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Magnesium 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 (Br) 4 atoms
Manganese (Mn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure and Mechanism of Action of Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase: Complex with the Bromohydrine of Ipp, PDB code: 1q54:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1q54

Go back to Magnesium Binding Sites List in 1q54
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg401

b:12.9
occ:1.00
 O4 A:BHI301 1.3 29.7 0.5
O8 A:BHI301 1.9 19.9 0.5
OE2 A:GLU87 1.9 28.0 1.0
O A:HOH502 2.0 21.9 1.0
O A:HOH503 2.0 30.0 1.0
O A:ALA67 2.2 23.6 1.0
O4 A:BHI301 2.3 19.4 0.5
O8 A:BHI301 2.5 30.5 0.5
P5 A:BHI301 2.7 76.1 0.5
CD A:GLU87 2.9 29.2 1.0
OE1 A:GLU87 3.2 27.9 1.0
P9 A:BHI301 3.3 44.2 0.5
O6 A:BHI301 3.3 20.2 0.5
O2 A:BHI301 3.3 31.4 0.5
C A:ALA67 3.4 24.0 1.0
P5 A:BHI301 3.4 19.8 0.5
P9 A:BHI301 3.5 19.8 0.5
O6 A:BHI301 3.6 19.3 0.5
O3 A:BHI301 3.7 19.5 0.5
N A:ALA67 3.9 26.6 1.0
O15 A:BHI301 3.9 30.0 0.5
O15 A:BHI301 3.9 29.8 0.5
O2 A:BHI301 4.1 12.5 0.5
CA A:ALA67 4.2 24.2 1.0
NH2 A:ARG83 4.2 28.9 1.0
O7 A:BHI301 4.2 20.7 0.5
CG A:GLU87 4.2 24.4 1.0
NE A:ARG83 4.3 26.1 1.0
OE1 A:GLU135 4.3 24.8 1.0
N A:GLY68 4.3 27.1 1.0
CA A:GLY68 4.4 25.0 1.0
O A:HOH508 4.4 23.1 1.0
O3 A:BHI301 4.5 18.0 0.5
O A:HOH504 4.5 27.5 1.0
NH1 A:ARG51 4.6 26.0 1.0
O7 A:BHI301 4.7 22.0 0.5
CZ A:ARG83 4.7 33.3 1.0
CB A:ALA67 4.7 20.7 1.0
NZ A:LYS55 4.8 25.1 1.0
CG2 A:VAL66 4.9 24.9 1.0

Magnesium binding site 2 out of 2 in 1q54

Go back to Magnesium Binding Sites List in 1q54
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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
B:Mg401

b:8.8
occ:1.00
 O8 B:BHI302 1.8 20.3 0.6
OE2 B:GLU87 1.9 25.4 1.0
O4 B:BHI302 2.0 19.2 0.6
O B:HOH520 2.1 29.7 1.0
O B:HOH519 2.1 23.6 1.0
O4 B:BHI302 2.1 18.9 0.5
O8 B:BHI302 2.2 24.1 0.5
O B:ALA67 2.2 22.4 1.0
CD B:GLU87 3.0 30.2 1.0
P9 B:BHI302 3.1 21.2 0.6
P5 B:BHI302 3.2 20.3 0.6
C B:ALA67 3.3 25.5 1.0
OE1 B:GLU87 3.4 24.1 1.0
O6 B:BHI302 3.4 15.2 0.6
P5 B:BHI302 3.4 37.6 0.5
P9 B:BHI302 3.5 29.0 0.5
O6 B:BHI302 3.8 20.7 0.5
O15 B:BHI302 3.8 27.3 0.6
O2 B:BHI302 3.9 25.6 0.6
O2 B:BHI302 4.0 19.4 0.5
O15 B:BHI302 4.0 30.5 0.5
N B:ALA67 4.0 24.4 1.0
O7 B:BHI302 4.1 16.8 0.6
NH2 B:ARG83 4.1 27.4 1.0
CA B:ALA67 4.2 25.4 1.0
NE B:ARG83 4.2 23.5 1.0
CA B:GLY68 4.3 26.6 1.0
O3 B:BHI302 4.3 28.9 0.6
N B:GLY68 4.3 27.1 1.0
CG B:GLU87 4.3 21.4 1.0
OE1 B:GLU135 4.3 24.5 1.0
O B:HOH516 4.4 26.2 1.0
O3 B:BHI302 4.5 27.1 0.5
NH1 B:ARG51 4.5 27.8 1.0
O7 B:BHI302 4.6 32.9 0.5
O B:HOH512 4.6 21.1 1.0
CZ B:ARG83 4.6 32.1 1.0
CB B:ALA67 4.7 21.2 1.0
NZ B:LYS55 4.8 26.5 1.0
CE B:LYS55 5.0 31.2 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: Tue Aug 13 11:05:46 2024

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