Chlorine 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:
Chlorine Binding Sites:
The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 2iga
Go back to
Chlorine Binding Sites List in 2iga
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl700
b:13.7
occ:0.40
|
O8
|
A:XXP600
|
1.0
|
40.5
|
0.6
|
C6
|
A:XXP600
|
2.2
|
44.7
|
0.6
|
N7
|
A:XXP600
|
2.2
|
41.2
|
0.6
|
C5
|
A:XXP600
|
2.7
|
41.4
|
0.6
|
NH1
|
A:ARG243
|
3.1
|
25.8
|
1.0
|
O10
|
A:XXP600
|
3.2
|
45.3
|
0.6
|
NH1
|
A:ARG293
|
3.3
|
25.7
|
1.0
|
O9
|
A:XXP600
|
3.3
|
40.4
|
0.6
|
CE1
|
A:HIS248
|
3.4
|
29.2
|
1.0
|
ND1
|
A:HIS248
|
3.5
|
29.4
|
1.0
|
NH2
|
A:ARG243
|
3.5
|
26.3
|
1.0
|
CB
|
A:ARG293
|
3.6
|
27.6
|
1.0
|
CG
|
A:ARG293
|
3.6
|
26.3
|
1.0
|
CD
|
A:ARG293
|
3.7
|
26.8
|
1.0
|
CZ
|
A:ARG243
|
3.7
|
30.2
|
1.0
|
O
|
A:ARG293
|
3.9
|
29.4
|
1.0
|
CA
|
A:ARG293
|
3.9
|
27.4
|
1.0
|
OH
|
A:TYR257
|
3.9
|
24.1
|
1.0
|
CH2
|
A:TRP304
|
4.0
|
31.7
|
1.0
|
CZ2
|
A:TRP304
|
4.1
|
29.4
|
1.0
|
C
|
A:ARG293
|
4.2
|
28.2
|
1.0
|
C4
|
A:XXP600
|
4.2
|
37.7
|
0.6
|
CZ
|
A:ARG293
|
4.3
|
28.3
|
1.0
|
NE
|
A:ARG293
|
4.5
|
27.1
|
1.0
|
NE2
|
A:HIS248
|
4.5
|
28.3
|
1.0
|
CZ3
|
A:TRP304
|
4.7
|
32.9
|
1.0
|
CG
|
A:HIS248
|
4.7
|
31.0
|
1.0
|
O12
|
A:XXP600
|
4.7
|
28.0
|
0.6
|
CE2
|
A:TRP304
|
4.8
|
26.1
|
1.0
|
C1
|
A:XXP600
|
4.9
|
26.4
|
0.6
|
CZ
|
A:TYR257
|
4.9
|
22.5
|
1.0
|
O13
|
A:XXP600
|
5.0
|
21.6
|
0.6
|
CE2
|
A:TYR257
|
5.0
|
25.1
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 2iga
Go back to
Chlorine Binding Sites List in 2iga
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl700
b:6.4
occ:0.25
|
O10
|
B:XX3600
|
0.6
|
39.8
|
0.8
|
N9
|
B:XX3600
|
2.0
|
43.7
|
0.8
|
O11
|
B:XX3600
|
2.8
|
45.2
|
0.8
|
C4
|
B:XX3600
|
3.1
|
41.4
|
0.8
|
NH1
|
B:ARG243
|
3.1
|
27.3
|
1.0
|
CE1
|
B:HIS248
|
3.2
|
27.9
|
1.0
|
ND1
|
B:HIS248
|
3.3
|
30.2
|
1.0
|
NH2
|
B:ARG243
|
3.3
|
30.0
|
1.0
|
CB
|
B:ARG293
|
3.4
|
25.7
|
1.0
|
C3
|
B:XX3600
|
3.4
|
38.9
|
0.8
|
NH1
|
B:ARG293
|
3.5
|
25.5
|
1.0
|
CG
|
B:ARG293
|
3.5
|
25.9
|
1.0
|
CD
|
B:ARG293
|
3.6
|
26.9
|
1.0
|
O
|
B:ARG293
|
3.6
|
27.8
|
1.0
|
CZ
|
B:ARG243
|
3.6
|
29.9
|
1.0
|
CA
|
B:ARG293
|
3.7
|
24.6
|
1.0
|
C
|
B:ARG293
|
3.9
|
25.3
|
1.0
|
OH
|
B:TYR257
|
4.0
|
23.7
|
1.0
|
C5
|
B:XX3600
|
4.3
|
40.7
|
0.8
|
NE2
|
B:HIS248
|
4.3
|
26.0
|
1.0
|
CZ
|
B:ARG293
|
4.4
|
25.7
|
1.0
|
NE
|
B:ARG293
|
4.4
|
27.7
|
1.0
|
CH2
|
B:TRP304
|
4.5
|
27.8
|
1.0
|
CZ2
|
B:TRP304
|
4.5
|
29.4
|
1.0
|
CG
|
B:HIS248
|
4.5
|
25.0
|
1.0
|
C2
|
B:XX3600
|
4.7
|
36.9
|
0.8
|
O8
|
B:XX3600
|
4.9
|
34.5
|
0.8
|
NE
|
B:ARG243
|
5.0
|
29.1
|
1.0
|
CE2
|
B:TYR257
|
5.0
|
25.1
|
1.0
|
CZ
|
B:TYR257
|
5.0
|
25.0
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 2iga
Go back to
Chlorine Binding Sites List in 2iga
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl700
b:11.7
occ:0.25
|
O10
|
C:XX2601
|
1.1
|
37.2
|
0.8
|
N9
|
C:XX2601
|
2.2
|
38.9
|
0.8
|
O11
|
C:XX2601
|
3.0
|
41.7
|
0.8
|
C4
|
C:XX2601
|
3.0
|
31.1
|
0.8
|
NH1
|
C:ARG243
|
3.1
|
34.4
|
1.0
|
CE1
|
C:HIS248
|
3.1
|
25.1
|
1.0
|
C3
|
C:XX2601
|
3.1
|
32.7
|
0.8
|
NH2
|
C:ARG243
|
3.2
|
33.2
|
1.0
|
ND1
|
C:HIS248
|
3.3
|
21.7
|
1.0
|
NH1
|
C:ARG293
|
3.4
|
31.3
|
1.0
|
CZ
|
C:ARG243
|
3.6
|
31.4
|
1.0
|
CB
|
C:ARG293
|
3.7
|
30.6
|
1.0
|
O
|
C:ARG293
|
3.7
|
29.4
|
1.0
|
CD
|
C:ARG293
|
3.7
|
31.4
|
1.0
|
CG
|
C:ARG293
|
3.9
|
31.0
|
1.0
|
CA
|
C:ARG293
|
3.9
|
30.8
|
1.0
|
OH
|
C:TYR257
|
3.9
|
28.1
|
1.0
|
C
|
C:ARG293
|
4.1
|
29.9
|
1.0
|
CH2
|
C:TRP304
|
4.2
|
33.9
|
1.0
|
NE2
|
C:HIS248
|
4.2
|
25.7
|
1.0
|
CZ2
|
C:TRP304
|
4.3
|
30.3
|
1.0
|
C5
|
C:XX2601
|
4.3
|
32.1
|
0.8
|
CZ
|
C:ARG293
|
4.4
|
29.2
|
1.0
|
C2
|
C:XX2601
|
4.4
|
27.8
|
0.8
|
NE
|
C:ARG293
|
4.5
|
29.4
|
1.0
|
CG
|
C:HIS248
|
4.5
|
26.6
|
1.0
|
CZ3
|
C:TRP304
|
4.8
|
33.4
|
1.0
|
O8
|
C:XX2601
|
4.8
|
19.6
|
0.8
|
CE2
|
C:TRP304
|
4.9
|
30.9
|
1.0
|
NE
|
C:ARG243
|
4.9
|
32.6
|
1.0
|
CZ
|
C:TYR257
|
4.9
|
28.0
|
1.0
|
CE2
|
C:TYR257
|
4.9
|
25.6
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 2iga
Go back to
Chlorine Binding Sites List in 2iga
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl700
b:6.9
occ:0.25
|
O10
|
D:XX3600
|
1.1
|
38.2
|
0.8
|
N9
|
D:XX3600
|
2.5
|
39.3
|
0.8
|
NH1
|
D:ARG243
|
3.0
|
29.1
|
1.0
|
NH2
|
D:ARG243
|
3.2
|
27.9
|
1.0
|
C4
|
D:XX3600
|
3.3
|
38.2
|
0.8
|
C3
|
D:XX3600
|
3.3
|
36.2
|
0.8
|
O11
|
D:XX3600
|
3.3
|
42.6
|
0.8
|
NH1
|
D:ARG293
|
3.4
|
26.0
|
1.0
|
CB
|
D:ARG293
|
3.4
|
25.0
|
1.0
|
CE1
|
D:HIS248
|
3.5
|
25.3
|
1.0
|
CZ
|
D:ARG243
|
3.5
|
28.0
|
1.0
|
ND1
|
D:HIS248
|
3.5
|
25.9
|
1.0
|
CG
|
D:ARG293
|
3.5
|
22.8
|
1.0
|
CD
|
D:ARG293
|
3.6
|
24.5
|
1.0
|
OH
|
D:TYR257
|
3.8
|
28.0
|
1.0
|
CA
|
D:ARG293
|
3.9
|
24.6
|
1.0
|
O
|
D:ARG293
|
3.9
|
26.1
|
1.0
|
CH2
|
D:TRP304
|
4.0
|
30.4
|
1.0
|
CZ2
|
D:TRP304
|
4.0
|
29.4
|
1.0
|
C
|
D:ARG293
|
4.2
|
25.8
|
1.0
|
CZ
|
D:ARG293
|
4.4
|
26.0
|
1.0
|
NE
|
D:ARG293
|
4.5
|
26.2
|
1.0
|
C2
|
D:XX3600
|
4.6
|
33.4
|
0.8
|
CZ3
|
D:TRP304
|
4.6
|
33.7
|
1.0
|
C5
|
D:XX3600
|
4.6
|
35.1
|
0.8
|
O8
|
D:XX3600
|
4.6
|
25.9
|
0.8
|
CE2
|
D:TRP304
|
4.6
|
26.9
|
1.0
|
NE2
|
D:HIS248
|
4.7
|
22.0
|
1.0
|
CZ
|
D:TYR257
|
4.8
|
29.2
|
1.0
|
CG
|
D:HIS248
|
4.8
|
25.5
|
1.0
|
NE
|
D:ARG243
|
4.8
|
26.9
|
1.0
|
CE2
|
D:TYR257
|
4.8
|
29.0
|
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 Jul 20 08:13:12 2024
|