Magnesium in PDB 1ppv: Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in Complex with the Bromohydrine of Ipp

All present enzymatic activity of Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in Complex with the Bromohydrine of Ipp:
5.3.3.2;

The structure of Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in Complex with the Bromohydrine of Ipp, PDB code: 1ppv was solved by J.Wouters, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.147, 71.821, 92.019, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.3

The structure of Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in Complex with the Bromohydrine of Ipp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in Complex with the Bromohydrine of Ipp (pdb code 1ppv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in Complex with the Bromohydrine of Ipp, PDB code: 1ppv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in 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 Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in Complex with the Bromohydrine of Ipp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:16.7 occ:1.00 O A:HOH504 2.0 18.0 1.0 O4 A:BHI301 2.1 18.2 1.0 O8 A:BHI301 2.1 18.9 1.0 OE2 A:GLU87 2.1 17.9 1.0 O A:HOH505 2.3 14.8 1.0 O A:CYS67 2.3 16.7 1.0 CD A:GLU87 3.0 19.7 1.0 P5 A:BHI301 3.3 18.9 1.0 OE1 A:GLU87 3.3 21.3 1.0 P9 A:BHI301 3.3 21.8 1.0 C A:CYS67 3.3 20.2 1.0 O6 A:BHI301 3.4 19.7 1.0 O15 A:BHI301 3.9 24.1 1.0 N A:CYS67 4.0 15.5 1.0 O2 A:BHI301 4.1 17.9 1.0 CA A:CYS67 4.1 16.2 1.0 NH2 A:ARG83 4.2 21.6 1.0 CB A:CYS67 4.3 24.0 1.0 OE1 A:GLU135 4.3 19.6 1.0 N A:GLY68 4.3 14.1 1.0 NE A:ARG83 4.3 15.4 1.0 O3 A:BHI301 4.3 17.6 1.0 O A:HOH506 4.4 17.4 1.0 O7 A:BHI301 4.4 24.2 1.0 CA A:GLY68 4.4 14.4 1.0 CG A:GLU87 4.4 16.2 1.0 O A:HOH507 4.4 16.4 1.0 NH1 A:ARG51 4.5 13.4 1.0 NZ A:LYS55 4.7 16.7 1.0 CZ A:ARG83 4.7 16.7 1.0

Magnesium binding site 2 out of 2 in the Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in 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 Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in Complex with the Bromohydrine of Ipp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:17.6 occ:1.00 O8 B:BHI301 2.1 14.0 0.8 OE2 B:GLU87 2.1 18.6 1.0 O4 B:BHI301 2.2 14.0 0.8 O B:HOH515 2.2 15.1 1.0 O B:CYS67 2.3 13.7 1.0 O B:HOH516 2.3 17.1 1.0 CD B:GLU87 3.0 21.4 1.0 P9 B:BHI301 3.3 15.1 0.8 OE1 B:GLU87 3.3 19.6 1.0 P5 B:BHI301 3.4 13.9 0.8 C B:CYS67 3.4 20.4 1.0 O6 B:BHI301 3.5 14.2 0.8 O15 B:BHI301 3.9 17.0 0.8 N B:CYS67 4.0 14.8 1.0 O2 B:BHI301 4.1 16.2 0.8 CA B:CYS67 4.2 20.9 1.0 NE B:ARG83 4.2 20.4 1.0 NH2 B:ARG83 4.3 21.5 1.0 OE1 B:GLU135 4.3 22.6 1.0 CA B:GLY68 4.3 16.4 1.0 N B:GLY68 4.3 13.7 1.0 O7 B:BHI301 4.4 18.5 0.8 CG B:GLU87 4.4 19.2 1.0 NH1 B:ARG51 4.4 19.5 1.0 O B:HOH509 4.4 16.3 1.0 O3 B:BHI301 4.4 12.4 0.8 CB B:CYS67 4.4 29.1 1.0 O B:HOH513 4.4 15.7 1.0 NZ B:LYS55 4.7 20.9 1.0 CZ B:ARG83 4.7 24.0 1.0

J.Wouters, F.Yin, Y.Song, Y.Zhang, Y.Oudjama, V.Stalon, L.Droogmans, C.T.Morita, E.Oldfield. A Crystallographic Investigation of Phosphoantigen Binding to Isopentenyl Pyrophosphate/Dimethylallyl Pyrophosphate Isomerase J.Am.Chem.Soc. V. 127 536 2005.
ISSN: ISSN 0002-7863
PubMed: 15643873
DOI: 10.1021/JA040207I