Bromine in PDB 1q54: Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp
Enzymatic activity of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp
All present enzymatic activity of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp:
5.3.3.2;
Protein crystallography data
The structure of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp, PDB code: 1q54
was solved by
J.Wouters,
Y.Oudjama,
S.Ghosh,
V.Stalon,
L.Droogmans,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
1.93
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.830,
71.350,
91.490,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21 /
26.6
|
Other elements in 1q54:
The structure of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp also contains other interesting chemical elements:
Bromine Binding Sites:
The binding sites of Bromine atom in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp
(pdb code 1q54). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the
Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp, PDB code: 1q54:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 1q54
Go back to
Bromine Binding Sites List in 1q54
Bromine binding site 1 out
of 4 in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br301
b:64.1
occ:0.51
|
BR
|
A:BHI301
|
0.0
|
64.1
|
0.5
|
C11
|
A:BHI301
|
1.5
|
23.5
|
0.5
|
C10
|
A:BHI301
|
1.8
|
49.2
|
0.5
|
C13
|
A:BHI301
|
2.6
|
42.9
|
0.5
|
C14
|
A:BHI301
|
2.6
|
46.5
|
0.5
|
C14
|
A:BHI301
|
2.8
|
42.7
|
0.5
|
C10
|
A:BHI301
|
3.1
|
48.2
|
0.5
|
C13
|
A:BHI301
|
3.4
|
37.1
|
0.5
|
O1
|
A:BHI301
|
3.4
|
34.8
|
0.5
|
SG
|
A:CYS118
|
3.4
|
38.1
|
1.0
|
CB
|
A:ALA67
|
3.7
|
20.7
|
1.0
|
CB
|
A:SER36
|
3.7
|
38.9
|
1.0
|
C11
|
A:BHI301
|
3.9
|
56.6
|
0.5
|
O
|
A:PHE35
|
4.0
|
23.4
|
1.0
|
O
|
A:HOH531
|
4.0
|
32.6
|
1.0
|
OG
|
A:SER36
|
4.0
|
40.0
|
1.0
|
CE3
|
A:TRP161
|
4.1
|
42.7
|
1.0
|
O1
|
A:BHI301
|
4.1
|
31.4
|
0.5
|
C12
|
A:BHI301
|
4.1
|
32.7
|
0.5
|
NE2
|
A:GLN165
|
4.2
|
37.8
|
1.0
|
OE1
|
A:GLU116
|
4.2
|
39.9
|
1.0
|
CB
|
A:TRP161
|
4.3
|
34.3
|
1.0
|
CD2
|
A:TRP161
|
4.3
|
46.0
|
1.0
|
CG
|
A:TRP161
|
4.5
|
44.5
|
1.0
|
CA
|
A:SER36
|
4.6
|
34.6
|
1.0
|
C
|
A:PHE35
|
4.6
|
27.6
|
1.0
|
C12
|
A:BHI301
|
4.7
|
31.0
|
0.5
|
O15
|
A:BHI301
|
4.7
|
29.8
|
0.5
|
BR
|
A:BHI301
|
4.8
|
85.5
|
0.5
|
CZ3
|
A:TRP161
|
4.8
|
38.5
|
1.0
|
CB
|
A:CYS118
|
4.8
|
29.7
|
1.0
|
O15
|
A:BHI301
|
4.8
|
30.0
|
0.5
|
N
|
A:SER36
|
4.9
|
30.1
|
1.0
|
|
Bromine binding site 2 out
of 4 in 1q54
Go back to
Bromine Binding Sites List in 1q54
Bromine binding site 2 out
of 4 in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br301
b:85.5
occ:0.49
|
BR
|
A:BHI301
|
0.0
|
85.5
|
0.5
|
C11
|
A:BHI301
|
1.2
|
56.6
|
0.5
|
C10
|
A:BHI301
|
1.9
|
48.2
|
0.5
|
C14
|
A:BHI301
|
2.2
|
46.5
|
0.5
|
O
|
A:HOH501
|
2.3
|
38.7
|
0.6
|
O1
|
A:BHI301
|
2.5
|
31.4
|
0.5
|
O1
|
A:BHI301
|
2.5
|
34.8
|
0.5
|
C14
|
A:BHI301
|
2.6
|
42.7
|
0.5
|
O7
|
A:BHI301
|
2.7
|
22.0
|
0.5
|
C12
|
A:BHI301
|
3.1
|
32.7
|
0.5
|
OE1
|
A:GLU114
|
3.2
|
33.4
|
1.0
|
O7
|
A:BHI301
|
3.2
|
20.7
|
0.5
|
C13
|
A:BHI301
|
3.2
|
42.9
|
0.5
|
C12
|
A:BHI301
|
3.3
|
31.0
|
0.5
|
C10
|
A:BHI301
|
3.3
|
49.2
|
0.5
|
O15
|
A:BHI301
|
3.5
|
30.0
|
0.5
|
C13
|
A:BHI301
|
3.5
|
37.1
|
0.5
|
P9
|
A:BHI301
|
3.6
|
19.8
|
0.5
|
CG
|
A:GLU114
|
3.6
|
28.8
|
1.0
|
O15
|
A:BHI301
|
3.6
|
29.8
|
0.5
|
CD
|
A:GLU114
|
3.7
|
35.7
|
1.0
|
C11
|
A:BHI301
|
3.8
|
23.5
|
0.5
|
P9
|
A:BHI301
|
3.9
|
44.2
|
0.5
|
O
|
A:HOH507
|
3.9
|
30.2
|
1.0
|
O
|
A:HOH526
|
4.1
|
20.4
|
1.0
|
NH2
|
A:ARG51
|
4.1
|
25.6
|
1.0
|
NH1
|
A:ARG51
|
4.2
|
26.0
|
1.0
|
CZ
|
A:ARG51
|
4.3
|
30.7
|
1.0
|
O8
|
A:BHI301
|
4.3
|
30.5
|
0.5
|
O
|
A:HOH531
|
4.6
|
32.6
|
1.0
|
CB
|
A:GLU114
|
4.6
|
29.6
|
1.0
|
BR
|
A:BHI301
|
4.8
|
64.1
|
0.5
|
OE2
|
A:GLU116
|
4.8
|
33.5
|
1.0
|
OE1
|
A:GLU116
|
4.8
|
39.9
|
1.0
|
CE3
|
A:TRP58
|
4.8
|
27.6
|
1.0
|
CB
|
A:ALA57
|
4.8
|
28.0
|
1.0
|
OE2
|
A:GLU114
|
4.9
|
33.4
|
1.0
|
O6
|
A:BHI301
|
5.0
|
19.3
|
0.5
|
O8
|
A:BHI301
|
5.0
|
19.9
|
0.5
|
O6
|
A:BHI301
|
5.0
|
20.2
|
0.5
|
|
Bromine binding site 3 out
of 4 in 1q54
Go back to
Bromine Binding Sites List in 1q54
Bromine binding site 3 out
of 4 in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br302
b:63.4
occ:0.55
|
BR
|
B:BHI302
|
0.0
|
63.4
|
0.6
|
O1
|
B:BHI302
|
1.4
|
46.7
|
0.5
|
C11
|
B:BHI302
|
1.8
|
2.8
|
0.5
|
C14
|
B:BHI302
|
1.8
|
33.0
|
0.5
|
C10
|
B:BHI302
|
1.8
|
36.1
|
0.6
|
C14
|
B:BHI302
|
2.6
|
30.0
|
0.6
|
O1
|
B:BHI302
|
2.7
|
27.7
|
0.6
|
C13
|
B:BHI302
|
2.9
|
25.1
|
0.5
|
C10
|
B:BHI302
|
3.1
|
37.1
|
0.5
|
OE1
|
B:GLU116
|
3.4
|
40.7
|
1.0
|
SG
|
B:CYS118
|
3.4
|
36.1
|
1.0
|
BR
|
B:BHI302
|
3.5
|
92.5
|
0.5
|
C13
|
B:BHI302
|
3.6
|
31.3
|
0.6
|
CD2
|
B:TYR104
|
3.7
|
44.6
|
1.0
|
C11
|
B:BHI302
|
3.8
|
27.6
|
0.6
|
CG
|
B:TRP161
|
4.0
|
44.4
|
1.0
|
CE2
|
B:TYR104
|
4.0
|
45.5
|
1.0
|
CB
|
B:TRP161
|
4.1
|
33.6
|
1.0
|
C12
|
B:BHI302
|
4.1
|
31.1
|
0.5
|
CD1
|
B:TRP161
|
4.2
|
47.1
|
1.0
|
CB
|
B:CYS118
|
4.2
|
28.9
|
1.0
|
CD2
|
B:TRP161
|
4.4
|
46.9
|
1.0
|
CG
|
B:TYR104
|
4.4
|
47.8
|
1.0
|
CD
|
B:GLU116
|
4.5
|
35.9
|
1.0
|
NE2
|
B:GLN165
|
4.5
|
38.3
|
1.0
|
NE1
|
B:TRP161
|
4.7
|
49.7
|
1.0
|
CE2
|
B:PHE102
|
4.8
|
31.9
|
1.0
|
CB
|
B:SER36
|
4.8
|
37.0
|
1.0
|
CE2
|
B:TRP161
|
4.8
|
44.8
|
1.0
|
CB
|
B:TYR104
|
4.9
|
42.7
|
1.0
|
CE3
|
B:TRP161
|
4.9
|
42.7
|
1.0
|
O
|
B:PHE35
|
4.9
|
24.2
|
1.0
|
CZ
|
B:TYR104
|
5.0
|
54.9
|
1.0
|
C12
|
B:BHI302
|
5.0
|
27.9
|
0.6
|
|
Bromine binding site 4 out
of 4 in 1q54
Go back to
Bromine Binding Sites List in 1q54
Bromine binding site 4 out
of 4 in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br302
b:92.5
occ:0.45
|
BR
|
B:BHI302
|
0.0
|
92.5
|
0.5
|
C11
|
B:BHI302
|
1.5
|
27.6
|
0.6
|
C10
|
B:BHI302
|
1.8
|
37.1
|
0.5
|
C14
|
B:BHI302
|
2.0
|
30.0
|
0.6
|
O1
|
B:BHI302
|
2.2
|
27.7
|
0.6
|
O1
|
B:BHI302
|
2.5
|
46.7
|
0.5
|
C14
|
B:BHI302
|
2.6
|
33.0
|
0.5
|
C10
|
B:BHI302
|
2.8
|
36.1
|
0.6
|
CE3
|
B:TRP161
|
3.2
|
42.7
|
1.0
|
CZ3
|
B:TRP161
|
3.2
|
39.6
|
1.0
|
C12
|
B:BHI302
|
3.4
|
31.1
|
0.5
|
CD2
|
B:TRP161
|
3.4
|
46.9
|
1.0
|
CH2
|
B:TRP161
|
3.4
|
34.1
|
1.0
|
C13
|
B:BHI302
|
3.5
|
31.3
|
0.6
|
BR
|
B:BHI302
|
3.5
|
63.4
|
0.6
|
C13
|
B:BHI302
|
3.6
|
25.1
|
0.5
|
CE2
|
B:TRP161
|
3.6
|
44.8
|
1.0
|
CZ2
|
B:TRP161
|
3.7
|
31.2
|
1.0
|
O7
|
B:BHI302
|
3.7
|
32.9
|
0.5
|
C11
|
B:BHI302
|
3.7
|
2.8
|
0.5
|
C12
|
B:BHI302
|
3.8
|
27.9
|
0.6
|
CE2
|
B:TYR104
|
4.0
|
45.5
|
1.0
|
O15
|
B:BHI302
|
4.2
|
30.5
|
0.5
|
CG
|
B:GLU114
|
4.2
|
28.3
|
1.0
|
CG
|
B:TRP161
|
4.2
|
44.4
|
1.0
|
O15
|
B:BHI302
|
4.3
|
27.3
|
0.6
|
OE1
|
B:GLU114
|
4.4
|
33.8
|
1.0
|
P9
|
B:BHI302
|
4.5
|
29.0
|
0.5
|
NE1
|
B:TRP161
|
4.5
|
49.7
|
1.0
|
OE1
|
B:GLU116
|
4.5
|
40.7
|
1.0
|
OH
|
B:TYR104
|
4.5
|
65.9
|
1.0
|
CE3
|
B:TRP58
|
4.6
|
26.8
|
1.0
|
CD
|
B:GLU114
|
4.6
|
34.5
|
1.0
|
CZ3
|
B:TRP58
|
4.6
|
25.7
|
1.0
|
CZ
|
B:TYR104
|
4.6
|
54.9
|
1.0
|
CD2
|
B:TYR104
|
4.7
|
44.6
|
1.0
|
CD1
|
B:TRP161
|
4.8
|
47.1
|
1.0
|
O7
|
B:BHI302
|
4.8
|
16.8
|
0.6
|
CB
|
B:GLU114
|
4.9
|
29.1
|
1.0
|
NH1
|
B:ARG51
|
4.9
|
27.8
|
1.0
|
CB
|
B:TRP161
|
5.0
|
33.6
|
1.0
|
|
Reference:
J.Wouters,
Y.Oudjama,
S.Ghosh,
V.Stalon,
L.Droogmans,
E.Oldfield.
Structure and Mechanism of Action of Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase. J.Am.Chem.Soc. V. 125 3198 2003.
ISSN: ISSN 0002-7863
PubMed: 12630859
DOI: 10.1021/JA029171P
Page generated: Wed Jul 10 17:14:02 2024
|