Iron in PDB 2iga: Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.
Enzymatic activity of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.
All present enzymatic activity of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.:
1.13.11.15;
Protein crystallography data
The structure of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations., PDB code: 2iga
was solved by
E.G.Kovaleva,
J.D.Lipscomb,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
52.70 /
1.95
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.678,
153.022,
96.389,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
24.5
|
Other elements in 2iga:
The structure of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.
(pdb code 2iga). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations., PDB code: 2iga:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2iga
Go back to
Iron Binding Sites List in 2iga
Iron binding site 1 out
of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:31.8
occ:1.00
|
O13
|
A:XXP600
|
2.0
|
21.6
|
0.6
|
OE1
|
A:GLU267
|
2.1
|
28.2
|
1.0
|
NE2
|
A:HIS155
|
2.2
|
26.6
|
1.0
|
O
|
A:HOH1042
|
2.2
|
25.4
|
1.0
|
O11
|
A:XXP600
|
2.2
|
15.4
|
0.6
|
NE2
|
A:HIS214
|
2.3
|
22.2
|
1.0
|
C1
|
A:XXP600
|
2.3
|
26.4
|
0.6
|
C2
|
A:XXP600
|
2.6
|
26.1
|
0.6
|
CE1
|
A:HIS155
|
2.9
|
23.8
|
1.0
|
CD
|
A:GLU267
|
3.1
|
29.6
|
1.0
|
CD2
|
A:HIS214
|
3.2
|
25.2
|
1.0
|
CE1
|
A:HIS214
|
3.3
|
27.9
|
1.0
|
O12
|
A:XXP600
|
3.3
|
28.0
|
0.6
|
CD2
|
A:HIS155
|
3.3
|
27.5
|
1.0
|
OE2
|
A:GLU267
|
3.6
|
27.7
|
1.0
|
NE2
|
A:HIS200
|
3.8
|
31.4
|
1.0
|
O10
|
A:XXP600
|
3.8
|
45.3
|
0.6
|
C3
|
A:XXP600
|
4.1
|
27.2
|
0.6
|
ND1
|
A:HIS155
|
4.1
|
26.2
|
1.0
|
OH
|
A:TYR257
|
4.2
|
24.1
|
1.0
|
CG
|
A:HIS155
|
4.3
|
31.1
|
1.0
|
ND1
|
A:HIS214
|
4.4
|
24.2
|
1.0
|
CG
|
A:HIS214
|
4.4
|
27.3
|
1.0
|
CG
|
A:GLU267
|
4.4
|
25.8
|
1.0
|
CE1
|
A:HIS200
|
4.4
|
32.0
|
1.0
|
ND2
|
A:ASN157
|
4.5
|
28.9
|
1.0
|
CB
|
A:ALA216
|
4.6
|
26.4
|
1.0
|
CB
|
A:GLU267
|
4.6
|
26.2
|
1.0
|
CE1
|
A:TYR257
|
4.7
|
21.1
|
1.0
|
CB
|
A:ASN157
|
4.7
|
27.8
|
1.0
|
C6
|
A:XXP600
|
4.9
|
44.7
|
0.6
|
CD1
|
A:TYR269
|
4.9
|
26.6
|
1.0
|
CZ
|
A:TYR257
|
5.0
|
22.5
|
1.0
|
CD2
|
A:HIS200
|
5.0
|
31.8
|
1.0
|
CE1
|
A:TYR269
|
5.0
|
28.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 2iga
Go back to
Iron Binding Sites List in 2iga
Iron binding site 2 out
of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:29.0
occ:1.00
|
OE1
|
B:GLU267
|
2.0
|
22.2
|
1.0
|
O7
|
B:XX3600
|
2.2
|
28.4
|
0.8
|
O13
|
B:XX3600
|
2.2
|
28.1
|
0.8
|
NE2
|
B:HIS155
|
2.2
|
22.2
|
1.0
|
O8
|
B:XX3600
|
2.3
|
34.5
|
0.8
|
NE2
|
B:HIS214
|
2.3
|
22.1
|
1.0
|
C2
|
B:XX3600
|
2.7
|
36.9
|
0.8
|
C1
|
B:XX3600
|
2.7
|
37.2
|
0.8
|
O12
|
B:XX3600
|
2.8
|
39.6
|
0.8
|
CD
|
B:GLU267
|
3.1
|
24.5
|
1.0
|
CE1
|
B:HIS214
|
3.1
|
24.6
|
1.0
|
CD2
|
B:HIS155
|
3.2
|
21.1
|
1.0
|
CE1
|
B:HIS155
|
3.2
|
26.4
|
1.0
|
CD2
|
B:HIS214
|
3.3
|
26.0
|
1.0
|
OE2
|
B:GLU267
|
3.5
|
26.1
|
1.0
|
NE2
|
B:HIS200
|
3.8
|
35.1
|
1.0
|
C3
|
B:XX3600
|
4.0
|
38.9
|
0.8
|
C6
|
B:XX3600
|
4.1
|
33.4
|
0.8
|
OH
|
B:TYR257
|
4.2
|
23.7
|
1.0
|
ND1
|
B:HIS214
|
4.3
|
21.6
|
1.0
|
ND1
|
B:HIS155
|
4.3
|
22.0
|
1.0
|
ND2
|
B:ASN157
|
4.3
|
21.3
|
1.0
|
CG
|
B:HIS155
|
4.3
|
22.2
|
1.0
|
CG
|
B:GLU267
|
4.4
|
19.1
|
1.0
|
CG
|
B:HIS214
|
4.4
|
24.2
|
1.0
|
CE1
|
B:HIS200
|
4.5
|
33.1
|
1.0
|
CB
|
B:GLU267
|
4.6
|
26.8
|
1.0
|
CE1
|
B:TYR257
|
4.6
|
21.6
|
1.0
|
CB
|
B:ALA216
|
4.7
|
25.9
|
1.0
|
CB
|
B:ASN157
|
4.7
|
26.1
|
1.0
|
CD2
|
B:HIS200
|
4.9
|
31.4
|
1.0
|
CZ
|
B:TYR257
|
4.9
|
25.0
|
1.0
|
C4
|
B:XX3600
|
5.0
|
41.4
|
0.8
|
|
Iron binding site 3 out
of 4 in 2iga
Go back to
Iron Binding Sites List in 2iga
Iron binding site 3 out
of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:32.8
occ:1.00
|
OE1
|
C:GLU267
|
2.1
|
23.9
|
1.0
|
O7
|
C:XX2601
|
2.2
|
30.3
|
0.8
|
NE2
|
C:HIS155
|
2.2
|
25.1
|
1.0
|
O8
|
C:XX2601
|
2.2
|
19.6
|
0.8
|
NE2
|
C:HIS214
|
2.3
|
24.7
|
1.0
|
O1
|
C:OXY600
|
2.4
|
39.7
|
1.0
|
O2
|
C:OXY600
|
2.5
|
35.9
|
1.0
|
C2
|
C:XX2601
|
2.8
|
27.8
|
0.8
|
C1
|
C:XX2601
|
2.9
|
30.3
|
0.8
|
CE1
|
C:HIS214
|
3.1
|
24.0
|
1.0
|
CE1
|
C:HIS155
|
3.1
|
29.6
|
1.0
|
CD
|
C:GLU267
|
3.2
|
27.0
|
1.0
|
CD2
|
C:HIS155
|
3.3
|
27.5
|
1.0
|
CD2
|
C:HIS214
|
3.4
|
26.8
|
1.0
|
OE2
|
C:GLU267
|
3.7
|
29.0
|
1.0
|
NE2
|
C:HIS200
|
3.7
|
39.7
|
1.0
|
OH
|
C:TYR257
|
4.2
|
28.1
|
1.0
|
C6
|
C:XX2601
|
4.2
|
27.0
|
0.8
|
ND1
|
C:HIS214
|
4.2
|
23.5
|
1.0
|
ND1
|
C:HIS155
|
4.2
|
25.2
|
1.0
|
C3
|
C:XX2601
|
4.3
|
32.7
|
0.8
|
CG
|
C:HIS155
|
4.4
|
27.6
|
1.0
|
CE1
|
C:HIS200
|
4.4
|
38.0
|
1.0
|
CG
|
C:HIS214
|
4.4
|
27.8
|
1.0
|
CG
|
C:GLU267
|
4.4
|
27.3
|
1.0
|
ND2
|
C:ASN157
|
4.5
|
30.1
|
1.0
|
CB
|
C:GLU267
|
4.5
|
25.6
|
1.0
|
CB
|
C:ALA216
|
4.6
|
28.9
|
1.0
|
CB
|
C:ASN157
|
4.7
|
29.7
|
1.0
|
CE1
|
C:TYR257
|
4.7
|
24.6
|
1.0
|
CD1
|
C:TYR269
|
4.8
|
31.6
|
1.0
|
CD2
|
C:HIS200
|
4.9
|
37.6
|
1.0
|
CE1
|
C:TYR269
|
4.9
|
31.6
|
1.0
|
CZ
|
C:TYR257
|
4.9
|
28.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 2iga
Go back to
Iron Binding Sites List in 2iga
Iron binding site 4 out
of 4 in the Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Homoprotocatechuate 2,3-Dioxygenase From B. Fuscum in Complex with Reactive Intermediates Formed Via in Crystallo Reaction with 4-Nitrocatechol at Low Oxygen Concentrations. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe500
b:32.0
occ:1.00
|
OE1
|
D:GLU267
|
2.0
|
27.5
|
1.0
|
O13
|
D:XX3600
|
2.1
|
20.5
|
0.8
|
NE2
|
D:HIS214
|
2.2
|
23.0
|
1.0
|
NE2
|
D:HIS155
|
2.2
|
24.8
|
1.0
|
O7
|
D:XX3600
|
2.2
|
36.5
|
0.8
|
O8
|
D:XX3600
|
2.3
|
25.9
|
0.8
|
C2
|
D:XX3600
|
2.7
|
33.4
|
0.8
|
O12
|
D:XX3600
|
2.8
|
34.1
|
0.8
|
C1
|
D:XX3600
|
2.8
|
36.0
|
0.8
|
CE1
|
D:HIS155
|
3.0
|
21.1
|
1.0
|
CE1
|
D:HIS214
|
3.1
|
22.1
|
1.0
|
CD
|
D:GLU267
|
3.1
|
27.7
|
1.0
|
CD2
|
D:HIS214
|
3.3
|
23.6
|
1.0
|
CD2
|
D:HIS155
|
3.4
|
25.7
|
1.0
|
OE2
|
D:GLU267
|
3.6
|
32.2
|
1.0
|
NE2
|
D:HIS200
|
3.9
|
36.0
|
1.0
|
ND1
|
D:HIS155
|
4.1
|
24.4
|
1.0
|
C3
|
D:XX3600
|
4.2
|
36.2
|
0.8
|
C6
|
D:XX3600
|
4.2
|
30.5
|
0.8
|
OH
|
D:TYR257
|
4.2
|
28.0
|
1.0
|
ND1
|
D:HIS214
|
4.2
|
25.6
|
1.0
|
CG
|
D:GLU267
|
4.3
|
26.2
|
1.0
|
CG
|
D:HIS214
|
4.4
|
23.2
|
1.0
|
CG
|
D:HIS155
|
4.4
|
25.3
|
1.0
|
ND2
|
D:ASN157
|
4.4
|
28.4
|
1.0
|
CB
|
D:GLU267
|
4.6
|
26.7
|
1.0
|
CE1
|
D:TYR257
|
4.6
|
27.8
|
1.0
|
CE1
|
D:HIS200
|
4.6
|
34.7
|
1.0
|
CB
|
D:ASN157
|
4.6
|
27.7
|
1.0
|
CB
|
D:ALA216
|
4.7
|
25.6
|
1.0
|
CZ
|
D:TYR257
|
4.9
|
29.2
|
1.0
|
CD1
|
D:TYR269
|
4.9
|
31.6
|
1.0
|
|
Reference:
E.G.Kovaleva,
J.D.Lipscomb.
Crystal Structures of FE2+ Dioxygenase Superoxo, Alkylperoxo, and Bound Product Intermediates Science V. 316 453 2007.
ISSN: ISSN 0036-8075
PubMed: 17446402
DOI: 10.1126/SCIENCE.1134697
Page generated: Sat Aug 3 23:20:28 2024
|