Magnesium in PDB 1ppw: 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: 1ppw 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)	8.00 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.090, 71.880, 91.730, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 28.7

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 1ppw). 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: 1ppw:
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:24.2 occ:1.00 O3 A:EIP301 2.0 22.2 1.0 O7 A:EIP301 2.1 18.3 1.0 O A:HOH501 2.1 18.5 1.0 OE2 A:GLU87 2.1 17.1 1.0 O A:CYS67 2.3 24.7 1.0 CD A:GLU87 3.0 19.3 1.0 OE1 A:GLU87 3.2 23.8 1.0 P4 A:EIP301 3.3 24.3 1.0 C A:CYS67 3.4 23.3 1.0 P8 A:EIP301 3.4 24.8 1.0 O5 A:EIP301 3.6 24.9 1.0 N A:CYS67 4.0 21.8 1.0 O1 A:EIP301 4.1 19.5 1.0 CA A:CYS67 4.1 25.4 1.0 O9 A:EIP301 4.2 27.1 1.0 O2 A:EIP301 4.2 19.7 1.0 NH2 A:ARG83 4.3 26.0 1.0 O6 A:EIP301 4.3 50.8 1.0 N A:GLY68 4.3 14.4 1.0 O A:HOH504 4.4 24.9 1.0 CG A:GLU87 4.4 14.7 1.0 OE1 A:GLU135 4.4 10.9 1.0 NE A:ARG83 4.4 19.9 1.0 CB A:CYS67 4.4 26.5 1.0 CA A:GLY68 4.4 14.1 1.0 NH1 A:ARG51 4.5 10.7 1.0 O A:HOH503 4.5 28.2 1.0 NZ A:LYS55 4.5 18.6 1.0 CZ A:ARG83 4.8 22.0 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:29.3 occ:1.00 OE2 B:GLU87 2.0 29.9 1.0 O7 B:EIP301 2.0 33.8 1.0 O B:HOH513 2.0 35.7 1.0 O B:CYS67 2.4 18.4 1.0 O B:HOH512 2.4 13.8 1.0 O3 B:EIP301 2.4 20.8 1.0 CD B:GLU87 2.9 27.4 1.0 OE1 B:GLU87 3.1 21.7 1.0 P8 B:EIP301 3.4 34.1 1.0 C B:CYS67 3.4 25.3 1.0 P4 B:EIP301 3.5 30.7 1.0 O5 B:EIP301 3.7 99.0 1.0 O9 B:EIP301 3.8 55.3 1.0 NE B:ARG83 3.9 22.1 1.0 NH2 B:ARG83 3.9 30.5 1.0 N B:CYS67 4.0 17.4 1.0 O1 B:EIP301 4.1 22.7 1.0 CA B:CYS67 4.2 26.9 1.0 CG B:GLU87 4.3 23.3 1.0 CA B:GLY68 4.3 26.4 1.0 N B:GLY68 4.3 28.8 1.0 CZ B:ARG83 4.4 28.4 1.0 O6 B:EIP301 4.4 44.6 1.0 O B:HOH506 4.4 17.5 1.0 O B:HOH510 4.5 23.0 1.0 CB B:CYS67 4.5 31.7 1.0 OE1 B:GLU135 4.6 27.9 1.0 O2 B:EIP301 4.6 53.6 1.0 NH1 B:ARG51 4.7 19.2 1.0 NZ B:LYS55 4.8 29.3 1.0 CG2 B:VAL66 4.9 26.8 1.0 CG B:ARG83 5.0 22.7 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