Iron in PDB 3pcf: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate
Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate
All present enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate:
1.13.11.3;
Protein crystallography data
The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate, PDB code: 3pcf
was solved by
A.M.Orville,
N.Elango,
J.D.Lipscomb,
D.H.Ohlendorf,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.00 /
2.15
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
196.030,
127.220,
133.700,
90.00,
97.70,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 3pcf:
The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate
(pdb code 3pcf). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate, PDB code: 3pcf:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3pcf
Go back to
Iron Binding Sites List in 3pcf
Iron binding site 1 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe600
b:21.6
occ:1.00
|
OH
|
M:TYR408
|
1.8
|
14.9
|
1.0
|
O4
|
M:FHB550
|
1.9
|
18.1
|
1.0
|
O
|
M:HOH747
|
2.1
|
17.3
|
1.0
|
OH
|
M:TYR447
|
2.2
|
21.1
|
1.0
|
NE2
|
M:HIS462
|
2.3
|
13.2
|
1.0
|
NE2
|
M:HIS460
|
2.3
|
12.7
|
1.0
|
CE1
|
M:HIS460
|
2.9
|
12.5
|
1.0
|
CZ
|
M:TYR408
|
2.9
|
16.4
|
1.0
|
C4
|
M:FHB550
|
3.0
|
18.8
|
1.0
|
CE1
|
M:HIS462
|
3.1
|
12.3
|
1.0
|
CD2
|
M:HIS462
|
3.3
|
12.8
|
1.0
|
CZ
|
M:TYR447
|
3.4
|
22.4
|
1.0
|
CE2
|
M:TYR408
|
3.5
|
17.1
|
1.0
|
CD2
|
M:HIS460
|
3.5
|
12.4
|
1.0
|
C5
|
M:FHB550
|
3.7
|
19.0
|
1.0
|
CE1
|
M:TYR447
|
3.9
|
23.0
|
1.0
|
CE1
|
M:TYR408
|
4.0
|
17.1
|
1.0
|
C3
|
M:FHB550
|
4.0
|
19.1
|
1.0
|
NH1
|
M:ARG457
|
4.1
|
9.9
|
1.0
|
ND1
|
M:HIS460
|
4.2
|
11.9
|
1.0
|
F3
|
M:FHB550
|
4.2
|
18.8
|
1.0
|
O
|
M:HOH624
|
4.2
|
10.9
|
1.0
|
ND1
|
M:HIS462
|
4.3
|
12.9
|
1.0
|
O
|
A:HOH606
|
4.4
|
15.0
|
1.0
|
CG
|
M:HIS462
|
4.4
|
13.2
|
1.0
|
CG
|
M:HIS460
|
4.5
|
11.6
|
1.0
|
CE2
|
M:TYR447
|
4.5
|
22.3
|
1.0
|
CD2
|
M:TYR408
|
4.8
|
18.2
|
1.0
|
OE1
|
M:GLN477
|
4.8
|
10.2
|
1.0
|
CD2
|
A:TYR16
|
4.9
|
22.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 3pcf
Go back to
Iron Binding Sites List in 3pcf
Iron binding site 2 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe600
b:21.2
occ:1.00
|
OH
|
N:TYR408
|
1.8
|
16.3
|
1.0
|
O4
|
N:FHB550
|
2.1
|
18.0
|
1.0
|
OH
|
N:TYR447
|
2.2
|
21.4
|
1.0
|
O
|
N:HOH861
|
2.2
|
16.9
|
0.8
|
NE2
|
N:HIS462
|
2.3
|
12.8
|
1.0
|
NE2
|
N:HIS460
|
2.4
|
12.8
|
1.0
|
CZ
|
N:TYR408
|
2.8
|
16.9
|
1.0
|
C4
|
N:FHB550
|
3.2
|
18.9
|
1.0
|
CE1
|
N:HIS462
|
3.2
|
11.8
|
1.0
|
CD2
|
N:HIS462
|
3.3
|
11.5
|
1.0
|
CE1
|
N:HIS460
|
3.3
|
11.7
|
1.0
|
CZ
|
N:TYR447
|
3.4
|
22.7
|
1.0
|
CD2
|
N:HIS460
|
3.4
|
11.4
|
1.0
|
CE1
|
N:TYR408
|
3.6
|
17.9
|
1.0
|
CE2
|
N:TYR408
|
3.7
|
17.7
|
1.0
|
C5
|
N:FHB550
|
3.9
|
19.4
|
1.0
|
CE1
|
N:TYR447
|
3.9
|
22.7
|
1.0
|
C3
|
N:FHB550
|
4.1
|
19.2
|
1.0
|
O
|
B:HOH606
|
4.2
|
15.1
|
1.0
|
F3
|
N:FHB550
|
4.2
|
19.0
|
1.0
|
ND1
|
N:HIS462
|
4.3
|
11.5
|
1.0
|
NH1
|
N:ARG457
|
4.4
|
9.0
|
1.0
|
O
|
N:HOH729
|
4.4
|
10.8
|
1.0
|
CG
|
N:HIS462
|
4.4
|
12.3
|
1.0
|
CE2
|
N:TYR447
|
4.5
|
22.2
|
1.0
|
ND1
|
N:HIS460
|
4.5
|
11.9
|
1.0
|
CG
|
N:HIS460
|
4.5
|
11.7
|
1.0
|
CD1
|
N:TYR408
|
4.8
|
18.1
|
1.0
|
CD2
|
B:TYR16
|
4.8
|
22.5
|
1.0
|
CD2
|
N:TYR408
|
4.9
|
18.3
|
1.0
|
|
Iron binding site 3 out
of 6 in 3pcf
Go back to
Iron Binding Sites List in 3pcf
Iron binding site 3 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe600
b:21.3
occ:1.00
|
OH
|
O:TYR408
|
1.9
|
17.5
|
1.0
|
O4
|
O:FHB550
|
1.9
|
18.2
|
1.0
|
OH
|
O:TYR447
|
2.0
|
21.4
|
1.0
|
NE2
|
O:HIS462
|
2.0
|
13.8
|
1.0
|
NE2
|
O:HIS460
|
2.3
|
12.8
|
1.0
|
O
|
O:HOH851
|
2.3
|
17.3
|
1.0
|
CE1
|
O:HIS462
|
3.0
|
13.6
|
1.0
|
CZ
|
O:TYR408
|
3.0
|
17.1
|
1.0
|
CD2
|
O:HIS462
|
3.1
|
12.7
|
1.0
|
CE1
|
O:HIS460
|
3.1
|
12.4
|
1.0
|
C4
|
O:FHB550
|
3.1
|
18.7
|
1.0
|
CZ
|
O:TYR447
|
3.3
|
21.9
|
1.0
|
CD2
|
O:HIS460
|
3.4
|
12.7
|
1.0
|
CE1
|
O:TYR408
|
3.7
|
18.2
|
1.0
|
C5
|
O:FHB550
|
3.8
|
18.9
|
1.0
|
CE2
|
O:TYR447
|
3.8
|
22.9
|
1.0
|
CE2
|
O:TYR408
|
3.9
|
17.4
|
1.0
|
O
|
O:HOH643
|
4.0
|
11.2
|
1.0
|
C3
|
O:FHB550
|
4.1
|
19.1
|
1.0
|
ND1
|
O:HIS462
|
4.1
|
12.4
|
1.0
|
F3
|
O:FHB550
|
4.1
|
19.1
|
1.0
|
CG
|
O:HIS462
|
4.2
|
12.2
|
1.0
|
NH1
|
O:ARG457
|
4.3
|
10.8
|
1.0
|
ND1
|
O:HIS460
|
4.3
|
12.7
|
1.0
|
O
|
C:HOH606
|
4.3
|
15.0
|
1.0
|
CE1
|
O:TYR447
|
4.3
|
22.0
|
1.0
|
CG
|
O:HIS460
|
4.5
|
11.6
|
1.0
|
OE1
|
O:GLN477
|
4.9
|
8.7
|
1.0
|
CD2
|
C:TYR16
|
4.9
|
22.0
|
1.0
|
|
Iron binding site 4 out
of 6 in 3pcf
Go back to
Iron Binding Sites List in 3pcf
Iron binding site 4 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Fe600
b:21.5
occ:1.00
|
OH
|
P:TYR408
|
1.7
|
14.7
|
1.0
|
O4
|
P:FHB550
|
2.0
|
18.1
|
1.0
|
OH
|
P:TYR447
|
2.2
|
21.9
|
1.0
|
NE2
|
P:HIS460
|
2.2
|
13.2
|
1.0
|
NE2
|
P:HIS462
|
2.2
|
12.4
|
1.0
|
O
|
P:HOH785
|
2.3
|
17.2
|
0.8
|
CZ
|
P:TYR408
|
2.8
|
16.4
|
1.0
|
CE1
|
P:HIS460
|
3.0
|
12.1
|
1.0
|
CE1
|
P:HIS462
|
3.0
|
12.4
|
1.0
|
C4
|
P:FHB550
|
3.1
|
18.8
|
1.0
|
CD2
|
P:HIS460
|
3.3
|
12.4
|
1.0
|
CD2
|
P:HIS462
|
3.3
|
11.8
|
1.0
|
CZ
|
P:TYR447
|
3.4
|
22.8
|
1.0
|
CE2
|
P:TYR408
|
3.5
|
17.4
|
1.0
|
CE1
|
P:TYR408
|
3.8
|
16.7
|
1.0
|
C5
|
P:FHB550
|
3.8
|
19.0
|
1.0
|
CE2
|
P:TYR447
|
3.9
|
23.3
|
1.0
|
C3
|
P:FHB550
|
4.1
|
19.0
|
1.0
|
O
|
P:HOH662
|
4.1
|
11.2
|
1.0
|
NH1
|
P:ARG457
|
4.2
|
10.7
|
1.0
|
ND1
|
P:HIS460
|
4.2
|
12.1
|
1.0
|
ND1
|
P:HIS462
|
4.2
|
12.1
|
1.0
|
F3
|
P:FHB550
|
4.3
|
19.2
|
1.0
|
CG
|
P:HIS460
|
4.4
|
12.8
|
1.0
|
O
|
D:HOH606
|
4.4
|
15.2
|
1.0
|
CG
|
P:HIS462
|
4.4
|
12.4
|
1.0
|
CE1
|
P:TYR447
|
4.5
|
22.6
|
1.0
|
OE1
|
P:GLN477
|
4.8
|
9.8
|
1.0
|
CD2
|
P:TYR408
|
4.8
|
18.2
|
1.0
|
CD2
|
D:TYR16
|
5.0
|
22.4
|
1.0
|
|
Iron binding site 5 out
of 6 in 3pcf
Go back to
Iron Binding Sites List in 3pcf
Iron binding site 5 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Fe600
b:22.9
occ:1.00
|
OH
|
Q:TYR408
|
1.8
|
16.5
|
1.0
|
OH
|
Q:TYR447
|
2.0
|
21.1
|
1.0
|
NE2
|
Q:HIS462
|
2.1
|
13.4
|
1.0
|
O4
|
Q:FHB550
|
2.1
|
18.4
|
1.0
|
NE2
|
Q:HIS460
|
2.3
|
13.3
|
1.0
|
O
|
Q:HOH776
|
2.4
|
17.4
|
1.0
|
CZ
|
Q:TYR408
|
2.9
|
16.9
|
1.0
|
CE1
|
Q:HIS462
|
2.9
|
12.4
|
1.0
|
CE1
|
Q:HIS460
|
3.2
|
12.2
|
1.0
|
CD2
|
Q:HIS462
|
3.2
|
13.1
|
1.0
|
CZ
|
Q:TYR447
|
3.2
|
22.3
|
1.0
|
C4
|
Q:FHB550
|
3.2
|
18.8
|
1.0
|
CD2
|
Q:HIS460
|
3.3
|
12.8
|
1.0
|
CE1
|
Q:TYR408
|
3.7
|
17.4
|
1.0
|
CE2
|
Q:TYR408
|
3.8
|
17.2
|
1.0
|
CE2
|
Q:TYR447
|
3.8
|
22.8
|
1.0
|
C5
|
Q:FHB550
|
4.0
|
19.1
|
1.0
|
O
|
Q:HOH648
|
4.1
|
11.8
|
1.0
|
ND1
|
Q:HIS462
|
4.1
|
12.1
|
1.0
|
C3
|
Q:FHB550
|
4.1
|
19.0
|
1.0
|
F3
|
Q:FHB550
|
4.2
|
18.9
|
1.0
|
NH1
|
Q:ARG457
|
4.2
|
10.4
|
1.0
|
CG
|
Q:HIS462
|
4.3
|
12.7
|
1.0
|
CE1
|
Q:TYR447
|
4.3
|
21.3
|
1.0
|
O
|
E:HOH606
|
4.3
|
15.2
|
1.0
|
ND1
|
Q:HIS460
|
4.3
|
12.8
|
1.0
|
CG
|
Q:HIS460
|
4.5
|
12.5
|
1.0
|
OE1
|
Q:GLN477
|
4.7
|
10.3
|
1.0
|
CD2
|
E:TYR16
|
4.9
|
22.4
|
1.0
|
|
Iron binding site 6 out
of 6 in 3pcf
Go back to
Iron Binding Sites List in 3pcf
Iron binding site 6 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Fe600
b:21.2
occ:1.00
|
O4
|
R:FHB550
|
1.9
|
17.7
|
1.0
|
OH
|
R:TYR408
|
1.9
|
16.8
|
1.0
|
OH
|
R:TYR447
|
2.1
|
21.6
|
1.0
|
NE2
|
R:HIS462
|
2.2
|
11.9
|
1.0
|
O
|
R:HOH897
|
2.3
|
17.4
|
1.0
|
NE2
|
R:HIS460
|
2.3
|
12.2
|
1.0
|
CZ
|
R:TYR408
|
2.9
|
17.3
|
1.0
|
C4
|
R:FHB550
|
3.0
|
18.9
|
1.0
|
CE1
|
R:HIS462
|
3.1
|
12.8
|
1.0
|
CE1
|
R:HIS460
|
3.1
|
11.9
|
1.0
|
CD2
|
R:HIS462
|
3.3
|
11.9
|
1.0
|
CZ
|
R:TYR447
|
3.3
|
22.0
|
1.0
|
CD2
|
R:HIS460
|
3.4
|
12.0
|
1.0
|
CE2
|
R:TYR408
|
3.5
|
17.6
|
1.0
|
C5
|
R:FHB550
|
3.8
|
19.1
|
1.0
|
CE1
|
R:TYR447
|
3.8
|
22.6
|
1.0
|
CE1
|
R:TYR408
|
3.9
|
17.6
|
1.0
|
C3
|
R:FHB550
|
3.9
|
18.8
|
1.0
|
F3
|
R:FHB550
|
4.0
|
18.8
|
1.0
|
NH1
|
R:ARG457
|
4.2
|
9.7
|
1.0
|
O
|
F:HOH606
|
4.3
|
15.7
|
1.0
|
O
|
R:HOH764
|
4.3
|
11.2
|
1.0
|
ND1
|
R:HIS462
|
4.3
|
12.2
|
1.0
|
ND1
|
R:HIS460
|
4.3
|
12.8
|
1.0
|
CG
|
R:HIS462
|
4.4
|
12.2
|
1.0
|
CE2
|
R:TYR447
|
4.4
|
21.8
|
1.0
|
CG
|
R:HIS460
|
4.5
|
12.2
|
1.0
|
CD2
|
R:TYR408
|
4.8
|
18.3
|
1.0
|
CD2
|
F:TYR16
|
4.9
|
22.6
|
1.0
|
OE1
|
R:GLN477
|
4.9
|
9.0
|
1.0
|
|
Reference:
A.M.Orville,
N.Elango,
J.D.Lipscomb,
D.H.Ohlendorf.
Structures of Competitive Inhibitor Complexes of Protocatechuate 3,4-Dioxygenase: Multiple Exogenous Ligand Binding Orientations Within the Active Site. Biochemistry V. 36 10039 1997.
ISSN: ISSN 0006-2960
PubMed: 9254599
DOI: 10.1021/BI970468N
Page generated: Sun Aug 4 17:49:34 2024
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