.8
|
1.0
|
CD2
|
B:HIS462
|
3.3
|
18.1
|
1.0
|
CD2
|
B:HIS460
|
3.3
|
16.4
|
1.0
|
CZ
|
B:TYR447
|
3.4
|
19.8
|
1.0
|
CE1
|
B:TYR408
|
3.6
|
16.5
|
1.0
|
CE2
|
B:TYR447
|
3.8
|
19.8
|
1.0
|
CE2
|
B:TYR408
|
3.9
|
16.6
|
1.0
|
O
|
B:HOH783
|
4.0
|
15.7
|
1.0
|
ND1
|
B:HIS460
|
4.2
|
15.4
|
1.0
|
ND1
|
B:HIS462
|
4.3
|
15.4
|
1.0
|
O
|
B:HOH870
|
4.3
|
19.9
|
1.0
|
CG
|
B:HIS462
|
4.4
|
15.5
|
1.0
|
CG
|
B:HIS460
|
4.4
|
15.4
|
1.0
|
O
|
A:HOH508
|
4.4
|
16.9
|
1.0
|
NH1
|
B:ARG457
|
4.5
|
16.9
|
1.0
|
CE1
|
B:TYR447
|
4.5
|
20.9
|
1.0
|
CD1
|
B:TYR408
|
4.9
|
16.3
|
1.0
|
OE1
|
B:GLN477
|
5.0
|
15.7
|
1.0
|
|
Iron binding site 2 out
of 3 in 4who
Go back to
Iron Binding Sites List in 4who
Iron binding site 2 out
of 3 in the Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe600
b:18.3
occ:0.75
|
OH
|
D:TYR408
|
1.8
|
20.8
|
1.0
|
O
|
D:HOH889
|
2.1
|
18.5
|
0.8
|
NE2
|
D:HIS460
|
2.2
|
16.9
|
1.0
|
NE2
|
D:HIS462
|
2.2
|
18.7
|
1.0
|
OH
|
D:TYR447
|
2.2
|
26.1
|
1.0
|
CZ
|
D:TYR408
|
2.9
|
18.7
|
1.0
|
CE1
|
D:HIS460
|
3.0
|
17.0
|
1.0
|
CE1
|
D:HIS462
|
3.2
|
17.9
|
1.0
|
O
|
D:HOH888
|
3.2
|
31.4
|
1.0
|
CD2
|
D:HIS462
|
3.2
|
17.5
|
1.0
|
CD2
|
D:HIS460
|
3.3
|
16.8
|
1.0
|
CZ
|
D:TYR447
|
3.4
|
23.8
|
1.0
|
CE2
|
D:TYR408
|
3.6
|
18.4
|
1.0
|
CE2
|
D:TYR447
|
3.8
|
23.3
|
1.0
|
CE1
|
D:TYR408
|
3.8
|
17.7
|
1.0
|
O
|
D:HOH758
|
4.0
|
16.0
|
1.0
|
ND1
|
D:HIS460
|
4.2
|
15.3
|
1.0
|
O
|
D:HOH887
|
4.3
|
21.1
|
1.0
|
ND1
|
D:HIS462
|
4.3
|
17.9
|
1.0
|
CG
|
D:HIS460
|
4.3
|
15.1
|
1.0
|
CG
|
D:HIS462
|
4.3
|
17.0
|
1.0
|
O
|
C:HOH421
|
4.4
|
15.8
|
1.0
|
NH1
|
D:ARG457
|
4.4
|
17.7
|
1.0
|
CE1
|
D:TYR447
|
4.6
|
24.6
|
1.0
|
CD2
|
D:TYR408
|
4.9
|
18.8
|
1.0
|
OE1
|
D:GLN477
|
5.0
|
16.8
|
1.0
|
|
Iron binding site 3 out
of 3 in 4who
Go back to
Iron Binding Sites List in 4who
Iron binding site 3 out
of 3 in the Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Resting Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe602
b:19.7
occ:0.75
|
OH
|
F:TYR408
|
1.8
|
20.4
|
1.0
|
NE2
|
F:HIS460
|
2.1
|
14.5
|
1.0
|
OH
|
F:TYR447
|
2.2
|
21.9
|
1.0
|
NE2
|
F:HIS462
|
2.3
|
18.6
|
1.0
|
O
|
F:HOH859
|
2.3
|
18.1
|
0.8
|
CZ
|
F:TYR408
|
2.9
|
19.8
|
1.0
|
CE1
|
F:HIS460
|
3.0
|
15.3
|
1.0
|
CE1
|
F:HIS462
|
3.2
|
16.4
|
1.0
|
CD2
|
F:HIS460
|
3.2
|
14.4
|
1.0
|
CD2
|
F:HIS462
|
3.3
|
16.4
|
1.0
|
O
|
F:HOH858
|
3.3
|
28.2
|
1.0
|
CZ
|
F:TYR447
|
3.3
|
21.9
|
1.0
|
CE1
|
F:TYR408
|
3.7
|
19.1
|
1.0
|
CE2
|
F:TYR447
|
3.7
|
22.6
|
1.0
|
CE2
|
F:TYR408
|
3.8
|
20.5
|
1.0
|
O
|
F:HOH754
|
4.0
|
16.2
|
1.0
|
ND1
|
F:HIS460
|
4.1
|
15.2
|
1.0
|
CG
|
F:HIS460
|
4.3
|
13.4
|
1.0
|
ND1
|
F:HIS462
|
4.3
|
18.1
|
1.0
|
O
|
F:HOH860
|
4.3
|
16.8
|
1.0
|
CG
|
F:HIS462
|
4.4
|
16.6
|
1.0
|
NH1
|
F:ARG457
|
4.4
|
17.6
|
1.0
|
O
|
E:HOH305
|
4.4
|
20.8
|
1.0
|
CE1
|
F:TYR447
|
4.5
|
23.4
|
1.0
|
OE1
|
F:GLN477
|
4.9
|
18.5
|
1.0
|
CD1
|
F:TYR408
|
5.0
|
19.8
|
1.0
|
|
Reference:
C.J.Knoot,
V.M.Purpero,
J.D.Lipscomb.
Crystal Structures of Alkylperoxo and Anhydride Intermediates in An Intradiol Ring-Cleaving Dioxygenase. Proc.Natl.Acad.Sci.Usa V. 112 388 2015.
ISSN: ESSN 1091-6490
PubMed: 25548185
DOI: 10.1073/PNAS.1419118112
Page generated: Mon Aug 5 14:49:06 2024
|