Iron in PDB 3pca: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate
Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate
All present enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate:
1.13.11.3;
Protein crystallography data
The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate, PDB code: 3pca
was solved by
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 /
2.20
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
196.300,
127.200,
133.800,
90.00,
97.60,
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 3,4- Dihydroxybenzoate
(pdb code 3pca). 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 3,4- Dihydroxybenzoate, PDB code: 3pca:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3pca
Go back to
Iron Binding Sites List in 3pca
Iron binding site 1 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate
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 3,4- Dihydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe600
b:24.5
occ:1.00
|
OH
|
M:TYR408
|
1.9
|
16.5
|
1.0
|
O4
|
M:DHB550
|
2.0
|
19.1
|
1.0
|
NE2
|
M:HIS462
|
2.2
|
13.0
|
1.0
|
NE2
|
M:HIS460
|
2.2
|
13.7
|
1.0
|
O3
|
M:DHB550
|
2.5
|
17.0
|
1.0
|
C4
|
M:DHB550
|
2.9
|
17.9
|
1.0
|
CE1
|
M:HIS460
|
3.0
|
12.4
|
1.0
|
CE1
|
M:HIS462
|
3.0
|
12.1
|
1.0
|
C3
|
M:DHB550
|
3.1
|
16.9
|
1.0
|
CZ
|
M:TYR408
|
3.1
|
17.4
|
1.0
|
CD2
|
M:HIS462
|
3.3
|
12.0
|
1.0
|
CD2
|
M:HIS460
|
3.4
|
13.2
|
1.0
|
CE2
|
M:TYR408
|
3.7
|
17.9
|
1.0
|
NH1
|
M:ARG457
|
4.1
|
13.2
|
1.0
|
CE1
|
M:TYR408
|
4.1
|
17.8
|
1.0
|
ND1
|
M:HIS460
|
4.2
|
12.9
|
1.0
|
ND1
|
M:HIS462
|
4.2
|
12.1
|
1.0
|
C5
|
M:DHB550
|
4.2
|
17.3
|
1.0
|
O
|
A:HOH206
|
4.3
|
16.2
|
1.0
|
O
|
M:HOH621
|
4.3
|
12.9
|
1.0
|
CG
|
M:HIS462
|
4.3
|
12.2
|
1.0
|
CG
|
M:HIS460
|
4.4
|
12.6
|
1.0
|
C2
|
M:DHB550
|
4.4
|
16.6
|
1.0
|
OE1
|
M:GLN477
|
4.7
|
13.1
|
1.0
|
CD2
|
M:TYR408
|
5.0
|
18.8
|
1.0
|
|
Iron binding site 2 out
of 6 in 3pca
Go back to
Iron Binding Sites List in 3pca
Iron binding site 2 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate
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 3,4- Dihydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe600
b:23.9
occ:1.00
|
OH
|
N:TYR408
|
2.0
|
17.0
|
1.0
|
NE2
|
N:HIS462
|
2.2
|
12.2
|
1.0
|
O4
|
N:DHB550
|
2.2
|
18.9
|
1.0
|
NE2
|
N:HIS460
|
2.3
|
13.3
|
1.0
|
O3
|
N:DHB550
|
2.5
|
16.9
|
1.0
|
CE1
|
N:HIS462
|
3.0
|
11.6
|
1.0
|
C4
|
N:DHB550
|
3.0
|
17.8
|
1.0
|
C3
|
N:DHB550
|
3.1
|
17.0
|
1.0
|
CZ
|
N:TYR408
|
3.1
|
17.7
|
1.0
|
CE1
|
N:HIS460
|
3.3
|
12.6
|
1.0
|
CD2
|
N:HIS462
|
3.3
|
11.3
|
1.0
|
CD2
|
N:HIS460
|
3.3
|
12.9
|
1.0
|
CE2
|
N:TYR408
|
3.7
|
18.0
|
1.0
|
CE1
|
N:TYR408
|
4.1
|
17.8
|
1.0
|
ND1
|
N:HIS462
|
4.2
|
11.4
|
1.0
|
O
|
B:HOH238
|
4.2
|
15.8
|
1.0
|
NH1
|
N:ARG457
|
4.3
|
12.9
|
1.0
|
O
|
N:HOH631
|
4.3
|
12.8
|
1.0
|
C5
|
N:DHB550
|
4.3
|
17.3
|
1.0
|
CG
|
N:HIS462
|
4.3
|
11.4
|
1.0
|
ND1
|
N:HIS460
|
4.4
|
13.1
|
1.0
|
C2
|
N:DHB550
|
4.4
|
16.6
|
1.0
|
CG
|
N:HIS460
|
4.5
|
12.8
|
1.0
|
OE1
|
N:GLN477
|
4.7
|
12.3
|
1.0
|
CD2
|
N:TYR408
|
5.0
|
18.7
|
1.0
|
|
Iron binding site 3 out
of 6 in 3pca
Go back to
Iron Binding Sites List in 3pca
Iron binding site 3 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate
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 3,4- Dihydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe600
b:23.6
occ:1.00
|
OH
|
O:TYR408
|
2.0
|
17.3
|
1.0
|
O4
|
O:DHB550
|
2.1
|
18.8
|
1.0
|
NE2
|
O:HIS460
|
2.2
|
13.2
|
1.0
|
NE2
|
O:HIS462
|
2.2
|
12.9
|
1.0
|
O3
|
O:DHB550
|
2.5
|
17.1
|
1.0
|
C4
|
O:DHB550
|
3.0
|
17.6
|
1.0
|
CE1
|
O:HIS460
|
3.0
|
12.7
|
1.0
|
C3
|
O:DHB550
|
3.1
|
16.8
|
1.0
|
CE1
|
O:HIS462
|
3.1
|
12.2
|
1.0
|
CZ
|
O:TYR408
|
3.2
|
17.4
|
1.0
|
CD2
|
O:HIS462
|
3.2
|
12.2
|
1.0
|
CD2
|
O:HIS460
|
3.2
|
13.0
|
1.0
|
CE1
|
O:TYR408
|
3.9
|
18.2
|
1.0
|
CE2
|
O:TYR408
|
4.1
|
17.6
|
1.0
|
NH1
|
O:ARG457
|
4.1
|
13.5
|
1.0
|
ND1
|
O:HIS460
|
4.2
|
13.4
|
1.0
|
O
|
O:HOH629
|
4.2
|
13.1
|
1.0
|
C5
|
O:DHB550
|
4.3
|
17.2
|
1.0
|
ND1
|
O:HIS462
|
4.3
|
12.0
|
1.0
|
O
|
C:HOH206
|
4.3
|
16.0
|
1.0
|
CG
|
O:HIS462
|
4.3
|
11.9
|
1.0
|
CG
|
O:HIS460
|
4.3
|
13.1
|
1.0
|
C2
|
O:DHB550
|
4.5
|
16.7
|
1.0
|
OE1
|
O:GLN477
|
4.7
|
13.1
|
1.0
|
|
Iron binding site 4 out
of 6 in 3pca
Go back to
Iron Binding Sites List in 3pca
Iron binding site 4 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate
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 3,4- Dihydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Fe600
b:24.8
occ:1.00
|
OH
|
P:TYR408
|
2.0
|
16.9
|
1.0
|
O4
|
P:DHB550
|
2.2
|
18.9
|
1.0
|
NE2
|
P:HIS462
|
2.2
|
12.2
|
1.0
|
NE2
|
P:HIS460
|
2.2
|
13.7
|
1.0
|
O3
|
P:DHB550
|
2.4
|
16.9
|
1.0
|
C4
|
P:DHB550
|
2.9
|
17.9
|
1.0
|
CE1
|
P:HIS462
|
3.0
|
11.8
|
1.0
|
C3
|
P:DHB550
|
3.0
|
16.9
|
1.0
|
CE1
|
P:HIS460
|
3.0
|
13.0
|
1.0
|
CZ
|
P:TYR408
|
3.0
|
17.5
|
1.0
|
CD2
|
P:HIS462
|
3.3
|
11.5
|
1.0
|
CD2
|
P:HIS460
|
3.4
|
13.1
|
1.0
|
CE2
|
P:TYR408
|
3.6
|
17.7
|
1.0
|
CE1
|
P:TYR408
|
4.1
|
17.8
|
1.0
|
NH1
|
P:ARG457
|
4.1
|
13.3
|
1.0
|
ND1
|
P:HIS462
|
4.2
|
11.6
|
1.0
|
C5
|
P:DHB550
|
4.2
|
17.4
|
1.0
|
ND1
|
P:HIS460
|
4.3
|
13.3
|
1.0
|
O
|
P:HOH630
|
4.3
|
13.0
|
1.0
|
O
|
D:HOH702
|
4.4
|
16.1
|
0.8
|
C2
|
P:DHB550
|
4.4
|
16.8
|
1.0
|
CG
|
P:HIS462
|
4.4
|
11.7
|
1.0
|
CG
|
P:HIS460
|
4.4
|
13.1
|
1.0
|
OE1
|
P:GLN477
|
4.7
|
12.8
|
1.0
|
CD2
|
P:TYR408
|
4.9
|
18.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 3pca
Go back to
Iron Binding Sites List in 3pca
Iron binding site 5 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate
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 3,4- Dihydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Fe600
b:24.4
occ:0.80
|
OH
|
Q:TYR408
|
1.9
|
17.3
|
1.0
|
NE2
|
Q:HIS462
|
2.1
|
12.9
|
1.0
|
O4
|
Q:DHB550
|
2.1
|
18.9
|
1.0
|
NE2
|
Q:HIS460
|
2.3
|
13.9
|
1.0
|
O3
|
Q:DHB550
|
2.7
|
17.1
|
1.0
|
CE1
|
Q:HIS462
|
3.0
|
12.2
|
1.0
|
C4
|
Q:DHB550
|
3.0
|
17.7
|
1.0
|
CZ
|
Q:TYR408
|
3.1
|
17.9
|
1.0
|
CD2
|
Q:HIS462
|
3.1
|
12.2
|
1.0
|
CD2
|
Q:HIS460
|
3.2
|
13.3
|
1.0
|
C3
|
Q:DHB550
|
3.2
|
17.0
|
1.0
|
CE1
|
Q:HIS460
|
3.3
|
13.0
|
1.0
|
CE2
|
Q:TYR408
|
3.7
|
18.2
|
1.0
|
CE1
|
Q:TYR408
|
4.1
|
18.0
|
1.0
|
NH1
|
Q:ARG457
|
4.1
|
13.7
|
1.0
|
ND1
|
Q:HIS462
|
4.2
|
11.6
|
1.0
|
CG
|
Q:HIS462
|
4.3
|
11.8
|
1.0
|
O
|
Q:HOH971
|
4.3
|
13.3
|
1.0
|
O
|
E:HOH206
|
4.3
|
16.2
|
0.8
|
C5
|
Q:DHB550
|
4.3
|
17.4
|
1.0
|
CG
|
Q:HIS460
|
4.4
|
13.0
|
1.0
|
ND1
|
Q:HIS460
|
4.4
|
13.3
|
1.0
|
OE1
|
Q:GLN477
|
4.6
|
13.1
|
1.0
|
C2
|
Q:DHB550
|
4.6
|
16.7
|
1.0
|
CD2
|
Q:TYR408
|
5.0
|
19.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 3pca
Go back to
Iron Binding Sites List in 3pca
Iron binding site 6 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3,4- Dihydroxybenzoate
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 3,4- Dihydroxybenzoate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Fe600
b:24.2
occ:1.00
|
O4
|
R:DHB550
|
1.9
|
18.7
|
1.0
|
OH
|
R:TYR408
|
2.1
|
17.4
|
1.0
|
NE2
|
R:HIS462
|
2.2
|
12.9
|
1.0
|
NE2
|
R:HIS460
|
2.3
|
13.4
|
1.0
|
O3
|
R:DHB550
|
2.4
|
16.9
|
1.0
|
C4
|
R:DHB550
|
2.8
|
17.7
|
1.0
|
C3
|
R:DHB550
|
3.0
|
16.8
|
1.0
|
CE1
|
R:HIS462
|
3.1
|
12.5
|
1.0
|
CE1
|
R:HIS460
|
3.2
|
12.4
|
1.0
|
CZ
|
R:TYR408
|
3.2
|
17.5
|
1.0
|
CD2
|
R:HIS460
|
3.3
|
12.7
|
1.0
|
CD2
|
R:HIS462
|
3.3
|
11.8
|
1.0
|
CE2
|
R:TYR408
|
3.8
|
18.1
|
1.0
|
NH1
|
R:ARG457
|
4.0
|
13.8
|
1.0
|
C5
|
R:DHB550
|
4.1
|
17.4
|
1.0
|
CE1
|
R:TYR408
|
4.2
|
18.0
|
1.0
|
ND1
|
R:HIS462
|
4.3
|
12.1
|
1.0
|
O
|
F:HOH1166
|
4.3
|
16.3
|
1.0
|
C2
|
R:DHB550
|
4.3
|
16.6
|
1.0
|
ND1
|
R:HIS460
|
4.3
|
12.9
|
1.0
|
O
|
R:HOH1203
|
4.3
|
13.0
|
1.0
|
CG
|
R:HIS462
|
4.4
|
11.7
|
1.0
|
CG
|
R:HIS460
|
4.4
|
12.7
|
1.0
|
OE1
|
R:GLN477
|
4.6
|
13.3
|
1.0
|
|
Reference:
A.M.Orville,
J.D.Lipscomb,
D.H.Ohlendorf.
Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-Dioxygenase: Endogenous FE3+ Ligand Displacement in Response to Substrate Binding. Biochemistry V. 36 10052 1997.
ISSN: ISSN 0006-2960
PubMed: 9254600
DOI: 10.1021/BI970469F
Page generated: Sun Aug 4 17:44:01 2024
|