Iron in PDB 3pcc: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 4- Hydroxybenzoate
Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 4- Hydroxybenzoate
All present enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 4- Hydroxybenzoate:
1.13.11.3;
Protein crystallography data
The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 4- Hydroxybenzoate, PDB code: 3pcc
was solved by
N.Elango,
A.M.Orville,
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 /
1.98
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
197.410,
127.970,
134.880,
90.00,
97.80,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 4- Hydroxybenzoate
(pdb code 3pcc). 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 4- Hydroxybenzoate, PDB code: 3pcc:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3pcc
Go back to
Iron Binding Sites List in 3pcc
Iron binding site 1 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 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 4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe600
b:22.6
occ:1.00
|
OH
|
M:TYR408
|
2.0
|
17.6
|
1.0
|
OH
|
M:TYR447
|
2.1
|
21.4
|
1.0
|
O
|
M:HOH743
|
2.1
|
18.9
|
1.0
|
O4
|
M:PHB550
|
2.1
|
19.6
|
1.0
|
NE2
|
M:HIS460
|
2.3
|
14.8
|
1.0
|
NE2
|
M:HIS462
|
2.3
|
14.4
|
1.0
|
CE1
|
M:HIS460
|
3.0
|
13.6
|
1.0
|
CZ
|
M:TYR408
|
3.0
|
18.2
|
1.0
|
CE1
|
M:HIS462
|
3.2
|
12.2
|
1.0
|
C4
|
M:PHB550
|
3.3
|
20.0
|
1.0
|
CZ
|
M:TYR447
|
3.3
|
21.4
|
1.0
|
CD2
|
M:HIS462
|
3.4
|
13.0
|
1.0
|
CD2
|
M:HIS460
|
3.5
|
13.6
|
1.0
|
CE2
|
M:TYR408
|
3.6
|
18.4
|
1.0
|
CE2
|
M:TYR447
|
3.8
|
21.8
|
1.0
|
C5
|
M:PHB550
|
3.9
|
20.3
|
1.0
|
CE1
|
M:TYR408
|
4.0
|
18.1
|
1.0
|
ND1
|
M:HIS460
|
4.2
|
13.5
|
1.0
|
O
|
M:HOH626
|
4.2
|
13.3
|
1.0
|
C3
|
M:PHB550
|
4.2
|
20.1
|
1.0
|
ND1
|
M:HIS462
|
4.3
|
12.7
|
1.0
|
NH1
|
M:ARG457
|
4.3
|
14.0
|
1.0
|
O
|
A:HOH606
|
4.4
|
15.5
|
1.0
|
CE1
|
M:TYR447
|
4.4
|
21.3
|
1.0
|
CG
|
M:HIS460
|
4.5
|
12.9
|
1.0
|
CG
|
M:HIS462
|
4.5
|
12.8
|
1.0
|
CD2
|
M:TYR408
|
4.9
|
18.9
|
1.0
|
CD2
|
A:TYR16
|
5.0
|
22.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 3pcc
Go back to
Iron Binding Sites List in 3pcc
Iron binding site 2 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 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 4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe600
b:21.4
occ:1.00
|
OH
|
N:TYR408
|
1.9
|
17.1
|
1.0
|
O4
|
N:PHB550
|
2.1
|
19.8
|
1.0
|
O
|
N:HOH854
|
2.1
|
18.5
|
1.0
|
NE2
|
N:HIS462
|
2.2
|
13.4
|
1.0
|
OH
|
N:TYR447
|
2.3
|
21.1
|
1.0
|
NE2
|
N:HIS460
|
2.4
|
14.6
|
1.0
|
CZ
|
N:TYR408
|
3.0
|
18.0
|
1.0
|
CE1
|
N:HIS462
|
3.0
|
12.3
|
1.0
|
C4
|
N:PHB550
|
3.2
|
20.1
|
1.0
|
CE1
|
N:HIS460
|
3.3
|
13.7
|
1.0
|
CD2
|
N:HIS462
|
3.4
|
13.4
|
1.0
|
CD2
|
N:HIS460
|
3.4
|
13.5
|
1.0
|
CZ
|
N:TYR447
|
3.4
|
22.3
|
1.0
|
CE2
|
N:TYR408
|
3.6
|
18.6
|
1.0
|
C5
|
N:PHB550
|
3.7
|
20.4
|
1.0
|
CE1
|
N:TYR447
|
3.9
|
22.2
|
1.0
|
CE1
|
N:TYR408
|
3.9
|
18.0
|
1.0
|
C3
|
N:PHB550
|
4.2
|
19.8
|
1.0
|
O
|
N:HOH728
|
4.2
|
12.8
|
1.0
|
ND1
|
N:HIS462
|
4.2
|
12.5
|
1.0
|
O
|
B:HOH606
|
4.3
|
15.2
|
1.0
|
NH1
|
N:ARG457
|
4.3
|
13.3
|
1.0
|
CG
|
N:HIS462
|
4.4
|
12.8
|
1.0
|
ND1
|
N:HIS460
|
4.4
|
13.9
|
1.0
|
CG
|
N:HIS460
|
4.5
|
13.8
|
1.0
|
CE2
|
N:TYR447
|
4.6
|
21.2
|
1.0
|
CD2
|
N:TYR408
|
4.9
|
18.4
|
1.0
|
OE1
|
N:GLN477
|
5.0
|
12.7
|
1.0
|
|
Iron binding site 3 out
of 6 in 3pcc
Go back to
Iron Binding Sites List in 3pcc
Iron binding site 3 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 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 4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe600
b:22.7
occ:1.00
|
OH
|
O:TYR408
|
1.9
|
18.2
|
1.0
|
O
|
O:HOH840
|
2.1
|
19.0
|
1.0
|
OH
|
O:TYR447
|
2.1
|
21.4
|
1.0
|
NE2
|
O:HIS462
|
2.2
|
14.6
|
1.0
|
O4
|
O:PHB550
|
2.2
|
19.9
|
1.0
|
NE2
|
O:HIS460
|
2.2
|
14.2
|
1.0
|
CE1
|
O:HIS460
|
3.0
|
13.5
|
1.0
|
CZ
|
O:TYR408
|
3.0
|
18.2
|
1.0
|
CE1
|
O:HIS462
|
3.0
|
13.6
|
1.0
|
CD2
|
O:HIS462
|
3.2
|
13.3
|
1.0
|
C4
|
O:PHB550
|
3.3
|
20.2
|
1.0
|
CD2
|
O:HIS460
|
3.3
|
12.9
|
1.0
|
CZ
|
O:TYR447
|
3.4
|
21.9
|
1.0
|
CE1
|
O:TYR408
|
3.8
|
18.7
|
1.0
|
CE2
|
O:TYR408
|
3.9
|
18.2
|
1.0
|
C5
|
O:PHB550
|
3.9
|
20.3
|
1.0
|
CE2
|
O:TYR447
|
4.0
|
21.7
|
1.0
|
O
|
O:HOH643
|
4.2
|
13.5
|
1.0
|
ND1
|
O:HIS460
|
4.2
|
13.6
|
1.0
|
C3
|
O:PHB550
|
4.2
|
19.9
|
1.0
|
ND1
|
O:HIS462
|
4.2
|
13.9
|
1.0
|
CG
|
O:HIS462
|
4.3
|
12.9
|
1.0
|
CG
|
O:HIS460
|
4.4
|
13.1
|
1.0
|
O
|
C:HOH606
|
4.4
|
15.8
|
1.0
|
NH1
|
O:ARG457
|
4.4
|
13.6
|
1.0
|
CE1
|
O:TYR447
|
4.5
|
21.3
|
1.0
|
OE1
|
O:GLN477
|
5.0
|
12.5
|
1.0
|
|
Iron binding site 4 out
of 6 in 3pcc
Go back to
Iron Binding Sites List in 3pcc
Iron binding site 4 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 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 4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Fe600
b:22.2
occ:1.00
|
OH
|
P:TYR408
|
1.8
|
17.8
|
1.0
|
OH
|
P:TYR447
|
2.1
|
21.4
|
1.0
|
O
|
P:HOH777
|
2.1
|
19.0
|
1.0
|
NE2
|
P:HIS462
|
2.2
|
13.7
|
1.0
|
NE2
|
P:HIS460
|
2.3
|
14.1
|
1.0
|
O4
|
P:PHB550
|
2.3
|
19.6
|
1.0
|
CZ
|
P:TYR408
|
3.0
|
17.9
|
1.0
|
CE1
|
P:HIS460
|
3.0
|
13.6
|
1.0
|
CE1
|
P:HIS462
|
3.0
|
11.7
|
1.0
|
CD2
|
P:HIS462
|
3.3
|
12.6
|
1.0
|
CD2
|
P:HIS460
|
3.3
|
12.8
|
1.0
|
CZ
|
P:TYR447
|
3.3
|
21.5
|
1.0
|
C4
|
P:PHB550
|
3.4
|
20.0
|
1.0
|
CE2
|
P:TYR408
|
3.6
|
18.7
|
1.0
|
CE2
|
P:TYR447
|
3.8
|
21.5
|
1.0
|
CE1
|
P:TYR408
|
3.9
|
17.7
|
1.0
|
C5
|
P:PHB550
|
4.0
|
20.4
|
1.0
|
O
|
P:HOH663
|
4.2
|
12.8
|
1.0
|
ND1
|
P:HIS462
|
4.2
|
12.0
|
1.0
|
ND1
|
P:HIS460
|
4.3
|
13.7
|
1.0
|
O
|
D:HOH606
|
4.3
|
16.0
|
1.0
|
CG
|
P:HIS462
|
4.4
|
12.9
|
1.0
|
CG
|
P:HIS460
|
4.4
|
13.8
|
1.0
|
NH1
|
P:ARG457
|
4.4
|
14.2
|
1.0
|
CE1
|
P:TYR447
|
4.5
|
21.0
|
1.0
|
C3
|
P:PHB550
|
4.5
|
19.9
|
1.0
|
CD2
|
P:TYR408
|
4.9
|
18.9
|
1.0
|
|
Iron binding site 5 out
of 6 in 3pcc
Go back to
Iron Binding Sites List in 3pcc
Iron binding site 5 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 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 4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Fe600
b:22.9
occ:1.00
|
OH
|
Q:TYR408
|
1.9
|
17.3
|
1.0
|
OH
|
Q:TYR447
|
2.0
|
21.7
|
1.0
|
O4
|
Q:PHB550
|
2.1
|
19.8
|
1.0
|
O
|
Q:HOH769
|
2.2
|
18.9
|
1.0
|
NE2
|
Q:HIS462
|
2.2
|
13.6
|
1.0
|
NE2
|
Q:HIS460
|
2.2
|
14.9
|
1.0
|
CZ
|
Q:TYR408
|
3.0
|
17.5
|
1.0
|
CE1
|
Q:HIS462
|
3.1
|
11.9
|
1.0
|
CE1
|
Q:HIS460
|
3.1
|
13.8
|
1.0
|
C4
|
Q:PHB550
|
3.2
|
20.0
|
1.0
|
CD2
|
Q:HIS462
|
3.3
|
13.2
|
1.0
|
CZ
|
Q:TYR447
|
3.3
|
22.4
|
1.0
|
CD2
|
Q:HIS460
|
3.3
|
13.7
|
1.0
|
CE1
|
Q:TYR408
|
3.7
|
18.0
|
1.0
|
CE2
|
Q:TYR447
|
3.8
|
22.4
|
1.0
|
C5
|
Q:PHB550
|
3.9
|
20.6
|
1.0
|
CE2
|
Q:TYR408
|
3.9
|
17.3
|
1.0
|
C3
|
Q:PHB550
|
4.2
|
19.8
|
1.0
|
O
|
Q:HOH646
|
4.2
|
14.0
|
1.0
|
ND1
|
Q:HIS462
|
4.2
|
12.9
|
1.0
|
ND1
|
Q:HIS460
|
4.3
|
14.0
|
1.0
|
NH1
|
Q:ARG457
|
4.3
|
13.7
|
1.0
|
CE1
|
Q:TYR447
|
4.4
|
21.7
|
1.0
|
CG
|
Q:HIS462
|
4.4
|
12.6
|
1.0
|
O
|
E:HOH606
|
4.4
|
15.6
|
1.0
|
CG
|
Q:HIS460
|
4.4
|
13.8
|
1.0
|
OE1
|
Q:GLN477
|
4.8
|
13.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 3pcc
Go back to
Iron Binding Sites List in 3pcc
Iron binding site 6 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 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 4- Hydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Fe600
b:22.5
occ:1.00
|
OH
|
R:TYR408
|
1.7
|
17.2
|
1.0
|
O4
|
R:PHB550
|
2.1
|
19.6
|
1.0
|
O
|
R:HOH899
|
2.2
|
18.7
|
1.0
|
OH
|
R:TYR447
|
2.2
|
21.6
|
1.0
|
NE2
|
R:HIS462
|
2.3
|
14.3
|
1.0
|
NE2
|
R:HIS460
|
2.3
|
14.7
|
1.0
|
CZ
|
R:TYR408
|
2.8
|
17.5
|
1.0
|
CE1
|
R:HIS460
|
3.2
|
14.0
|
1.0
|
C4
|
R:PHB550
|
3.2
|
20.0
|
1.0
|
CE1
|
R:HIS462
|
3.3
|
13.3
|
1.0
|
CD2
|
R:HIS462
|
3.3
|
13.3
|
1.0
|
CD2
|
R:HIS460
|
3.3
|
14.5
|
1.0
|
CZ
|
R:TYR447
|
3.4
|
21.8
|
1.0
|
CE1
|
R:TYR408
|
3.5
|
18.3
|
1.0
|
CE2
|
R:TYR408
|
3.8
|
17.6
|
1.0
|
C5
|
R:PHB550
|
3.8
|
20.5
|
1.0
|
CE2
|
R:TYR447
|
3.8
|
21.8
|
1.0
|
O
|
R:HOH770
|
4.2
|
13.2
|
1.0
|
O
|
F:HOH606
|
4.2
|
15.8
|
1.0
|
C3
|
R:PHB550
|
4.2
|
19.9
|
1.0
|
NH1
|
R:ARG457
|
4.3
|
13.6
|
1.0
|
ND1
|
R:HIS460
|
4.4
|
13.8
|
1.0
|
ND1
|
R:HIS462
|
4.4
|
12.5
|
1.0
|
CG
|
R:HIS462
|
4.5
|
12.8
|
1.0
|
CG
|
R:HIS460
|
4.5
|
14.1
|
1.0
|
CE1
|
R:TYR447
|
4.6
|
21.5
|
1.0
|
CD1
|
R:TYR408
|
4.8
|
19.0
|
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 17:45:24 2024
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