Iron in PDB 3pcm: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide
Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide
All present enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide:
1.13.11.3;
Protein crystallography data
The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide, PDB code: 3pcm
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 /
2.25
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
196.100,
127.300,
134.500,
90.00,
97.70,
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 6- Hydroxynicotinic Acid N-Oxide and Cyanide
(pdb code 3pcm). 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 6- Hydroxynicotinic Acid N-Oxide and Cyanide, PDB code: 3pcm:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3pcm
Go back to
Iron Binding Sites List in 3pcm
Iron binding site 1 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide
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 6- Hydroxynicotinic Acid N-Oxide and Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe600
b:21.0
occ:0.80
|
OH
|
M:TYR408
|
2.0
|
15.8
|
1.0
|
O4
|
M:NNO550
|
2.1
|
18.7
|
0.9
|
NE2
|
M:HIS462
|
2.2
|
12.9
|
1.0
|
O3
|
M:NNO550
|
2.3
|
16.3
|
0.9
|
NE2
|
M:HIS460
|
2.3
|
12.9
|
1.0
|
C
|
M:CYN575
|
2.4
|
17.5
|
1.0
|
C6
|
M:NNO550
|
2.8
|
19.0
|
0.9
|
N1
|
M:NNO550
|
2.8
|
18.1
|
0.9
|
CZ
|
M:TYR408
|
3.0
|
16.7
|
1.0
|
CE1
|
M:HIS462
|
3.1
|
11.9
|
1.0
|
CE1
|
M:HIS460
|
3.1
|
12.1
|
1.0
|
CD2
|
M:HIS462
|
3.3
|
12.2
|
1.0
|
N
|
M:CYN575
|
3.3
|
18.1
|
1.0
|
CD2
|
M:HIS460
|
3.5
|
12.3
|
1.0
|
CE2
|
M:TYR408
|
3.6
|
17.0
|
1.0
|
C5
|
M:NNO550
|
4.0
|
19.4
|
0.9
|
CE1
|
M:TYR408
|
4.0
|
17.3
|
1.0
|
C2
|
M:NNO550
|
4.1
|
19.0
|
0.9
|
NH1
|
M:ARG457
|
4.2
|
12.6
|
1.0
|
ND1
|
M:HIS462
|
4.3
|
12.0
|
1.0
|
ND1
|
M:HIS460
|
4.3
|
12.0
|
1.0
|
O
|
M:HOH624
|
4.3
|
11.8
|
1.0
|
CG
|
M:HIS462
|
4.4
|
12.0
|
1.0
|
CG
|
M:HIS460
|
4.5
|
11.7
|
1.0
|
O
|
M:HOH602
|
4.6
|
16.4
|
1.0
|
OE1
|
M:GLN477
|
4.9
|
11.9
|
1.0
|
CD2
|
M:TYR408
|
4.9
|
17.7
|
1.0
|
|
Iron binding site 2 out
of 6 in 3pcm
Go back to
Iron Binding Sites List in 3pcm
Iron binding site 2 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide
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 6- Hydroxynicotinic Acid N-Oxide and Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe600
b:20.5
occ:0.80
|
OH
|
N:TYR408
|
2.0
|
15.6
|
1.0
|
NE2
|
N:HIS462
|
2.1
|
12.5
|
1.0
|
C
|
N:CYN575
|
2.2
|
17.3
|
1.0
|
O4
|
N:NNO550
|
2.2
|
18.6
|
0.9
|
O3
|
N:NNO550
|
2.4
|
16.3
|
0.9
|
NE2
|
N:HIS460
|
2.4
|
12.3
|
1.0
|
C6
|
N:NNO550
|
2.9
|
19.1
|
0.9
|
N1
|
N:NNO550
|
3.0
|
18.1
|
0.9
|
CE1
|
N:HIS462
|
3.0
|
12.1
|
1.0
|
CZ
|
N:TYR408
|
3.0
|
16.2
|
1.0
|
CD2
|
N:HIS462
|
3.2
|
12.1
|
1.0
|
N
|
N:CYN575
|
3.3
|
17.9
|
1.0
|
CE1
|
N:HIS460
|
3.3
|
12.0
|
1.0
|
CD2
|
N:HIS460
|
3.5
|
12.2
|
1.0
|
CE2
|
N:TYR408
|
3.7
|
16.8
|
1.0
|
CE1
|
N:TYR408
|
4.0
|
16.7
|
1.0
|
C5
|
N:NNO550
|
4.2
|
19.4
|
0.9
|
ND1
|
N:HIS462
|
4.2
|
11.9
|
1.0
|
C2
|
N:NNO550
|
4.2
|
19.1
|
0.9
|
CG
|
N:HIS462
|
4.3
|
12.0
|
1.0
|
O
|
N:HOH629
|
4.4
|
11.6
|
1.0
|
NH1
|
N:ARG457
|
4.4
|
11.6
|
1.0
|
ND1
|
N:HIS460
|
4.5
|
11.7
|
1.0
|
O
|
B:HOH242
|
4.5
|
16.6
|
1.0
|
CG
|
N:HIS460
|
4.6
|
11.9
|
1.0
|
OE1
|
N:GLN477
|
4.7
|
10.9
|
1.0
|
CD2
|
N:TYR408
|
5.0
|
17.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 3pcm
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Iron Binding Sites List in 3pcm
Iron binding site 3 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide
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 6- Hydroxynicotinic Acid N-Oxide and Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe600
b:21.2
occ:0.80
|
C
|
O:CYN575
|
2.0
|
17.3
|
1.0
|
OH
|
O:TYR408
|
2.0
|
15.8
|
1.0
|
O4
|
O:NNO550
|
2.1
|
18.7
|
0.9
|
NE2
|
O:HIS462
|
2.2
|
12.6
|
1.0
|
NE2
|
O:HIS460
|
2.2
|
12.6
|
1.0
|
O3
|
O:NNO550
|
2.3
|
16.6
|
0.9
|
C6
|
O:NNO550
|
2.8
|
19.1
|
0.9
|
N1
|
O:NNO550
|
2.8
|
18.1
|
0.9
|
CE1
|
O:HIS460
|
3.1
|
12.1
|
1.0
|
CZ
|
O:TYR408
|
3.1
|
16.8
|
1.0
|
N
|
O:CYN575
|
3.1
|
17.9
|
1.0
|
CE1
|
O:HIS462
|
3.2
|
12.1
|
1.0
|
CD2
|
O:HIS462
|
3.2
|
12.4
|
1.0
|
CD2
|
O:HIS460
|
3.3
|
12.0
|
1.0
|
CE1
|
O:TYR408
|
3.7
|
17.4
|
1.0
|
CE2
|
O:TYR408
|
4.0
|
17.4
|
1.0
|
C5
|
O:NNO550
|
4.1
|
19.3
|
0.9
|
C2
|
O:NNO550
|
4.1
|
19.0
|
0.9
|
O
|
O:HOH632
|
4.2
|
11.8
|
1.0
|
NH1
|
O:ARG457
|
4.2
|
12.1
|
1.0
|
ND1
|
O:HIS460
|
4.3
|
12.2
|
1.0
|
ND1
|
O:HIS462
|
4.3
|
12.0
|
1.0
|
CG
|
O:HIS462
|
4.4
|
12.2
|
1.0
|
CG
|
O:HIS460
|
4.4
|
11.9
|
1.0
|
O
|
O:HOH608
|
4.4
|
16.4
|
1.0
|
OE1
|
O:GLN477
|
4.9
|
11.2
|
1.0
|
|
Iron binding site 4 out
of 6 in 3pcm
Go back to
Iron Binding Sites List in 3pcm
Iron binding site 4 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide
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 6- Hydroxynicotinic Acid N-Oxide and Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Fe600
b:21.8
occ:0.80
|
OH
|
P:TYR408
|
1.9
|
15.2
|
1.0
|
C
|
P:CYN575
|
2.1
|
17.4
|
1.0
|
O4
|
P:NNO550
|
2.2
|
18.7
|
0.9
|
NE2
|
P:HIS460
|
2.2
|
12.6
|
1.0
|
NE2
|
P:HIS462
|
2.2
|
12.7
|
1.0
|
O3
|
P:NNO550
|
2.3
|
16.3
|
0.9
|
C6
|
P:NNO550
|
2.8
|
19.2
|
0.9
|
N1
|
P:NNO550
|
2.8
|
18.1
|
0.9
|
CE1
|
P:HIS460
|
2.9
|
11.7
|
1.0
|
CZ
|
P:TYR408
|
2.9
|
16.6
|
1.0
|
CE1
|
P:HIS462
|
3.1
|
12.4
|
1.0
|
N
|
P:CYN575
|
3.2
|
18.2
|
1.0
|
CD2
|
P:HIS462
|
3.3
|
12.1
|
1.0
|
CD2
|
P:HIS460
|
3.4
|
12.2
|
1.0
|
CE2
|
P:TYR408
|
3.5
|
17.1
|
1.0
|
CE1
|
P:TYR408
|
4.0
|
16.6
|
1.0
|
C5
|
P:NNO550
|
4.1
|
19.4
|
0.9
|
C2
|
P:NNO550
|
4.1
|
19.1
|
0.9
|
ND1
|
P:HIS460
|
4.2
|
12.2
|
1.0
|
O
|
P:HOH630
|
4.2
|
11.4
|
0.8
|
ND1
|
P:HIS462
|
4.3
|
12.6
|
1.0
|
CG
|
P:HIS462
|
4.4
|
11.9
|
1.0
|
CG
|
P:HIS460
|
4.4
|
12.0
|
1.0
|
NH1
|
P:ARG457
|
4.5
|
11.4
|
1.0
|
O
|
P:HOH610
|
4.5
|
16.6
|
0.8
|
CD2
|
P:TYR408
|
4.8
|
17.5
|
1.0
|
OE1
|
P:GLN477
|
5.0
|
11.4
|
1.0
|
|
Iron binding site 5 out
of 6 in 3pcm
Go back to
Iron Binding Sites List in 3pcm
Iron binding site 5 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide
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 6- Hydroxynicotinic Acid N-Oxide and Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Fe600
b:21.5
occ:0.80
|
OH
|
Q:TYR408
|
1.9
|
16.1
|
1.0
|
C
|
Q:CYN575
|
2.1
|
17.5
|
1.0
|
O4
|
Q:NNO550
|
2.2
|
18.7
|
0.9
|
NE2
|
Q:HIS462
|
2.2
|
13.0
|
1.0
|
NE2
|
Q:HIS460
|
2.3
|
13.1
|
1.0
|
O3
|
Q:NNO550
|
2.6
|
16.6
|
0.9
|
C6
|
Q:NNO550
|
3.0
|
19.1
|
0.9
|
CZ
|
Q:TYR408
|
3.0
|
16.7
|
1.0
|
N1
|
Q:NNO550
|
3.1
|
18.2
|
0.9
|
CE1
|
Q:HIS462
|
3.1
|
12.1
|
1.0
|
CE1
|
Q:HIS460
|
3.2
|
12.0
|
1.0
|
CD2
|
Q:HIS462
|
3.2
|
12.7
|
1.0
|
N
|
Q:CYN575
|
3.3
|
18.1
|
1.0
|
CD2
|
Q:HIS460
|
3.4
|
12.3
|
1.0
|
CE1
|
Q:TYR408
|
3.7
|
17.1
|
1.0
|
CE2
|
Q:TYR408
|
3.8
|
16.9
|
1.0
|
O
|
Q:HOH987
|
4.2
|
11.9
|
1.0
|
C5
|
Q:NNO550
|
4.2
|
19.4
|
0.9
|
ND1
|
Q:HIS462
|
4.3
|
11.8
|
1.0
|
NH1
|
Q:ARG457
|
4.3
|
12.5
|
1.0
|
ND1
|
Q:HIS460
|
4.3
|
12.1
|
1.0
|
CG
|
Q:HIS462
|
4.3
|
12.1
|
1.0
|
C2
|
Q:NNO550
|
4.4
|
19.2
|
0.9
|
CG
|
Q:HIS460
|
4.5
|
12.0
|
1.0
|
O
|
E:HOH206
|
4.6
|
16.8
|
0.8
|
OE1
|
Q:GLN477
|
4.8
|
11.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 3pcm
Go back to
Iron Binding Sites List in 3pcm
Iron binding site 6 out
of 6 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 6- Hydroxynicotinic Acid N-Oxide and Cyanide
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 6- Hydroxynicotinic Acid N-Oxide and Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Fe600
b:22.6
occ:1.00
|
OH
|
R:TYR408
|
2.0
|
16.5
|
1.0
|
C
|
R:CYN575
|
2.1
|
17.3
|
1.0
|
O4
|
R:NNO550
|
2.2
|
18.7
|
0.9
|
NE2
|
R:HIS462
|
2.2
|
13.0
|
1.0
|
NE2
|
R:HIS460
|
2.3
|
12.8
|
1.0
|
O3
|
R:NNO550
|
2.4
|
16.5
|
0.9
|
C6
|
R:NNO550
|
2.9
|
19.0
|
0.9
|
N1
|
R:NNO550
|
2.9
|
18.1
|
0.9
|
CE1
|
R:HIS462
|
3.0
|
12.1
|
1.0
|
CZ
|
R:TYR408
|
3.1
|
16.9
|
1.0
|
CE1
|
R:HIS460
|
3.2
|
11.8
|
1.0
|
N
|
R:CYN575
|
3.2
|
17.9
|
1.0
|
CD2
|
R:HIS462
|
3.4
|
12.5
|
1.0
|
CD2
|
R:HIS460
|
3.4
|
12.3
|
1.0
|
CE2
|
R:TYR408
|
3.7
|
17.2
|
1.0
|
C5
|
R:NNO550
|
4.1
|
19.3
|
0.9
|
CE1
|
R:TYR408
|
4.1
|
17.5
|
1.0
|
C2
|
R:NNO550
|
4.2
|
19.0
|
0.9
|
ND1
|
R:HIS462
|
4.2
|
11.7
|
1.0
|
NH1
|
R:ARG457
|
4.3
|
11.9
|
1.0
|
ND1
|
R:HIS460
|
4.4
|
11.8
|
1.0
|
O
|
R:HOH1223
|
4.4
|
11.5
|
1.0
|
CG
|
R:HIS462
|
4.4
|
11.9
|
1.0
|
CG
|
R:HIS460
|
4.5
|
12.0
|
1.0
|
O
|
R:HOH1186
|
4.6
|
16.7
|
1.0
|
OE1
|
R:GLN477
|
4.9
|
10.7
|
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 17:55:26 2024
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