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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:

Magnesium (Mg) 2 atoms
Manganese (Mn) 2 atoms

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: Sat Dec 12 02:03:39 2020

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