Iron in PDB 1ndo: Napthalene 1,2-Dioxygenase
Enzymatic activity of Napthalene 1,2-Dioxygenase
All present enzymatic activity of Napthalene 1,2-Dioxygenase:
1.14.12.12;
Protein crystallography data
The structure of Napthalene 1,2-Dioxygenase, PDB code: 1ndo
was solved by
S.Ramaswamy,
B.Kauppi,
E.Carredano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.25
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.000,
174.000,
282.500,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19 /
24
|
Iron Binding Sites:
The binding sites of Iron atom in the Napthalene 1,2-Dioxygenase
(pdb code 1ndo). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the
Napthalene 1,2-Dioxygenase, PDB code: 1ndo:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Iron binding site 1 out
of 9 in 1ndo
Go back to
Iron Binding Sites List in 1ndo
Iron binding site 1 out
of 9 in the Napthalene 1,2-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe452
b:36.3
occ:1.00
|
NE2
|
A:HIS208
|
2.0
|
26.9
|
1.0
|
NE2
|
A:HIS213
|
2.1
|
32.1
|
1.0
|
OD2
|
A:ASP362
|
2.3
|
35.3
|
1.0
|
OD1
|
A:ASP362
|
2.7
|
42.9
|
1.0
|
CG
|
A:ASP362
|
2.8
|
35.8
|
1.0
|
CD2
|
A:HIS208
|
3.0
|
29.6
|
1.0
|
CD2
|
A:HIS213
|
3.0
|
26.5
|
1.0
|
CE1
|
A:HIS208
|
3.0
|
32.0
|
1.0
|
CE1
|
A:HIS213
|
3.2
|
28.8
|
1.0
|
OD1
|
A:ASN201
|
3.8
|
43.2
|
1.0
|
ND1
|
A:HIS208
|
4.1
|
33.7
|
1.0
|
CG
|
A:HIS208
|
4.2
|
27.9
|
1.0
|
CG
|
A:HIS213
|
4.2
|
30.2
|
1.0
|
ND1
|
A:HIS213
|
4.2
|
30.1
|
1.0
|
ND2
|
A:ASN201
|
4.3
|
29.6
|
1.0
|
CB
|
A:ASP362
|
4.3
|
28.3
|
1.0
|
CG
|
A:ASN201
|
4.5
|
37.7
|
1.0
|
CG2
|
A:THR212
|
4.5
|
30.0
|
1.0
|
O
|
A:HOH712
|
4.6
|
49.2
|
1.0
|
|
Iron binding site 2 out
of 9 in 1ndo
Go back to
Iron Binding Sites List in 1ndo
Iron binding site 2 out
of 9 in the Napthalene 1,2-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe451
b:28.2
occ:1.00
|
FE1
|
A:FES451
|
0.0
|
28.2
|
1.0
|
ND1
|
A:HIS104
|
2.0
|
34.7
|
1.0
|
S1
|
A:FES451
|
2.2
|
28.9
|
1.0
|
ND1
|
A:HIS83
|
2.2
|
24.1
|
1.0
|
S2
|
A:FES451
|
2.3
|
26.1
|
1.0
|
FE2
|
A:FES451
|
2.8
|
25.2
|
1.0
|
CE1
|
A:HIS104
|
2.9
|
32.2
|
1.0
|
CG
|
A:HIS104
|
3.1
|
29.6
|
1.0
|
CG
|
A:HIS83
|
3.2
|
27.1
|
1.0
|
CE1
|
A:HIS83
|
3.2
|
24.8
|
1.0
|
CB
|
A:HIS83
|
3.4
|
24.7
|
1.0
|
CB
|
A:HIS104
|
3.5
|
25.4
|
1.0
|
N
|
A:HIS104
|
3.8
|
32.0
|
1.0
|
NE2
|
A:HIS104
|
4.0
|
32.8
|
1.0
|
CB
|
A:TYR103
|
4.1
|
29.7
|
1.0
|
CD2
|
A:HIS104
|
4.1
|
31.1
|
1.0
|
N
|
A:ARG84
|
4.1
|
23.9
|
1.0
|
CA
|
A:HIS104
|
4.2
|
33.8
|
1.0
|
SG
|
A:CYS81
|
4.3
|
22.9
|
1.0
|
NE2
|
A:HIS83
|
4.3
|
26.8
|
1.0
|
CG
|
A:TYR103
|
4.3
|
30.6
|
1.0
|
CD2
|
A:HIS83
|
4.4
|
27.9
|
1.0
|
CD2
|
A:TYR103
|
4.4
|
32.1
|
1.0
|
CG
|
A:ARG84
|
4.5
|
33.8
|
1.0
|
CB
|
A:ARG84
|
4.5
|
31.2
|
1.0
|
SG
|
A:CYS101
|
4.5
|
25.2
|
1.0
|
C
|
A:TYR103
|
4.6
|
32.7
|
1.0
|
CA
|
A:HIS83
|
4.7
|
27.5
|
1.0
|
C
|
A:HIS83
|
4.9
|
26.8
|
1.0
|
CA
|
A:TYR103
|
4.9
|
30.2
|
1.0
|
CA
|
A:ARG84
|
4.9
|
25.5
|
1.0
|
CD1
|
A:TRP106
|
5.0
|
28.4
|
1.0
|
|
Iron binding site 3 out
of 9 in 1ndo
Go back to
Iron Binding Sites List in 1ndo
Iron binding site 3 out
of 9 in the Napthalene 1,2-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe451
b:25.2
occ:1.00
|
FE2
|
A:FES451
|
0.0
|
25.2
|
1.0
|
SG
|
A:CYS81
|
2.2
|
22.9
|
1.0
|
S2
|
A:FES451
|
2.2
|
26.1
|
1.0
|
SG
|
A:CYS101
|
2.3
|
25.2
|
1.0
|
S1
|
A:FES451
|
2.3
|
28.9
|
1.0
|
FE1
|
A:FES451
|
2.8
|
28.2
|
1.0
|
CB
|
A:CYS81
|
3.0
|
22.8
|
1.0
|
CB
|
A:CYS101
|
3.1
|
23.7
|
1.0
|
CB
|
A:HIS83
|
4.1
|
24.7
|
1.0
|
CB
|
A:TYR103
|
4.3
|
29.7
|
1.0
|
CA
|
A:CYS81
|
4.5
|
24.8
|
1.0
|
ND1
|
A:HIS104
|
4.5
|
34.7
|
1.0
|
CB
|
A:LYS86
|
4.5
|
24.0
|
1.0
|
ND1
|
A:HIS83
|
4.5
|
24.1
|
1.0
|
CA
|
A:CYS101
|
4.5
|
26.6
|
1.0
|
N
|
A:HIS104
|
4.7
|
32.0
|
1.0
|
N
|
A:ARG84
|
4.7
|
23.9
|
1.0
|
CG
|
A:HIS83
|
4.8
|
27.1
|
1.0
|
N
|
A:HIS83
|
4.9
|
27.9
|
1.0
|
N
|
A:TYR103
|
4.9
|
28.7
|
1.0
|
N
|
A:LYS86
|
5.0
|
23.5
|
1.0
|
C
|
A:CYS81
|
5.0
|
25.6
|
1.0
|
CB
|
A:TRP106
|
5.0
|
27.4
|
1.0
|
|
Iron binding site 4 out
of 9 in 1ndo
Go back to
Iron Binding Sites List in 1ndo
Iron binding site 4 out
of 9 in the Napthalene 1,2-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe452
b:35.1
occ:1.00
|
NE2
|
C:HIS208
|
2.1
|
27.0
|
1.0
|
OD2
|
C:ASP362
|
2.2
|
35.1
|
1.0
|
NE2
|
C:HIS213
|
2.2
|
31.8
|
1.0
|
OD1
|
C:ASP362
|
2.6
|
42.6
|
1.0
|
CG
|
C:ASP362
|
2.7
|
35.6
|
1.0
|
CD2
|
C:HIS208
|
3.0
|
29.8
|
1.0
|
CD2
|
C:HIS213
|
3.1
|
26.8
|
1.0
|
CE1
|
C:HIS208
|
3.1
|
32.5
|
1.0
|
CE1
|
C:HIS213
|
3.2
|
29.1
|
1.0
|
OD1
|
C:ASN201
|
3.7
|
43.0
|
1.0
|
CG
|
C:HIS208
|
4.2
|
28.8
|
1.0
|
CB
|
C:ASP362
|
4.2
|
28.5
|
1.0
|
ND1
|
C:HIS208
|
4.2
|
33.7
|
1.0
|
CG
|
C:HIS213
|
4.3
|
31.0
|
1.0
|
ND2
|
C:ASN201
|
4.3
|
30.1
|
1.0
|
ND1
|
C:HIS213
|
4.3
|
30.7
|
1.0
|
CG
|
C:ASN201
|
4.4
|
37.8
|
1.0
|
CG2
|
C:THR212
|
4.4
|
29.9
|
1.0
|
|
Iron binding site 5 out
of 9 in 1ndo
Go back to
Iron Binding Sites List in 1ndo
Iron binding site 5 out
of 9 in the Napthalene 1,2-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe451
b:24.5
occ:1.00
|
FE1
|
C:FES451
|
0.0
|
24.5
|
1.0
|
ND1
|
C:HIS104
|
2.0
|
34.4
|
1.0
|
ND1
|
C:HIS83
|
2.2
|
23.6
|
1.0
|
S1
|
C:FES451
|
2.2
|
26.6
|
1.0
|
S2
|
C:FES451
|
2.4
|
24.0
|
1.0
|
FE2
|
C:FES451
|
2.7
|
22.6
|
1.0
|
CE1
|
C:HIS104
|
2.9
|
31.9
|
1.0
|
CG
|
C:HIS104
|
3.0
|
28.9
|
1.0
|
CG
|
C:HIS83
|
3.1
|
27.2
|
1.0
|
CE1
|
C:HIS83
|
3.2
|
24.8
|
1.0
|
CB
|
C:HIS104
|
3.4
|
24.8
|
1.0
|
CB
|
C:HIS83
|
3.4
|
24.8
|
1.0
|
N
|
C:HIS104
|
3.7
|
31.1
|
1.0
|
NE2
|
C:HIS104
|
4.0
|
32.9
|
1.0
|
CD2
|
C:HIS104
|
4.1
|
30.4
|
1.0
|
CA
|
C:HIS104
|
4.1
|
33.5
|
1.0
|
CB
|
C:TYR103
|
4.1
|
29.4
|
1.0
|
N
|
C:ARG84
|
4.2
|
23.2
|
1.0
|
CD2
|
C:HIS83
|
4.3
|
27.8
|
1.0
|
NE2
|
C:HIS83
|
4.3
|
25.8
|
1.0
|
SG
|
C:CYS81
|
4.3
|
22.6
|
1.0
|
CG
|
C:TYR103
|
4.4
|
30.2
|
1.0
|
SG
|
C:CYS101
|
4.5
|
23.0
|
1.0
|
CG
|
C:ARG84
|
4.5
|
33.4
|
1.0
|
CD2
|
C:TYR103
|
4.5
|
31.8
|
1.0
|
C
|
C:TYR103
|
4.6
|
32.5
|
1.0
|
CB
|
C:ARG84
|
4.7
|
31.5
|
1.0
|
CA
|
C:HIS83
|
4.7
|
27.8
|
1.0
|
C
|
C:HIS83
|
4.9
|
26.6
|
1.0
|
CD1
|
C:TRP106
|
4.9
|
28.3
|
1.0
|
C
|
C:HIS104
|
4.9
|
34.1
|
1.0
|
CA
|
C:TYR103
|
4.9
|
29.9
|
1.0
|
CA
|
C:ARG84
|
5.0
|
25.4
|
1.0
|
|
Iron binding site 6 out
of 9 in 1ndo
Go back to
Iron Binding Sites List in 1ndo
Iron binding site 6 out
of 9 in the Napthalene 1,2-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe451
b:22.6
occ:1.00
|
FE2
|
C:FES451
|
0.0
|
22.6
|
1.0
|
S2
|
C:FES451
|
2.2
|
24.0
|
1.0
|
SG
|
C:CYS101
|
2.2
|
23.0
|
1.0
|
S1
|
C:FES451
|
2.3
|
26.6
|
1.0
|
SG
|
C:CYS81
|
2.3
|
22.6
|
1.0
|
FE1
|
C:FES451
|
2.7
|
24.5
|
1.0
|
CB
|
C:CYS101
|
3.1
|
23.1
|
1.0
|
CB
|
C:CYS81
|
3.2
|
22.3
|
1.0
|
CB
|
C:HIS83
|
4.1
|
24.8
|
1.0
|
CB
|
C:TYR103
|
4.2
|
29.4
|
1.0
|
ND1
|
C:HIS104
|
4.4
|
34.4
|
1.0
|
N
|
C:HIS104
|
4.4
|
31.1
|
1.0
|
ND1
|
C:HIS83
|
4.4
|
23.6
|
1.0
|
CA
|
C:CYS101
|
4.5
|
27.0
|
1.0
|
CB
|
C:LYS86
|
4.6
|
23.8
|
1.0
|
CA
|
C:CYS81
|
4.6
|
24.6
|
1.0
|
N
|
C:ARG84
|
4.7
|
23.2
|
1.0
|
CG
|
C:HIS83
|
4.8
|
27.2
|
1.0
|
CB
|
C:TRP106
|
4.8
|
27.7
|
1.0
|
N
|
C:TYR103
|
4.9
|
28.2
|
1.0
|
C
|
C:CYS101
|
5.0
|
27.5
|
1.0
|
N
|
C:HIS83
|
5.0
|
27.4
|
1.0
|
CA
|
C:TYR103
|
5.0
|
29.9
|
1.0
|
|
Iron binding site 7 out
of 9 in 1ndo
Go back to
Iron Binding Sites List in 1ndo
Iron binding site 7 out
of 9 in the Napthalene 1,2-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe452
b:36.7
occ:1.00
|
NE2
|
E:HIS213
|
2.0
|
32.0
|
1.0
|
NE2
|
E:HIS208
|
2.1
|
27.1
|
1.0
|
OD2
|
E:ASP362
|
2.2
|
35.3
|
1.0
|
OD1
|
E:ASP362
|
2.6
|
42.7
|
1.0
|
CG
|
E:ASP362
|
2.7
|
35.9
|
1.0
|
CD2
|
E:HIS213
|
2.9
|
26.6
|
1.0
|
CE1
|
E:HIS213
|
3.0
|
29.4
|
1.0
|
CD2
|
E:HIS208
|
3.1
|
29.7
|
1.0
|
CE1
|
E:HIS208
|
3.2
|
32.4
|
1.0
|
OD1
|
E:ASN201
|
4.0
|
43.6
|
1.0
|
O
|
E:HOH563
|
4.0
|
47.9
|
1.0
|
CG
|
E:HIS213
|
4.1
|
30.9
|
1.0
|
ND1
|
E:HIS213
|
4.1
|
30.4
|
1.0
|
CB
|
E:ASP362
|
4.2
|
28.8
|
1.0
|
CG
|
E:HIS208
|
4.2
|
28.6
|
1.0
|
ND1
|
E:HIS208
|
4.3
|
34.0
|
1.0
|
ND2
|
E:ASN201
|
4.4
|
30.4
|
1.0
|
CG2
|
E:THR212
|
4.5
|
29.9
|
1.0
|
CG
|
E:ASN201
|
4.7
|
37.6
|
1.0
|
|
Iron binding site 8 out
of 9 in 1ndo
Go back to
Iron Binding Sites List in 1ndo
Iron binding site 8 out
of 9 in the Napthalene 1,2-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe451
b:27.8
occ:1.00
|
FE1
|
E:FES451
|
0.0
|
27.8
|
1.0
|
ND1
|
E:HIS104
|
2.0
|
34.6
|
1.0
|
ND1
|
E:HIS83
|
2.1
|
23.8
|
1.0
|
S1
|
E:FES451
|
2.2
|
28.8
|
1.0
|
S2
|
E:FES451
|
2.3
|
26.1
|
1.0
|
FE2
|
E:FES451
|
2.8
|
25.6
|
1.0
|
CE1
|
E:HIS104
|
2.9
|
32.1
|
1.0
|
CG
|
E:HIS104
|
3.1
|
29.3
|
1.0
|
CE1
|
E:HIS83
|
3.1
|
25.1
|
1.0
|
CG
|
E:HIS83
|
3.1
|
27.2
|
1.0
|
CB
|
E:HIS83
|
3.4
|
24.5
|
1.0
|
CB
|
E:HIS104
|
3.5
|
25.6
|
1.0
|
N
|
E:HIS104
|
3.8
|
31.4
|
1.0
|
NE2
|
E:HIS104
|
4.0
|
33.0
|
1.0
|
N
|
E:ARG84
|
4.1
|
23.6
|
1.0
|
CB
|
E:TYR103
|
4.1
|
29.4
|
1.0
|
CD2
|
E:HIS104
|
4.1
|
30.9
|
1.0
|
NE2
|
E:HIS83
|
4.2
|
26.1
|
1.0
|
CA
|
E:HIS104
|
4.2
|
33.6
|
1.0
|
CD2
|
E:HIS83
|
4.2
|
27.4
|
1.0
|
SG
|
E:CYS81
|
4.4
|
23.9
|
1.0
|
CG
|
E:TYR103
|
4.4
|
30.4
|
1.0
|
CD2
|
E:TYR103
|
4.4
|
31.9
|
1.0
|
CG
|
E:ARG84
|
4.4
|
34.1
|
1.0
|
SG
|
E:CYS101
|
4.5
|
25.4
|
1.0
|
CB
|
E:ARG84
|
4.6
|
31.7
|
1.0
|
CA
|
E:HIS83
|
4.7
|
27.5
|
1.0
|
C
|
E:TYR103
|
4.7
|
32.5
|
1.0
|
C
|
E:HIS83
|
4.8
|
27.1
|
1.0
|
CA
|
E:ARG84
|
4.9
|
25.3
|
1.0
|
CD1
|
E:TRP106
|
4.9
|
28.3
|
1.0
|
CA
|
E:TYR103
|
4.9
|
30.0
|
1.0
|
|
Iron binding site 9 out
of 9 in 1ndo
Go back to
Iron Binding Sites List in 1ndo
Iron binding site 9 out
of 9 in the Napthalene 1,2-Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Napthalene 1,2-Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe451
b:25.6
occ:1.00
|
FE2
|
E:FES451
|
0.0
|
25.6
|
1.0
|
SG
|
E:CYS101
|
2.3
|
25.4
|
1.0
|
S2
|
E:FES451
|
2.3
|
26.1
|
1.0
|
SG
|
E:CYS81
|
2.3
|
23.9
|
1.0
|
S1
|
E:FES451
|
2.4
|
28.8
|
1.0
|
FE1
|
E:FES451
|
2.8
|
27.8
|
1.0
|
CB
|
E:CYS81
|
3.1
|
22.5
|
1.0
|
CB
|
E:CYS101
|
3.1
|
23.6
|
1.0
|
CB
|
E:HIS83
|
4.2
|
24.5
|
1.0
|
CB
|
E:TYR103
|
4.2
|
29.4
|
1.0
|
ND1
|
E:HIS83
|
4.4
|
23.8
|
1.0
|
CB
|
E:LYS86
|
4.4
|
23.6
|
1.0
|
ND1
|
E:HIS104
|
4.5
|
34.6
|
1.0
|
CA
|
E:CYS101
|
4.5
|
26.6
|
1.0
|
CA
|
E:CYS81
|
4.5
|
24.4
|
1.0
|
N
|
E:HIS104
|
4.6
|
31.4
|
1.0
|
N
|
E:ARG84
|
4.6
|
23.6
|
1.0
|
CG
|
E:HIS83
|
4.8
|
27.2
|
1.0
|
CB
|
E:TRP106
|
4.9
|
27.2
|
1.0
|
N
|
E:TYR103
|
4.9
|
28.8
|
1.0
|
N
|
E:HIS83
|
5.0
|
27.9
|
1.0
|
C
|
E:CYS101
|
5.0
|
28.0
|
1.0
|
|
Reference:
B.Kauppi,
K.Lee,
E.Carredano,
R.E.Parales,
D.T.Gibson,
H.Eklund,
S.Ramaswamy.
Structure of An Aromatic-Ring-Hydroxylating Dioxygenase-Naphthalene 1,2-Dioxygenase. Structure V. 6 571 1998.
ISSN: ISSN 0969-2126
PubMed: 9634695
DOI: 10.1016/S0969-2126(98)00059-8
Page generated: Sat Aug 3 11:30:08 2024
|