Chlorine in PDB 6oo8: Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Protein crystallography data
The structure of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol, PDB code: 6oo8
was solved by
R.A.Ghiladi,
V.S.De Serrano,
T.Malewschik,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.51 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.690,
67.220,
67.580,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.6 /
21.8
|
Other elements in 6oo8:
The structure of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol also contains other interesting chemical elements:
Chlorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Binding sites:
The binding sites of Chlorine atom in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
(pdb code 6oo8). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 20 binding sites of Chlorine where determined in the
Dehaloperoxidase B in Complex with Substrate Pentachlorophenol, PDB code: 6oo8:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Chlorine binding site 1 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 1 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:31.1
occ:0.15
|
CL1
|
A:PCI202
|
0.0
|
31.1
|
0.1
|
CB
|
A:HIS55
|
1.4
|
20.0
|
0.7
|
CB
|
A:HIS55
|
1.5
|
19.5
|
0.3
|
CG
|
A:HIS55
|
1.5
|
19.8
|
0.3
|
C2
|
A:PCI202
|
1.7
|
31.1
|
0.1
|
CG
|
A:HIS55
|
1.9
|
21.4
|
0.7
|
ND1
|
A:HIS55
|
2.1
|
23.0
|
0.7
|
ND1
|
A:HIS55
|
2.2
|
20.4
|
0.3
|
CD2
|
A:HIS55
|
2.4
|
20.0
|
0.3
|
CA
|
A:HIS55
|
2.4
|
19.1
|
0.7
|
O1D
|
A:HEM201
|
2.5
|
23.8
|
0.5
|
CA
|
A:HIS55
|
2.6
|
18.7
|
0.3
|
C1
|
A:PCI202
|
2.7
|
31.6
|
0.1
|
C3
|
A:PCI202
|
2.7
|
31.5
|
0.1
|
CL1
|
A:PCI202
|
2.9
|
95.1
|
0.4
|
O1
|
A:PCI202
|
3.0
|
29.7
|
0.1
|
CL2
|
A:PCI202
|
3.1
|
32.7
|
0.1
|
CE1
|
A:HIS55
|
3.1
|
20.4
|
0.3
|
C
|
A:HIS55
|
3.2
|
17.8
|
0.7
|
C2
|
A:PCI202
|
3.2
|
90.2
|
0.4
|
O1
|
A:PCI202
|
3.2
|
84.5
|
0.4
|
CD2
|
A:HIS55
|
3.2
|
22.2
|
0.7
|
NE2
|
A:HIS55
|
3.3
|
20.3
|
0.3
|
C
|
A:HIS55
|
3.3
|
17.7
|
0.3
|
CGD
|
A:HEM201
|
3.3
|
25.3
|
0.5
|
C1
|
A:PCI202
|
3.3
|
89.4
|
0.4
|
O2D
|
A:HEM201
|
3.4
|
23.6
|
0.2
|
CE1
|
A:HIS55
|
3.4
|
23.7
|
0.7
|
O1D
|
A:HEM201
|
3.5
|
34.9
|
0.5
|
CBA
|
A:HEM201
|
3.5
|
32.1
|
1.0
|
O
|
A:HIS55
|
3.6
|
17.7
|
0.7
|
N
|
A:HIS55
|
3.7
|
19.1
|
0.7
|
O1A
|
A:HEM201
|
3.7
|
35.6
|
1.0
|
CGA
|
A:HEM201
|
3.7
|
34.1
|
1.0
|
O
|
A:HIS55
|
3.7
|
17.7
|
0.3
|
N
|
A:HIS55
|
3.9
|
18.6
|
0.3
|
NE2
|
A:HIS55
|
3.9
|
23.6
|
0.7
|
C6
|
A:PCI202
|
4.0
|
32.5
|
0.1
|
C4
|
A:PCI202
|
4.0
|
32.1
|
0.1
|
N
|
A:THR56
|
4.0
|
16.8
|
1.0
|
C3
|
A:PCI202
|
4.1
|
90.8
|
0.4
|
CGD
|
A:HEM201
|
4.2
|
30.9
|
0.5
|
O
|
A:LYS51
|
4.2
|
18.1
|
0.3
|
O
|
A:LYS51
|
4.3
|
17.7
|
0.7
|
C6
|
A:PCI202
|
4.3
|
91.0
|
0.4
|
O2D
|
A:HEM201
|
4.3
|
29.6
|
0.2
|
O2A
|
A:HEM201
|
4.4
|
43.3
|
1.0
|
C5
|
A:PCI202
|
4.5
|
32.3
|
0.1
|
CHA
|
A:HEM201
|
4.6
|
21.2
|
1.0
|
CBD
|
A:HEM201
|
4.7
|
25.2
|
0.5
|
CG2
|
A:VAL59
|
4.7
|
17.4
|
1.0
|
C
|
A:ASP54
|
4.8
|
19.5
|
0.5
|
OH
|
A:TYR38
|
4.8
|
27.1
|
1.0
|
CAA
|
A:HEM201
|
4.8
|
27.1
|
1.0
|
CL2
|
A:PCI202
|
4.9
|
94.2
|
0.4
|
C4
|
A:PCI202
|
5.0
|
91.3
|
0.4
|
|
Chlorine binding site 2 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 2 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:95.1
occ:0.40
|
CL1
|
A:PCI202
|
0.0
|
95.1
|
0.4
|
C1
|
A:PCI202
|
1.6
|
31.6
|
0.1
|
O2D
|
A:HEM201
|
1.6
|
23.6
|
0.2
|
C2
|
A:PCI202
|
1.7
|
90.2
|
0.4
|
C2
|
A:PCI202
|
1.8
|
31.1
|
0.1
|
CGD
|
A:HEM201
|
1.8
|
25.3
|
0.5
|
O1D
|
A:HEM201
|
2.0
|
23.8
|
0.5
|
O2D
|
A:HEM201
|
2.0
|
29.6
|
0.2
|
C6
|
A:PCI202
|
2.1
|
32.5
|
0.1
|
NE2
|
A:HIS55
|
2.2
|
20.3
|
0.3
|
O1
|
A:PCI202
|
2.3
|
29.7
|
0.1
|
CD2
|
A:HIS55
|
2.4
|
20.0
|
0.3
|
C3
|
A:PCI202
|
2.4
|
31.5
|
0.1
|
CGD
|
A:HEM201
|
2.5
|
30.9
|
0.5
|
CE1
|
A:HIS55
|
2.7
|
20.4
|
0.3
|
C5
|
A:PCI202
|
2.7
|
32.3
|
0.1
|
C1
|
A:PCI202
|
2.7
|
89.4
|
0.4
|
C3
|
A:PCI202
|
2.7
|
90.8
|
0.4
|
C4
|
A:PCI202
|
2.8
|
32.1
|
0.1
|
O1D
|
A:HEM201
|
2.8
|
34.9
|
0.5
|
CL1
|
A:PCI202
|
2.9
|
31.1
|
0.1
|
CG
|
A:HIS55
|
2.9
|
19.8
|
0.3
|
O1
|
A:PCI202
|
2.9
|
84.5
|
0.4
|
ND1
|
A:HIS55
|
3.0
|
20.4
|
0.3
|
CBD
|
A:HEM201
|
3.1
|
25.2
|
0.5
|
CL2
|
A:PCI202
|
3.1
|
94.2
|
0.4
|
CL5
|
A:PCI202
|
3.3
|
32.8
|
0.1
|
CE1
|
A:PHE35
|
3.5
|
30.5
|
1.0
|
CBD
|
A:HEM201
|
3.5
|
29.1
|
0.5
|
C3D
|
A:HEM201
|
3.6
|
25.4
|
1.0
|
CD1
|
A:PHE35
|
3.7
|
29.6
|
1.0
|
CAD
|
A:HEM201
|
3.7
|
27.6
|
0.5
|
CAD
|
A:HEM201
|
3.8
|
25.5
|
0.5
|
CL2
|
A:PCI202
|
3.8
|
32.7
|
0.1
|
ND1
|
A:HIS55
|
3.8
|
23.0
|
0.7
|
C4D
|
A:HEM201
|
3.9
|
25.5
|
1.0
|
CB
|
A:HIS55
|
3.9
|
20.0
|
0.7
|
C2D
|
A:HEM201
|
4.0
|
27.6
|
1.0
|
C6
|
A:PCI202
|
4.0
|
91.0
|
0.4
|
C4
|
A:PCI202
|
4.0
|
91.3
|
0.4
|
CB
|
A:HIS55
|
4.0
|
19.5
|
0.3
|
CL4
|
A:PCI202
|
4.2
|
35.2
|
0.1
|
CHA
|
A:HEM201
|
4.3
|
21.2
|
1.0
|
CG
|
A:HIS55
|
4.3
|
21.4
|
0.7
|
CL3
|
A:PCI202
|
4.3
|
30.3
|
0.1
|
OH
|
A:TYR38
|
4.4
|
27.1
|
1.0
|
ND
|
A:HEM201
|
4.4
|
25.6
|
1.0
|
C1D
|
A:HEM201
|
4.5
|
26.6
|
1.0
|
C5
|
A:PCI202
|
4.5
|
91.1
|
0.4
|
CMD
|
A:HEM201
|
4.6
|
28.3
|
1.0
|
O
|
A:HOH317
|
4.8
|
21.9
|
0.5
|
CZ
|
A:PHE35
|
4.8
|
31.8
|
1.0
|
CE1
|
A:HIS55
|
4.9
|
23.7
|
0.7
|
CE2
|
A:TYR38
|
5.0
|
24.7
|
1.0
|
|
Chlorine binding site 3 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 3 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:32.7
occ:0.15
|
CL2
|
A:PCI202
|
0.0
|
32.7
|
0.1
|
C3
|
A:PCI202
|
1.7
|
31.5
|
0.1
|
C1A
|
A:HEM201
|
2.3
|
24.4
|
1.0
|
C2A
|
A:HEM201
|
2.6
|
24.1
|
1.0
|
CHA
|
A:HEM201
|
2.6
|
21.2
|
1.0
|
CG2
|
A:VAL59
|
2.7
|
17.4
|
1.0
|
C2
|
A:PCI202
|
2.7
|
31.1
|
0.1
|
C4
|
A:PCI202
|
2.7
|
32.1
|
0.1
|
CBA
|
A:HEM201
|
2.7
|
32.1
|
1.0
|
NA
|
A:HEM201
|
2.9
|
23.5
|
1.0
|
CL1
|
A:PCI202
|
3.1
|
31.1
|
0.1
|
ND1
|
A:HIS55
|
3.1
|
20.4
|
0.3
|
CL3
|
A:PCI202
|
3.1
|
30.3
|
0.1
|
CAA
|
A:HEM201
|
3.2
|
27.1
|
1.0
|
C3A
|
A:HEM201
|
3.2
|
24.4
|
1.0
|
O1D
|
A:HEM201
|
3.2
|
23.8
|
0.5
|
CL2
|
A:PCI202
|
3.3
|
94.2
|
0.4
|
C3
|
A:PCI202
|
3.3
|
90.8
|
0.4
|
C4D
|
A:HEM201
|
3.3
|
25.5
|
1.0
|
C4A
|
A:HEM201
|
3.4
|
24.9
|
1.0
|
C2
|
A:PCI202
|
3.5
|
90.2
|
0.4
|
O
|
A:HIS55
|
3.6
|
17.7
|
0.7
|
CE1
|
A:HIS55
|
3.7
|
20.4
|
0.3
|
O
|
A:HIS55
|
3.8
|
17.7
|
0.3
|
CL1
|
A:PCI202
|
3.8
|
95.1
|
0.4
|
CG
|
A:HIS55
|
3.8
|
19.8
|
0.3
|
ND
|
A:HEM201
|
3.9
|
25.6
|
1.0
|
C5
|
A:PCI202
|
4.0
|
32.3
|
0.1
|
O
|
A:HOH317
|
4.0
|
21.9
|
0.5
|
C4
|
A:PCI202
|
4.0
|
91.3
|
0.4
|
C1
|
A:PCI202
|
4.0
|
31.6
|
0.1
|
CGA
|
A:HEM201
|
4.0
|
34.1
|
1.0
|
FE
|
A:HEM201
|
4.1
|
26.5
|
1.0
|
CB
|
A:VAL59
|
4.1
|
16.8
|
1.0
|
C
|
A:HIS55
|
4.2
|
17.8
|
0.7
|
CB
|
A:HIS55
|
4.2
|
19.5
|
0.3
|
C
|
A:HIS55
|
4.3
|
17.7
|
0.3
|
CB
|
A:HIS55
|
4.3
|
20.0
|
0.7
|
CMA
|
A:HEM201
|
4.3
|
23.8
|
1.0
|
CGD
|
A:HEM201
|
4.4
|
25.3
|
0.5
|
C3D
|
A:HEM201
|
4.4
|
25.4
|
1.0
|
C1
|
A:PCI202
|
4.4
|
89.4
|
0.4
|
CA
|
A:HIS55
|
4.4
|
19.1
|
0.7
|
N
|
A:VAL59
|
4.5
|
16.2
|
1.0
|
C6
|
A:PCI202
|
4.5
|
32.5
|
0.1
|
CA
|
A:HIS55
|
4.5
|
18.7
|
0.3
|
CHB
|
A:HEM201
|
4.5
|
25.4
|
1.0
|
CA
|
A:VAL59
|
4.5
|
16.3
|
1.0
|
NE2
|
A:HIS55
|
4.6
|
20.3
|
0.3
|
O1A
|
A:HEM201
|
4.6
|
35.6
|
1.0
|
CD2
|
A:HIS55
|
4.6
|
20.0
|
0.3
|
CL3
|
A:PCI202
|
4.6
|
90.7
|
0.4
|
ND1
|
A:HIS55
|
4.7
|
23.0
|
0.7
|
C5
|
A:PCI202
|
4.7
|
91.1
|
0.4
|
O2A
|
A:HEM201
|
4.8
|
43.3
|
1.0
|
CG
|
A:HIS55
|
4.9
|
21.4
|
0.7
|
C6
|
A:PCI202
|
4.9
|
91.0
|
0.4
|
CAD
|
A:HEM201
|
4.9
|
27.6
|
0.5
|
C1D
|
A:HEM201
|
4.9
|
26.6
|
1.0
|
CAD
|
A:HEM201
|
4.9
|
25.5
|
0.5
|
O2D
|
A:HEM201
|
5.0
|
23.6
|
0.2
|
|
Chlorine binding site 4 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 4 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:94.2
occ:0.40
|
CL2
|
A:PCI202
|
0.0
|
94.2
|
0.4
|
C4
|
A:PCI202
|
1.3
|
32.1
|
0.1
|
CL3
|
A:PCI202
|
1.5
|
30.3
|
0.1
|
C3
|
A:PCI202
|
1.7
|
90.8
|
0.4
|
O
|
A:HOH317
|
1.8
|
21.9
|
0.5
|
C5
|
A:PCI202
|
1.9
|
32.3
|
0.1
|
ND
|
A:HEM201
|
2.2
|
25.6
|
1.0
|
C3
|
A:PCI202
|
2.3
|
31.5
|
0.1
|
C1D
|
A:HEM201
|
2.5
|
26.6
|
1.0
|
CL4
|
A:PCI202
|
2.5
|
35.2
|
0.1
|
C4
|
A:PCI202
|
2.7
|
91.3
|
0.4
|
C2
|
A:PCI202
|
2.7
|
90.2
|
0.4
|
C4D
|
A:HEM201
|
2.7
|
25.5
|
1.0
|
FE
|
A:HEM201
|
2.9
|
26.5
|
1.0
|
C6
|
A:PCI202
|
3.1
|
32.5
|
0.1
|
CL3
|
A:PCI202
|
3.1
|
90.7
|
0.4
|
CL1
|
A:PCI202
|
3.1
|
95.1
|
0.4
|
CHD
|
A:HEM201
|
3.2
|
27.8
|
1.0
|
C2D
|
A:HEM201
|
3.2
|
27.6
|
1.0
|
CL2
|
A:PCI202
|
3.3
|
32.7
|
0.1
|
C3D
|
A:HEM201
|
3.3
|
25.4
|
1.0
|
C2
|
A:PCI202
|
3.3
|
31.1
|
0.1
|
NC
|
A:HEM201
|
3.4
|
26.7
|
1.0
|
C4C
|
A:HEM201
|
3.4
|
29.4
|
1.0
|
CE1
|
A:HIS55
|
3.4
|
20.4
|
0.3
|
CHA
|
A:HEM201
|
3.5
|
21.2
|
1.0
|
CE1
|
A:PHE35
|
3.6
|
30.5
|
1.0
|
NA
|
A:HEM201
|
3.6
|
23.5
|
1.0
|
C1
|
A:PCI202
|
3.7
|
31.6
|
0.1
|
C1A
|
A:HEM201
|
3.8
|
24.4
|
1.0
|
CG2
|
A:VAL59
|
3.8
|
17.4
|
1.0
|
O1D
|
A:HEM201
|
3.9
|
23.8
|
0.5
|
C5
|
A:PCI202
|
4.0
|
91.1
|
0.4
|
C1
|
A:PCI202
|
4.0
|
89.4
|
0.4
|
NE2
|
A:HIS55
|
4.0
|
20.3
|
0.3
|
CZ
|
A:PHE35
|
4.1
|
31.8
|
1.0
|
ND1
|
A:HIS55
|
4.1
|
20.4
|
0.3
|
CGD
|
A:HEM201
|
4.2
|
25.3
|
0.5
|
CMD
|
A:HEM201
|
4.4
|
28.3
|
1.0
|
NB
|
A:HEM201
|
4.4
|
24.2
|
1.0
|
CL5
|
A:PCI202
|
4.4
|
32.8
|
0.1
|
C1C
|
A:HEM201
|
4.4
|
27.6
|
1.0
|
C6
|
A:PCI202
|
4.5
|
91.0
|
0.4
|
C3C
|
A:HEM201
|
4.5
|
30.0
|
1.0
|
O2D
|
A:HEM201
|
4.5
|
29.6
|
0.2
|
CAD
|
A:HEM201
|
4.6
|
27.6
|
0.5
|
CAD
|
A:HEM201
|
4.6
|
25.5
|
0.5
|
O2D
|
A:HEM201
|
4.6
|
23.6
|
0.2
|
CD1
|
A:PHE35
|
4.7
|
29.6
|
1.0
|
C4A
|
A:HEM201
|
4.7
|
24.9
|
1.0
|
CL1
|
A:PCI202
|
4.9
|
31.1
|
0.1
|
CZ
|
A:PHE21
|
4.9
|
25.1
|
1.0
|
CBD
|
A:HEM201
|
4.9
|
25.2
|
0.5
|
NE2
|
A:HIS89
|
4.9
|
36.9
|
1.0
|
CD2
|
A:HIS55
|
4.9
|
20.0
|
0.3
|
CGD
|
A:HEM201
|
4.9
|
30.9
|
0.5
|
CG
|
A:HIS55
|
4.9
|
19.8
|
0.3
|
O1
|
A:PCI202
|
4.9
|
29.7
|
0.1
|
C2A
|
A:HEM201
|
5.0
|
24.1
|
1.0
|
CE1
|
A:PHE21
|
5.0
|
24.4
|
1.0
|
|
Chlorine binding site 5 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 5 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:30.3
occ:0.15
|
CL3
|
A:PCI202
|
0.0
|
30.3
|
0.1
|
O
|
A:HOH317
|
0.9
|
21.9
|
0.5
|
CL2
|
A:PCI202
|
1.5
|
94.2
|
0.4
|
C4
|
A:PCI202
|
1.7
|
32.1
|
0.1
|
CL3
|
A:PCI202
|
2.2
|
90.7
|
0.4
|
FE
|
A:HEM201
|
2.2
|
26.5
|
1.0
|
C3
|
A:PCI202
|
2.3
|
90.8
|
0.4
|
C4
|
A:PCI202
|
2.5
|
91.3
|
0.4
|
ND
|
A:HEM201
|
2.7
|
25.6
|
1.0
|
C5
|
A:PCI202
|
2.7
|
32.3
|
0.1
|
C3
|
A:PCI202
|
2.7
|
31.5
|
0.1
|
CG2
|
A:VAL59
|
2.9
|
17.4
|
1.0
|
NA
|
A:HEM201
|
2.9
|
23.5
|
1.0
|
NC
|
A:HEM201
|
3.0
|
26.7
|
1.0
|
CL4
|
A:PCI202
|
3.0
|
35.2
|
0.1
|
CL2
|
A:PCI202
|
3.1
|
32.7
|
0.1
|
NB
|
A:HEM201
|
3.2
|
24.2
|
1.0
|
C1D
|
A:HEM201
|
3.4
|
26.6
|
1.0
|
C4D
|
A:HEM201
|
3.4
|
25.5
|
1.0
|
C2
|
A:PCI202
|
3.5
|
90.2
|
0.4
|
C1A
|
A:HEM201
|
3.5
|
24.4
|
1.0
|
C4C
|
A:HEM201
|
3.6
|
29.4
|
1.0
|
C4A
|
A:HEM201
|
3.8
|
24.9
|
1.0
|
C1C
|
A:HEM201
|
3.8
|
27.6
|
1.0
|
CHA
|
A:HEM201
|
3.8
|
21.2
|
1.0
|
CHD
|
A:HEM201
|
3.8
|
27.8
|
1.0
|
C5
|
A:PCI202
|
3.8
|
91.1
|
0.4
|
CG1
|
A:VAL59
|
3.9
|
17.2
|
1.0
|
CE1
|
A:HIS55
|
3.9
|
20.4
|
0.3
|
C4B
|
A:HEM201
|
3.9
|
25.4
|
1.0
|
CB
|
A:VAL59
|
3.9
|
16.8
|
1.0
|
C1B
|
A:HEM201
|
3.9
|
24.5
|
1.0
|
C6
|
A:PCI202
|
4.0
|
32.5
|
0.1
|
C2
|
A:PCI202
|
4.0
|
31.1
|
0.1
|
CHC
|
A:HEM201
|
4.2
|
25.4
|
1.0
|
CHB
|
A:HEM201
|
4.2
|
25.4
|
1.0
|
ND1
|
A:HIS55
|
4.3
|
20.4
|
0.3
|
CL1
|
A:PCI202
|
4.3
|
95.1
|
0.4
|
C2D
|
A:HEM201
|
4.4
|
27.6
|
1.0
|
NE2
|
A:HIS89
|
4.4
|
36.9
|
1.0
|
C3D
|
A:HEM201
|
4.4
|
25.4
|
1.0
|
C1
|
A:PCI202
|
4.5
|
31.6
|
0.1
|
C2A
|
A:HEM201
|
4.6
|
24.1
|
1.0
|
C3C
|
A:HEM201
|
4.6
|
30.0
|
1.0
|
C1
|
A:PCI202
|
4.6
|
89.4
|
0.4
|
C2C
|
A:HEM201
|
4.7
|
28.5
|
1.0
|
C3A
|
A:HEM201
|
4.7
|
24.4
|
1.0
|
C6
|
A:PCI202
|
4.7
|
91.0
|
0.4
|
CE1
|
A:PHE35
|
4.8
|
30.5
|
1.0
|
O1D
|
A:HEM201
|
4.9
|
23.8
|
0.5
|
NE2
|
A:HIS55
|
4.9
|
20.3
|
0.3
|
CL4
|
A:PCI202
|
4.9
|
91.6
|
0.4
|
CE1
|
A:PHE21
|
4.9
|
24.4
|
1.0
|
CA
|
A:VAL59
|
5.0
|
16.3
|
1.0
|
|
Chlorine binding site 6 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 6 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:90.7
occ:0.40
|
CL3
|
A:PCI202
|
0.0
|
90.7
|
0.4
|
O
|
A:HOH317
|
1.7
|
21.9
|
0.5
|
C4
|
A:PCI202
|
1.7
|
91.3
|
0.4
|
CL3
|
A:PCI202
|
2.2
|
30.3
|
0.1
|
CL4
|
A:PCI202
|
2.6
|
35.2
|
0.1
|
C3
|
A:PCI202
|
2.7
|
90.8
|
0.4
|
C5
|
A:PCI202
|
2.7
|
91.1
|
0.4
|
C4
|
A:PCI202
|
2.8
|
32.1
|
0.1
|
C5
|
A:PCI202
|
2.9
|
32.3
|
0.1
|
CG1
|
A:VAL59
|
2.9
|
17.2
|
1.0
|
CL2
|
A:PCI202
|
3.1
|
94.2
|
0.4
|
CG2
|
A:VAL59
|
3.1
|
17.4
|
1.0
|
CL4
|
A:PCI202
|
3.2
|
91.6
|
0.4
|
CE1
|
A:PHE21
|
3.2
|
24.4
|
1.0
|
CB
|
A:VAL59
|
3.5
|
16.8
|
1.0
|
CD1
|
A:PHE21
|
3.8
|
23.0
|
1.0
|
C3
|
A:PCI202
|
3.9
|
31.5
|
0.1
|
CZ
|
A:PHE21
|
3.9
|
25.1
|
1.0
|
CE1
|
A:HIS55
|
3.9
|
20.4
|
0.3
|
NC
|
A:HEM201
|
4.0
|
26.7
|
1.0
|
C2
|
A:PCI202
|
4.0
|
90.2
|
0.4
|
FE
|
A:HEM201
|
4.0
|
26.5
|
1.0
|
C6
|
A:PCI202
|
4.0
|
91.0
|
0.4
|
NB
|
A:HEM201
|
4.0
|
24.2
|
1.0
|
C1C
|
A:HEM201
|
4.1
|
27.6
|
1.0
|
C6
|
A:PCI202
|
4.1
|
32.5
|
0.1
|
C4B
|
A:HEM201
|
4.2
|
25.4
|
1.0
|
CHC
|
A:HEM201
|
4.2
|
25.4
|
1.0
|
C4C
|
A:HEM201
|
4.5
|
29.4
|
1.0
|
C1
|
A:PCI202
|
4.5
|
89.4
|
0.4
|
ND1
|
A:HIS55
|
4.6
|
20.4
|
0.3
|
CL2
|
A:PCI202
|
4.6
|
32.7
|
0.1
|
C2C
|
A:HEM201
|
4.7
|
28.5
|
1.0
|
ND
|
A:HEM201
|
4.7
|
25.6
|
1.0
|
C1B
|
A:HEM201
|
4.7
|
24.5
|
1.0
|
NA
|
A:HEM201
|
4.8
|
23.5
|
1.0
|
CG
|
A:PHE21
|
4.8
|
21.0
|
1.0
|
CD2
|
A:LEU100
|
4.8
|
25.5
|
1.0
|
C2
|
A:PCI202
|
4.8
|
31.1
|
0.1
|
CA
|
A:VAL59
|
4.9
|
16.3
|
1.0
|
CE2
|
A:PHE21
|
4.9
|
24.1
|
1.0
|
C3C
|
A:HEM201
|
4.9
|
30.0
|
1.0
|
NE2
|
A:HIS55
|
5.0
|
20.3
|
0.3
|
C3B
|
A:HEM201
|
5.0
|
25.0
|
1.0
|
C1
|
A:PCI202
|
5.0
|
31.6
|
0.1
|
|
Chlorine binding site 7 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 7 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:35.2
occ:0.15
|
CL4
|
A:PCI202
|
0.0
|
35.2
|
0.1
|
C5
|
A:PCI202
|
1.7
|
32.3
|
0.1
|
C3
|
A:PCI202
|
2.2
|
90.8
|
0.4
|
C4
|
A:PCI202
|
2.3
|
91.3
|
0.4
|
CZ
|
A:PHE21
|
2.5
|
25.1
|
1.0
|
CL2
|
A:PCI202
|
2.5
|
94.2
|
0.4
|
O
|
A:HOH317
|
2.6
|
21.9
|
0.5
|
CL3
|
A:PCI202
|
2.6
|
90.7
|
0.4
|
CZ
|
A:PHE35
|
2.6
|
31.8
|
1.0
|
C4
|
A:PCI202
|
2.7
|
32.1
|
0.1
|
CE1
|
A:PHE21
|
2.7
|
24.4
|
1.0
|
C6
|
A:PCI202
|
2.7
|
32.5
|
0.1
|
CE1
|
A:PHE35
|
2.7
|
30.5
|
1.0
|
CL3
|
A:PCI202
|
3.0
|
30.3
|
0.1
|
C2
|
A:PCI202
|
3.1
|
90.2
|
0.4
|
CL5
|
A:PCI202
|
3.2
|
32.8
|
0.1
|
C5
|
A:PCI202
|
3.2
|
91.1
|
0.4
|
CE2
|
A:PHE21
|
3.6
|
24.1
|
1.0
|
CE1
|
A:HIS55
|
3.6
|
20.4
|
0.3
|
CE2
|
A:PHE35
|
3.7
|
31.5
|
1.0
|
C1
|
A:PCI202
|
3.9
|
89.4
|
0.4
|
C6
|
A:PCI202
|
3.9
|
91.0
|
0.4
|
C4C
|
A:HEM201
|
3.9
|
29.4
|
1.0
|
CD1
|
A:PHE35
|
3.9
|
29.6
|
1.0
|
NE2
|
A:HIS55
|
4.0
|
20.3
|
0.3
|
CHD
|
A:HEM201
|
4.0
|
27.8
|
1.0
|
C3
|
A:PCI202
|
4.0
|
31.5
|
0.1
|
CD1
|
A:PHE21
|
4.0
|
23.0
|
1.0
|
C1
|
A:PCI202
|
4.0
|
31.6
|
0.1
|
CL1
|
A:PCI202
|
4.2
|
95.1
|
0.4
|
C1D
|
A:HEM201
|
4.2
|
26.6
|
1.0
|
NC
|
A:HEM201
|
4.2
|
26.7
|
1.0
|
C3C
|
A:HEM201
|
4.2
|
30.0
|
1.0
|
CL4
|
A:PCI202
|
4.3
|
91.6
|
0.4
|
ND
|
A:HEM201
|
4.4
|
25.6
|
1.0
|
C2
|
A:PCI202
|
4.5
|
31.1
|
0.1
|
CD2
|
A:PHE21
|
4.6
|
23.3
|
1.0
|
CAC
|
A:HEM201
|
4.6
|
30.5
|
1.0
|
C1C
|
A:HEM201
|
4.6
|
27.6
|
1.0
|
C2C
|
A:HEM201
|
4.6
|
28.5
|
1.0
|
CD2
|
A:PHE35
|
4.6
|
31.5
|
1.0
|
FE
|
A:HEM201
|
4.7
|
26.5
|
1.0
|
CG
|
A:PHE35
|
4.7
|
29.5
|
1.0
|
CG
|
A:PHE21
|
4.8
|
21.0
|
1.0
|
ND1
|
A:HIS55
|
4.8
|
20.4
|
0.3
|
C2D
|
A:HEM201
|
4.8
|
27.6
|
1.0
|
CE2
|
A:PHE24
|
4.9
|
19.1
|
1.0
|
CG2
|
A:VAL59
|
4.9
|
17.4
|
1.0
|
|
Chlorine binding site 8 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 8 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:91.6
occ:0.40
|
CL4
|
A:PCI202
|
0.0
|
91.6
|
0.4
|
C5
|
A:PCI202
|
1.7
|
91.1
|
0.4
|
CD1
|
A:PHE21
|
2.5
|
23.0
|
1.0
|
C6
|
A:PCI202
|
2.7
|
91.0
|
0.4
|
C4
|
A:PCI202
|
2.7
|
91.3
|
0.4
|
CG
|
A:PHE21
|
2.7
|
21.0
|
1.0
|
CE1
|
A:PHE21
|
3.0
|
24.4
|
1.0
|
CG2
|
A:THR56
|
3.1
|
17.2
|
0.4
|
CL5
|
A:PCI202
|
3.1
|
93.4
|
0.4
|
CL3
|
A:PCI202
|
3.2
|
90.7
|
0.4
|
CG2
|
A:THR56
|
3.2
|
15.7
|
0.6
|
CB
|
A:PHE21
|
3.3
|
18.4
|
1.0
|
CB
|
A:THR56
|
3.4
|
15.7
|
0.6
|
CD2
|
A:PHE21
|
3.4
|
23.3
|
1.0
|
CA
|
A:THR56
|
3.5
|
16.3
|
0.6
|
CA
|
A:THR56
|
3.5
|
16.8
|
0.4
|
CB
|
A:THR56
|
3.6
|
16.8
|
0.4
|
CZ
|
A:PHE21
|
3.7
|
25.1
|
1.0
|
CE1
|
A:HIS55
|
3.7
|
20.4
|
0.3
|
OG1
|
A:THR56
|
3.8
|
17.0
|
0.4
|
CE1
|
A:PHE60
|
3.8
|
17.2
|
1.0
|
CE2
|
A:PHE21
|
3.8
|
24.1
|
1.0
|
CG1
|
A:VAL59
|
3.9
|
17.2
|
1.0
|
CB
|
A:VAL59
|
3.9
|
16.8
|
1.0
|
C3
|
A:PCI202
|
4.0
|
90.8
|
0.4
|
O
|
A:THR56
|
4.0
|
17.8
|
1.0
|
C1
|
A:PCI202
|
4.0
|
89.4
|
0.4
|
CG2
|
A:VAL59
|
4.0
|
17.4
|
1.0
|
CD1
|
A:PHE60
|
4.1
|
16.9
|
1.0
|
C5
|
A:PCI202
|
4.2
|
32.3
|
0.1
|
C
|
A:THR56
|
4.3
|
16.7
|
1.0
|
CL4
|
A:PCI202
|
4.3
|
35.2
|
0.1
|
ND1
|
A:HIS55
|
4.3
|
20.4
|
0.3
|
C4
|
A:PCI202
|
4.5
|
32.1
|
0.1
|
C6
|
A:PCI202
|
4.5
|
32.5
|
0.1
|
C2
|
A:PCI202
|
4.5
|
90.2
|
0.4
|
CA
|
A:PHE21
|
4.5
|
17.0
|
1.0
|
N
|
A:THR56
|
4.6
|
16.8
|
1.0
|
O
|
A:ALA17
|
4.6
|
14.8
|
1.0
|
NE2
|
A:HIS55
|
4.7
|
20.3
|
0.3
|
O
|
A:HOH317
|
4.7
|
21.9
|
0.5
|
OG1
|
A:THR56
|
4.8
|
14.9
|
0.6
|
CL3
|
A:PCI202
|
4.9
|
30.3
|
0.1
|
CZ
|
A:PHE60
|
5.0
|
17.8
|
1.0
|
CL5
|
A:PCI202
|
5.0
|
32.8
|
0.1
|
|
Chlorine binding site 9 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 9 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 9 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:32.8
occ:0.15
|
CL5
|
A:PCI202
|
0.0
|
32.8
|
0.1
|
C6
|
A:PCI202
|
1.7
|
32.5
|
0.1
|
NE2
|
A:HIS55
|
2.2
|
20.3
|
0.3
|
C1
|
A:PCI202
|
2.5
|
89.4
|
0.4
|
C2
|
A:PCI202
|
2.7
|
90.2
|
0.4
|
CE2
|
A:PHE21
|
2.7
|
24.1
|
1.0
|
C1
|
A:PCI202
|
2.7
|
31.6
|
0.1
|
CD1
|
A:PHE35
|
2.7
|
29.6
|
1.0
|
C5
|
A:PCI202
|
2.7
|
32.3
|
0.1
|
CE1
|
A:PHE35
|
2.8
|
30.5
|
1.0
|
O1
|
A:PCI202
|
2.9
|
84.5
|
0.4
|
O1
|
A:PCI202
|
2.9
|
29.7
|
0.1
|
CZ
|
A:PHE21
|
2.9
|
25.1
|
1.0
|
CE2
|
A:TYR38
|
2.9
|
24.7
|
1.0
|
CE1
|
A:HIS55
|
3.0
|
20.4
|
0.3
|
C6
|
A:PCI202
|
3.1
|
91.0
|
0.4
|
CL4
|
A:PCI202
|
3.2
|
35.2
|
0.1
|
C3
|
A:PCI202
|
3.3
|
90.8
|
0.4
|
CL1
|
A:PCI202
|
3.3
|
95.1
|
0.4
|
CD2
|
A:HIS55
|
3.3
|
20.0
|
0.3
|
CG
|
A:PHE35
|
3.4
|
29.5
|
1.0
|
CZ
|
A:PHE35
|
3.6
|
31.8
|
1.0
|
C5
|
A:PCI202
|
3.6
|
91.1
|
0.4
|
C4
|
A:PCI202
|
3.7
|
91.3
|
0.4
|
CD2
|
A:TYR38
|
3.8
|
24.6
|
1.0
|
CD2
|
A:PHE21
|
3.8
|
23.3
|
1.0
|
CZ
|
A:TYR38
|
3.9
|
25.2
|
1.0
|
OH
|
A:TYR38
|
3.9
|
27.1
|
1.0
|
O2D
|
A:HEM201
|
3.9
|
29.6
|
0.2
|
C2
|
A:PCI202
|
4.0
|
31.1
|
0.1
|
CD2
|
A:PHE35
|
4.0
|
31.5
|
1.0
|
C4
|
A:PCI202
|
4.0
|
32.1
|
0.1
|
O2D
|
A:HEM201
|
4.0
|
23.6
|
0.2
|
CL5
|
A:PCI202
|
4.0
|
93.4
|
0.4
|
CE2
|
A:PHE35
|
4.1
|
31.5
|
1.0
|
CE1
|
A:PHE21
|
4.1
|
24.4
|
1.0
|
CB
|
A:PHE35
|
4.1
|
30.8
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
20.4
|
0.3
|
CG
|
A:HIS55
|
4.4
|
19.8
|
0.3
|
CL2
|
A:PCI202
|
4.4
|
94.2
|
0.4
|
C3
|
A:PCI202
|
4.5
|
31.5
|
0.1
|
CG
|
A:PHE21
|
4.8
|
21.0
|
1.0
|
CG2
|
A:THR56
|
4.8
|
15.7
|
0.6
|
CGD
|
A:HEM201
|
4.9
|
25.3
|
0.5
|
CD1
|
A:PHE21
|
4.9
|
23.0
|
1.0
|
CL4
|
A:PCI202
|
5.0
|
91.6
|
0.4
|
|
Chlorine binding site 10 out
of 20 in 6oo8
Go back to
Chlorine Binding Sites List in 6oo8
Chlorine binding site 10 out
of 20 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 10 of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:93.4
occ:0.40
|
CL5
|
A:PCI202
|
0.0
|
93.4
|
0.4
|
CG2
|
A:THR56
|
0.9
|
15.7
|
0.6
|
OG1
|
A:THR56
|
1.1
|
17.0
|
0.4
|
C6
|
A:PCI202
|
1.7
|
91.0
|
0.4
|
CB
|
A:THR56
|
2.2
|
15.7
|
0.6
|
CB
|
A:THR56
|
2.2
|
16.8
|
0.4
|
CA
|
A:THR56
|
2.7
|
16.8
|
0.4
|
C1
|
A:PCI202
|
2.7
|
89.4
|
0.4
|
CA
|
A:THR56
|
2.7
|
16.3
|
0.6
|
C5
|
A:PCI202
|
2.7
|
91.1
|
0.4
|
CG2
|
A:THR56
|
2.9
|
17.2
|
0.4
|
O1
|
A:PCI202
|
2.9
|
84.5
|
0.4
|
N
|
A:THR56
|
3.0
|
16.8
|
1.0
|
CE1
|
A:HIS55
|
3.0
|
20.4
|
0.3
|
CL4
|
A:PCI202
|
3.1
|
91.6
|
0.4
|
OG1
|
A:THR56
|
3.1
|
14.9
|
0.6
|
NE2
|
A:HIS55
|
3.2
|
20.3
|
0.3
|
O
|
A:PHE52
|
3.3
|
17.6
|
1.0
|
CD2
|
A:PHE21
|
3.4
|
23.3
|
1.0
|
ND1
|
A:HIS55
|
3.4
|
20.4
|
0.3
|
CD2
|
A:HIS55
|
3.7
|
20.0
|
0.3
|
CE2
|
A:PHE21
|
3.8
|
24.1
|
1.0
|
CG
|
A:PHE21
|
3.8
|
21.0
|
1.0
|
CG
|
A:HIS55
|
3.8
|
19.8
|
0.3
|
C1
|
A:PCI202
|
3.8
|
31.6
|
0.1
|
O1
|
A:PCI202
|
3.9
|
29.7
|
0.1
|
C6
|
A:PCI202
|
3.9
|
32.5
|
0.1
|
CE1
|
A:PHE52
|
4.0
|
18.1
|
1.0
|
C2
|
A:PCI202
|
4.0
|
90.2
|
0.4
|
C4
|
A:PCI202
|
4.0
|
91.3
|
0.4
|
CL5
|
A:PCI202
|
4.0
|
32.8
|
0.1
|
C
|
A:HIS55
|
4.0
|
17.8
|
0.7
|
CD1
|
A:PHE52
|
4.1
|
17.4
|
1.0
|
C
|
A:HIS55
|
4.1
|
17.7
|
0.3
|
C
|
A:THR56
|
4.2
|
16.7
|
1.0
|
CZ
|
A:PHE52
|
4.3
|
17.4
|
1.0
|
C
|
A:PHE52
|
4.3
|
17.5
|
1.0
|
CB
|
A:PHE21
|
4.3
|
18.4
|
1.0
|
C2
|
A:PCI202
|
4.5
|
31.1
|
0.1
|
C3
|
A:PCI202
|
4.5
|
90.8
|
0.4
|
CZ
|
A:PHE21
|
4.5
|
25.1
|
1.0
|
CG
|
A:PHE52
|
4.5
|
17.0
|
1.0
|
CD1
|
A:PHE21
|
4.5
|
23.0
|
1.0
|
C5
|
A:PCI202
|
4.5
|
32.3
|
0.1
|
CA
|
A:PHE52
|
4.6
|
17.5
|
1.0
|
CE2
|
A:PHE52
|
4.6
|
17.4
|
1.0
|
O
|
A:HIS55
|
4.7
|
17.7
|
0.7
|
OH
|
A:TYR38
|
4.7
|
27.1
|
1.0
|
CD2
|
A:PHE52
|
4.8
|
16.6
|
1.0
|
CB
|
A:HIS55
|
4.8
|
20.0
|
0.7
|
CE1
|
A:PHE21
|
4.8
|
24.4
|
1.0
|
O
|
A:HIS55
|
4.8
|
17.7
|
0.3
|
O
|
A:THR56
|
4.8
|
17.8
|
1.0
|
CB
|
A:HIS55
|
4.8
|
19.5
|
0.3
|
CA
|
A:HIS55
|
4.9
|
19.1
|
0.7
|
CE2
|
A:TYR38
|
5.0
|
24.7
|
1.0
|
CA
|
A:HIS55
|
5.0
|
18.7
|
0.3
|
|
Reference:
T.Malewschik,
V.De Serrano,
A.H.Mcguire,
R.A.Ghiladi.
The Multifunctional Globin Dehaloperoxidase Strikes Again: Simultaneous Peroxidase and Peroxygenase Mechanisms in the Oxidation of Epa Pollutants. Arch.Biochem.Biophys. V. 673 08079 2019.
ISSN: ESSN 1096-0384
PubMed: 31445024
DOI: 10.1016/J.ABB.2019.108079
Page generated: Mon Jul 29 12:46:51 2024
|