Chlorine in PDB 2xsh: Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl
Enzymatic activity of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl
All present enzymatic activity of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl:
1.14.12.18;
Protein crystallography data
The structure of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl, PDB code: 2xsh
was solved by
P.Kumar,
J.T.Bolin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
138.68 /
2.29
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.728,
276.762,
92.317,
90.00,
117.37,
90.00
|
R / Rfree (%)
|
18.571 /
24.456
|
Other elements in 2xsh:
The structure of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl
(pdb code 2xsh). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl, PDB code: 2xsh:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 2xsh
Go back to
Chlorine Binding Sites List in 2xsh
Chlorine binding site 1 out
of 6 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl902
b:61.2
occ:1.00
|
CL6
|
A:DC5902
|
0.0
|
61.2
|
1.0
|
CB6
|
A:DC5902
|
1.7
|
59.8
|
1.0
|
CB5
|
A:DC5902
|
2.7
|
60.2
|
1.0
|
CB1
|
A:DC5902
|
2.7
|
58.8
|
1.0
|
CA1
|
A:DC5902
|
3.0
|
57.4
|
1.0
|
CA2
|
A:DC5902
|
3.2
|
55.1
|
1.0
|
C
|
A:GLN322
|
3.2
|
39.2
|
1.0
|
O
|
A:GLN322
|
3.3
|
38.4
|
1.0
|
CE
|
A:MET231
|
3.5
|
33.4
|
1.0
|
N
|
A:HIS323
|
3.5
|
38.3
|
1.0
|
N
|
A:GLN322
|
3.6
|
41.6
|
1.0
|
SD
|
A:MET231
|
3.6
|
35.2
|
1.0
|
CB
|
A:HIS323
|
3.6
|
37.4
|
1.0
|
CA
|
A:GLN322
|
3.7
|
40.4
|
1.0
|
CD2
|
A:HIS323
|
3.9
|
40.3
|
1.0
|
CA6
|
A:DC5902
|
3.9
|
56.2
|
1.0
|
CB2
|
A:DC5902
|
4.0
|
59.9
|
1.0
|
CB4
|
A:DC5902
|
4.0
|
59.9
|
1.0
|
CA
|
A:HIS323
|
4.0
|
37.5
|
1.0
|
C
|
A:GLY321
|
4.0
|
42.9
|
1.0
|
CG
|
A:HIS323
|
4.1
|
39.0
|
1.0
|
CA3
|
A:DC5902
|
4.2
|
54.5
|
1.0
|
O
|
A:GLY321
|
4.3
|
43.9
|
1.0
|
CD2
|
A:LEU333
|
4.4
|
38.1
|
1.0
|
CB3
|
A:DC5902
|
4.5
|
60.5
|
1.0
|
CA
|
A:GLY321
|
4.8
|
43.4
|
1.0
|
CA5
|
A:DC5902
|
4.8
|
55.1
|
1.0
|
O
|
A:GLY275
|
4.8
|
38.4
|
1.0
|
CA4
|
A:DC5902
|
4.9
|
55.2
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 2xsh
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Chlorine Binding Sites List in 2xsh
Chlorine binding site 2 out
of 6 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl902
b:61.5
occ:1.00
|
CL1
|
A:DC5902
|
0.0
|
61.5
|
1.0
|
CB2
|
A:DC5902
|
1.7
|
59.9
|
1.0
|
CB1
|
A:DC5902
|
2.7
|
58.8
|
1.0
|
CB3
|
A:DC5902
|
2.7
|
60.5
|
1.0
|
CA1
|
A:DC5902
|
3.0
|
57.4
|
1.0
|
CA6
|
A:DC5902
|
3.2
|
56.2
|
1.0
|
O
|
A:HOH2109
|
3.5
|
47.1
|
1.0
|
CD2
|
A:HIS239
|
3.5
|
33.4
|
1.0
|
CD2
|
A:PHE384
|
3.5
|
35.3
|
1.0
|
CB
|
A:ALA234
|
3.7
|
35.5
|
1.0
|
CE2
|
A:PHE384
|
3.8
|
34.7
|
1.0
|
NE2
|
A:HIS239
|
3.9
|
33.1
|
1.0
|
CA2
|
A:DC5902
|
3.9
|
55.1
|
1.0
|
CB6
|
A:DC5902
|
4.0
|
59.8
|
1.0
|
CB4
|
A:DC5902
|
4.0
|
59.9
|
1.0
|
CA5
|
A:DC5902
|
4.2
|
55.1
|
1.0
|
CG
|
A:HIS239
|
4.3
|
33.0
|
1.0
|
FE
|
A:FE2901
|
4.4
|
34.6
|
1.0
|
CB5
|
A:DC5902
|
4.5
|
60.2
|
1.0
|
NE2
|
A:HIS233
|
4.6
|
34.1
|
1.0
|
CG
|
A:PHE384
|
4.6
|
35.4
|
1.0
|
CE1
|
A:HIS233
|
4.7
|
30.5
|
1.0
|
CE1
|
A:HIS239
|
4.7
|
31.6
|
1.0
|
CA3
|
A:DC5902
|
4.8
|
54.5
|
1.0
|
CA
|
A:ALA234
|
4.9
|
35.9
|
1.0
|
CA4
|
A:DC5902
|
4.9
|
55.2
|
1.0
|
ND1
|
A:HIS239
|
4.9
|
30.4
|
1.0
|
CB
|
A:HIS239
|
5.0
|
33.4
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 2xsh
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Chlorine Binding Sites List in 2xsh
Chlorine binding site 3 out
of 6 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl902
b:74.8
occ:1.00
|
CL6
|
C:DC5902
|
0.0
|
74.8
|
1.0
|
CB6
|
C:DC5902
|
1.7
|
73.9
|
1.0
|
CB5
|
C:DC5902
|
2.7
|
74.3
|
1.0
|
CB1
|
C:DC5902
|
2.7
|
73.3
|
1.0
|
CA1
|
C:DC5902
|
3.1
|
72.8
|
1.0
|
CA2
|
C:DC5902
|
3.3
|
72.2
|
1.0
|
O
|
C:GLN322
|
3.3
|
42.2
|
1.0
|
C
|
C:GLN322
|
3.4
|
43.0
|
1.0
|
SD
|
C:MET231
|
3.4
|
43.8
|
1.0
|
N
|
C:GLN322
|
3.5
|
45.8
|
1.0
|
CE
|
C:MET231
|
3.5
|
43.7
|
1.0
|
N
|
C:HIS323
|
3.7
|
41.9
|
1.0
|
CA
|
C:GLN322
|
3.8
|
44.7
|
1.0
|
C
|
C:GLY321
|
3.9
|
47.5
|
1.0
|
CB4
|
C:DC5902
|
4.0
|
74.4
|
1.0
|
CB
|
C:HIS323
|
4.0
|
39.9
|
1.0
|
CB2
|
C:DC5902
|
4.0
|
74.0
|
1.0
|
CA6
|
C:DC5902
|
4.1
|
72.1
|
1.0
|
CE
|
C:MET336
|
4.2
|
49.5
|
1.0
|
CA3
|
C:DC5902
|
4.3
|
71.3
|
1.0
|
CD2
|
C:HIS323
|
4.3
|
40.5
|
1.0
|
CA
|
C:HIS323
|
4.3
|
40.3
|
1.0
|
O
|
C:GLY321
|
4.3
|
48.0
|
1.0
|
CD2
|
C:LEU333
|
4.5
|
42.9
|
1.0
|
CB3
|
C:DC5902
|
4.5
|
74.5
|
1.0
|
CG
|
C:HIS323
|
4.5
|
40.5
|
1.0
|
CA
|
C:GLY321
|
4.5
|
48.4
|
1.0
|
CA5
|
C:DC5902
|
5.0
|
71.7
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 2xsh
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Chlorine Binding Sites List in 2xsh
Chlorine binding site 4 out
of 6 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl902
b:74.8
occ:1.00
|
CL1
|
C:DC5902
|
0.0
|
74.8
|
1.0
|
CB2
|
C:DC5902
|
1.7
|
74.0
|
1.0
|
CB3
|
C:DC5902
|
2.7
|
74.5
|
1.0
|
CB1
|
C:DC5902
|
2.7
|
73.3
|
1.0
|
O
|
C:HOH2073
|
3.0
|
43.7
|
1.0
|
CA1
|
C:DC5902
|
3.0
|
72.8
|
1.0
|
CA6
|
C:DC5902
|
3.2
|
72.1
|
1.0
|
CD2
|
C:PHE384
|
3.3
|
41.8
|
1.0
|
CD2
|
C:HIS239
|
3.4
|
37.6
|
1.0
|
CE2
|
C:PHE384
|
3.5
|
41.7
|
1.0
|
CB
|
C:ALA234
|
3.7
|
40.5
|
1.0
|
NE2
|
C:HIS239
|
3.8
|
39.2
|
1.0
|
CB4
|
C:DC5902
|
4.0
|
74.4
|
1.0
|
CB6
|
C:DC5902
|
4.0
|
73.9
|
1.0
|
CA2
|
C:DC5902
|
4.0
|
72.2
|
1.0
|
CG
|
C:HIS239
|
4.1
|
37.8
|
1.0
|
FE
|
C:FE2901
|
4.2
|
37.4
|
1.0
|
CA5
|
C:DC5902
|
4.2
|
71.7
|
1.0
|
CG
|
C:PHE384
|
4.5
|
41.1
|
1.0
|
CB5
|
C:DC5902
|
4.5
|
74.3
|
1.0
|
NE2
|
C:HIS233
|
4.5
|
38.4
|
1.0
|
CE1
|
C:HIS233
|
4.6
|
37.5
|
1.0
|
CE1
|
C:HIS239
|
4.7
|
39.1
|
1.0
|
CZ
|
C:PHE384
|
4.8
|
42.6
|
1.0
|
CB
|
C:HIS239
|
4.8
|
38.6
|
1.0
|
CE1
|
C:PHE378
|
4.8
|
38.4
|
1.0
|
ND1
|
C:HIS239
|
4.8
|
37.9
|
1.0
|
CA
|
C:ALA234
|
4.9
|
41.3
|
1.0
|
CA3
|
C:DC5902
|
4.9
|
71.3
|
1.0
|
CA4
|
C:DC5902
|
5.0
|
71.8
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 2xsh
Go back to
Chlorine Binding Sites List in 2xsh
Chlorine binding site 5 out
of 6 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl900
b:76.8
occ:1.00
|
CL6
|
E:DC5900
|
0.0
|
76.8
|
1.0
|
CB6
|
E:DC5900
|
1.7
|
75.8
|
1.0
|
CB5
|
E:DC5900
|
2.7
|
76.0
|
1.0
|
CB1
|
E:DC5900
|
2.7
|
74.8
|
1.0
|
CA1
|
E:DC5900
|
3.0
|
73.9
|
1.0
|
C
|
E:GLN322
|
3.3
|
46.4
|
1.0
|
O
|
E:GLN322
|
3.3
|
45.2
|
1.0
|
CA2
|
E:DC5900
|
3.4
|
72.9
|
1.0
|
N
|
E:HIS323
|
3.5
|
45.1
|
1.0
|
N
|
E:GLN322
|
3.7
|
49.8
|
1.0
|
CE
|
E:MET231
|
3.7
|
45.6
|
1.0
|
CB
|
E:HIS323
|
3.8
|
42.7
|
1.0
|
CA6
|
E:DC5900
|
3.9
|
73.2
|
1.0
|
CA
|
E:GLN322
|
3.9
|
48.4
|
1.0
|
SD
|
E:MET231
|
3.9
|
45.7
|
1.0
|
CB4
|
E:DC5900
|
4.0
|
76.2
|
1.0
|
CB2
|
E:DC5900
|
4.0
|
76.0
|
1.0
|
CA
|
E:HIS323
|
4.0
|
43.7
|
1.0
|
C
|
E:GLY321
|
4.0
|
51.6
|
1.0
|
CD2
|
E:LEU333
|
4.2
|
45.5
|
1.0
|
CD2
|
E:HIS323
|
4.3
|
42.1
|
1.0
|
CA3
|
E:DC5900
|
4.4
|
72.2
|
1.0
|
O
|
E:GLY321
|
4.4
|
52.2
|
1.0
|
CG
|
E:HIS323
|
4.4
|
42.6
|
1.0
|
CB3
|
E:DC5900
|
4.5
|
76.5
|
1.0
|
CA
|
E:GLY321
|
4.6
|
52.6
|
1.0
|
CA5
|
E:DC5900
|
4.8
|
72.5
|
1.0
|
SD
|
E:MET336
|
4.9
|
49.2
|
1.0
|
CA4
|
E:DC5900
|
5.0
|
72.8
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 2xsh
Go back to
Chlorine Binding Sites List in 2xsh
Chlorine binding site 6 out
of 6 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl900
b:76.5
occ:1.00
|
CL1
|
E:DC5900
|
0.0
|
76.5
|
1.0
|
CB2
|
E:DC5900
|
1.7
|
76.0
|
1.0
|
CB3
|
E:DC5900
|
2.7
|
76.5
|
1.0
|
CB1
|
E:DC5900
|
2.7
|
74.8
|
1.0
|
CA1
|
E:DC5900
|
3.0
|
73.9
|
1.0
|
O
|
E:HOH2101
|
3.2
|
34.5
|
1.0
|
CA6
|
E:DC5900
|
3.3
|
73.2
|
1.0
|
CD2
|
E:PHE384
|
3.3
|
44.5
|
1.0
|
CD2
|
E:HIS239
|
3.4
|
37.2
|
1.0
|
CE2
|
E:PHE384
|
3.4
|
44.8
|
1.0
|
CB
|
E:ALA234
|
3.6
|
41.5
|
1.0
|
CA2
|
E:DC5900
|
3.7
|
72.9
|
1.0
|
NE2
|
E:HIS239
|
3.8
|
36.5
|
1.0
|
CB4
|
E:DC5900
|
4.0
|
76.2
|
1.0
|
CB6
|
E:DC5900
|
4.0
|
75.8
|
1.0
|
FE
|
E:FE2902
|
4.1
|
40.1
|
1.0
|
CG
|
E:HIS239
|
4.2
|
37.0
|
1.0
|
CA5
|
E:DC5900
|
4.3
|
72.5
|
1.0
|
CG
|
E:PHE384
|
4.5
|
43.5
|
1.0
|
NE2
|
E:HIS233
|
4.5
|
36.1
|
1.0
|
CB5
|
E:DC5900
|
4.5
|
76.0
|
1.0
|
CE1
|
E:HIS233
|
4.5
|
36.9
|
1.0
|
CA3
|
E:DC5900
|
4.6
|
72.2
|
1.0
|
CZ
|
E:PHE384
|
4.6
|
45.2
|
1.0
|
CA
|
E:ALA234
|
4.7
|
41.5
|
1.0
|
CE1
|
E:HIS239
|
4.8
|
36.0
|
1.0
|
CA4
|
E:DC5900
|
4.8
|
72.8
|
1.0
|
CB
|
E:HIS239
|
4.9
|
37.9
|
1.0
|
ND1
|
E:HIS239
|
5.0
|
36.2
|
1.0
|
|
Reference:
P.Kumar,
M.Mohammadi,
J.F.Viger,
D.Barriault,
L.Gomez-Gil,
L.D.Eltis,
J.T.Bolin,
M.Sylvestre.
Structural Insight Into the Expanded Pcb-Degrading Abilities of A Biphenyl Dioxygenase Obtained By Directed Evolution. J.Mol.Biol. V. 405 531 2011.
ISSN: ISSN 0022-2836
PubMed: 21073881
DOI: 10.1016/J.JMB.2010.11.009
Page generated: Sat Jul 20 14:10:01 2024
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