Iron in PDB 3lkt: Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
Enzymatic activity of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
All present enzymatic activity of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis:
1.13.11.3;
Protein crystallography data
The structure of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis, PDB code: 3lkt
was solved by
J.D.Lipscomb,
V.M.Purpero,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.57 /
1.65
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
190.310,
168.040,
128.160,
90.00,
132.30,
90.00
|
R / Rfree (%)
|
14.8 /
17.3
|
Other elements in 3lkt:
The structure of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
(pdb code 3lkt). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis, PDB code: 3lkt:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3lkt
Go back to
Iron Binding Sites List in 3lkt
Iron binding site 1 out
of 6 in the Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe600
b:15.9
occ:1.00
|
OH
|
M:TYR408
|
1.9
|
20.9
|
1.0
|
NE2
|
M:HIS462
|
2.1
|
13.1
|
1.0
|
NE2
|
M:HIS460
|
2.1
|
15.1
|
1.0
|
O1
|
M:BME29
|
2.3
|
23.5
|
0.9
|
S2
|
M:BME29
|
2.5
|
28.5
|
0.9
|
C1
|
M:BME29
|
2.6
|
21.6
|
0.9
|
CZ
|
M:TYR408
|
2.9
|
19.2
|
1.0
|
C2
|
M:BME29
|
3.0
|
25.3
|
0.9
|
CE1
|
M:HIS460
|
3.0
|
14.6
|
1.0
|
CE1
|
M:HIS462
|
3.1
|
16.0
|
1.0
|
CD2
|
M:HIS462
|
3.1
|
13.8
|
1.0
|
CD2
|
M:HIS460
|
3.2
|
14.8
|
1.0
|
CE2
|
M:TYR408
|
3.6
|
17.7
|
1.0
|
CE1
|
M:TYR408
|
3.8
|
17.3
|
1.0
|
O
|
M:HOH165
|
4.1
|
15.4
|
1.0
|
ND1
|
M:HIS460
|
4.2
|
14.1
|
1.0
|
ND1
|
M:HIS462
|
4.2
|
14.4
|
1.0
|
CG
|
M:HIS462
|
4.3
|
15.1
|
1.0
|
NH1
|
M:ARG457
|
4.3
|
14.8
|
1.0
|
O
|
M:HOH874
|
4.3
|
19.8
|
1.0
|
CG
|
M:HIS460
|
4.3
|
14.5
|
1.0
|
O
|
M:HOH225
|
4.4
|
18.5
|
1.0
|
CD2
|
M:TYR408
|
4.9
|
17.5
|
1.0
|
OE1
|
M:GLN477
|
4.9
|
14.5
|
1.0
|
|
Iron binding site 2 out
of 6 in 3lkt
Go back to
Iron Binding Sites List in 3lkt
Iron binding site 2 out
of 6 in the Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe600
b:16.6
occ:1.00
|
OH
|
N:TYR408
|
1.9
|
21.0
|
1.0
|
NE2
|
N:HIS462
|
2.1
|
15.0
|
1.0
|
NE2
|
N:HIS460
|
2.1
|
13.8
|
1.0
|
O1
|
N:BME32
|
2.3
|
17.4
|
0.5
|
O1
|
N:BME32
|
2.4
|
43.5
|
0.5
|
C2
|
N:BME32
|
2.4
|
42.7
|
0.5
|
S2
|
N:BME32
|
2.4
|
44.5
|
0.5
|
S2
|
N:BME32
|
2.4
|
23.2
|
0.5
|
C1
|
N:BME32
|
2.7
|
17.3
|
0.5
|
C1
|
N:BME32
|
2.7
|
43.3
|
0.5
|
CZ
|
N:TYR408
|
2.9
|
19.3
|
1.0
|
C2
|
N:BME32
|
3.0
|
18.7
|
0.5
|
CE1
|
N:HIS460
|
3.0
|
14.0
|
1.0
|
CE1
|
N:HIS462
|
3.1
|
14.3
|
1.0
|
CD2
|
N:HIS462
|
3.1
|
14.2
|
1.0
|
CD2
|
N:HIS460
|
3.2
|
14.5
|
1.0
|
CE2
|
N:TYR408
|
3.7
|
17.4
|
1.0
|
CE1
|
N:TYR408
|
3.8
|
18.1
|
1.0
|
O
|
N:HOH285
|
4.1
|
15.4
|
1.0
|
ND1
|
N:HIS462
|
4.2
|
14.9
|
1.0
|
ND1
|
N:HIS460
|
4.2
|
14.8
|
1.0
|
CG
|
N:HIS462
|
4.2
|
14.9
|
1.0
|
NH1
|
N:ARG457
|
4.3
|
16.4
|
1.0
|
O
|
N:HOH2285
|
4.3
|
18.5
|
1.0
|
CG
|
N:HIS460
|
4.3
|
13.8
|
1.0
|
O
|
N:HOH552
|
4.3
|
19.1
|
1.0
|
OE1
|
N:GLN477
|
4.9
|
15.7
|
1.0
|
CD2
|
N:TYR408
|
4.9
|
16.5
|
1.0
|
|
Iron binding site 3 out
of 6 in 3lkt
Go back to
Iron Binding Sites List in 3lkt
Iron binding site 3 out
of 6 in the Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe600
b:16.0
occ:1.00
|
OH
|
O:TYR408
|
1.9
|
20.5
|
1.0
|
NE2
|
O:HIS462
|
2.1
|
13.5
|
1.0
|
NE2
|
O:HIS460
|
2.1
|
15.0
|
1.0
|
O1
|
O:BME30
|
2.3
|
24.8
|
0.9
|
S2
|
O:BME30
|
2.4
|
28.7
|
0.9
|
C1
|
O:BME30
|
2.5
|
23.1
|
0.9
|
CZ
|
O:TYR408
|
2.9
|
18.6
|
1.0
|
C2
|
O:BME30
|
3.0
|
26.3
|
0.9
|
CE1
|
O:HIS460
|
3.0
|
15.6
|
1.0
|
CE1
|
O:HIS462
|
3.1
|
13.1
|
1.0
|
CD2
|
O:HIS462
|
3.1
|
13.7
|
1.0
|
CD2
|
O:HIS460
|
3.2
|
14.4
|
1.0
|
CE2
|
O:TYR408
|
3.7
|
17.9
|
1.0
|
CE1
|
O:TYR408
|
3.7
|
17.6
|
1.0
|
O
|
O:HOH119
|
4.2
|
15.9
|
1.0
|
ND1
|
O:HIS460
|
4.2
|
13.6
|
1.0
|
ND1
|
O:HIS462
|
4.2
|
13.4
|
1.0
|
O
|
O:HOH704
|
4.2
|
18.7
|
1.0
|
CG
|
O:HIS462
|
4.2
|
13.4
|
1.0
|
NH1
|
O:ARG457
|
4.3
|
15.5
|
1.0
|
CG
|
O:HIS460
|
4.3
|
13.4
|
1.0
|
O
|
O:HOH605
|
4.3
|
17.1
|
1.0
|
OE1
|
O:GLN477
|
4.8
|
15.2
|
1.0
|
CD2
|
O:TYR408
|
4.9
|
17.1
|
1.0
|
CD1
|
O:TYR408
|
5.0
|
16.9
|
1.0
|
|
Iron binding site 4 out
of 6 in 3lkt
Go back to
Iron Binding Sites List in 3lkt
Iron binding site 4 out
of 6 in the Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Fe600
b:16.0
occ:1.00
|
OH
|
P:TYR408
|
1.9
|
19.4
|
1.0
|
NE2
|
P:HIS460
|
2.1
|
16.1
|
1.0
|
NE2
|
P:HIS462
|
2.1
|
13.8
|
1.0
|
O1
|
P:BME31
|
2.3
|
24.1
|
0.9
|
S2
|
P:BME31
|
2.5
|
28.6
|
0.9
|
C1
|
P:BME31
|
2.6
|
23.2
|
0.9
|
CZ
|
P:TYR408
|
2.9
|
16.4
|
1.0
|
C2
|
P:BME31
|
3.0
|
26.3
|
0.9
|
CE1
|
P:HIS460
|
3.0
|
14.7
|
1.0
|
CE1
|
P:HIS462
|
3.1
|
15.8
|
1.0
|
CD2
|
P:HIS462
|
3.1
|
14.5
|
1.0
|
CD2
|
P:HIS460
|
3.2
|
14.7
|
1.0
|
CE2
|
P:TYR408
|
3.6
|
16.2
|
1.0
|
CE1
|
P:TYR408
|
3.8
|
17.5
|
1.0
|
O
|
P:HOH147
|
4.1
|
14.9
|
1.0
|
ND1
|
P:HIS460
|
4.1
|
14.1
|
1.0
|
ND1
|
P:HIS462
|
4.2
|
14.5
|
1.0
|
CG
|
P:HIS460
|
4.3
|
14.6
|
1.0
|
CG
|
P:HIS462
|
4.3
|
14.0
|
1.0
|
NH1
|
P:ARG457
|
4.3
|
16.6
|
1.0
|
O
|
P:HOH2287
|
4.3
|
20.1
|
1.0
|
O
|
P:HOH540
|
4.3
|
17.6
|
1.0
|
CD2
|
P:TYR408
|
4.9
|
16.7
|
1.0
|
OE1
|
P:GLN477
|
4.9
|
15.4
|
1.0
|
|
Iron binding site 5 out
of 6 in 3lkt
Go back to
Iron Binding Sites List in 3lkt
Iron binding site 5 out
of 6 in the Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Fe600
b:16.5
occ:1.00
|
OH
|
Q:TYR408
|
1.9
|
20.4
|
1.0
|
NE2
|
Q:HIS462
|
2.1
|
15.6
|
1.0
|
NE2
|
Q:HIS460
|
2.1
|
13.5
|
1.0
|
C2
|
Q:BME34
|
2.3
|
57.0
|
0.5
|
O1
|
Q:BME34
|
2.3
|
57.7
|
0.5
|
O1
|
Q:BME34
|
2.4
|
14.0
|
0.5
|
C1
|
Q:BME34
|
2.5
|
11.4
|
0.5
|
S2
|
Q:BME34
|
2.5
|
57.0
|
0.5
|
S2
|
Q:BME34
|
2.5
|
16.8
|
0.5
|
C1
|
Q:BME34
|
2.7
|
57.1
|
0.5
|
CZ
|
Q:TYR408
|
3.0
|
18.9
|
1.0
|
C2
|
Q:BME34
|
3.0
|
13.7
|
0.5
|
CE1
|
Q:HIS460
|
3.0
|
13.7
|
1.0
|
CE1
|
Q:HIS462
|
3.1
|
13.9
|
1.0
|
CD2
|
Q:HIS462
|
3.1
|
14.7
|
1.0
|
CD2
|
Q:HIS460
|
3.2
|
16.0
|
1.0
|
CE2
|
Q:TYR408
|
3.7
|
18.2
|
1.0
|
CE1
|
Q:TYR408
|
3.8
|
18.4
|
1.0
|
O
|
Q:HOH184
|
4.1
|
14.6
|
1.0
|
ND1
|
Q:HIS460
|
4.2
|
15.0
|
1.0
|
ND1
|
Q:HIS462
|
4.2
|
15.6
|
1.0
|
CG
|
Q:HIS462
|
4.2
|
14.3
|
1.0
|
CG
|
Q:HIS460
|
4.3
|
14.1
|
1.0
|
O
|
Q:HOH623
|
4.3
|
18.1
|
1.0
|
NH1
|
Q:ARG457
|
4.3
|
15.3
|
1.0
|
O
|
Q:HOH251
|
4.4
|
18.1
|
1.0
|
OE1
|
Q:GLN477
|
4.9
|
15.5
|
1.0
|
CD2
|
Q:TYR408
|
4.9
|
16.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 3lkt
Go back to
Iron Binding Sites List in 3lkt
Iron binding site 6 out
of 6 in the Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Fe600
b:15.6
occ:1.00
|
OH
|
R:TYR408
|
2.0
|
19.7
|
1.0
|
NE2
|
R:HIS460
|
2.1
|
15.2
|
1.0
|
NE2
|
R:HIS462
|
2.1
|
13.5
|
1.0
|
O1
|
R:BME28
|
2.1
|
15.0
|
0.9
|
S2
|
R:BME28
|
2.4
|
18.4
|
0.9
|
C1
|
R:BME28
|
2.8
|
14.8
|
0.9
|
CZ
|
R:TYR408
|
2.9
|
18.1
|
1.0
|
CE1
|
R:HIS460
|
3.0
|
15.8
|
1.0
|
CE1
|
R:HIS462
|
3.1
|
13.8
|
1.0
|
CD2
|
R:HIS462
|
3.1
|
13.2
|
1.0
|
C2
|
R:BME28
|
3.1
|
15.2
|
0.9
|
CD2
|
R:HIS460
|
3.2
|
15.5
|
1.0
|
CE2
|
R:TYR408
|
3.7
|
17.0
|
1.0
|
CE1
|
R:TYR408
|
3.8
|
17.5
|
1.0
|
O
|
R:HOH174
|
4.2
|
16.8
|
1.0
|
ND1
|
R:HIS460
|
4.2
|
14.3
|
1.0
|
ND1
|
R:HIS462
|
4.2
|
14.0
|
1.0
|
NH1
|
R:ARG457
|
4.2
|
15.5
|
1.0
|
CG
|
R:HIS462
|
4.2
|
13.1
|
1.0
|
CG
|
R:HIS460
|
4.3
|
13.7
|
1.0
|
O
|
R:HOH757
|
4.3
|
19.1
|
1.0
|
O
|
R:HOH35
|
4.3
|
16.9
|
1.0
|
OE1
|
R:GLN477
|
4.9
|
15.0
|
1.0
|
CD2
|
R:TYR408
|
5.0
|
17.5
|
1.0
|
CD1
|
R:TYR408
|
5.0
|
18.4
|
1.0
|
|
Reference:
V.M.Purpero,
M.P.Valley,
D.H.Ohlendorf,
J.D.Lipscomb,
D.Burk,
K.B.Dolbeare,
K.C.Brown.
Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis To Be Published.
Page generated: Sun Aug 4 14:30:19 2024
|