Manganese 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:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Isopentenylpyrophosphate-Dimethylallylpyrophosphate Isomerase in Complex with the Bromohydrine of Ipp, PDB code: 1ppv:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn201 b:15.0 occ:1.00 OE2 A:GLU116 2.0 24.7 1.0 NE2 A:HIS25 2.1 15.4 1.0 NE2 A:HIS69 2.1 19.1 1.0 NE2 A:HIS32 2.2 15.3 1.0 OE1 A:GLU114 2.2 15.4 1.0 OE2 A:GLU114 2.2 20.0 1.0 CD A:GLU114 2.5 24.3 1.0 CE1 A:HIS32 2.9 21.8 1.0 CE1 A:HIS69 3.0 13.9 1.0 CD2 A:HIS25 3.1 16.8 1.0 CE1 A:HIS25 3.1 12.9 1.0 CD A:GLU116 3.1 23.2 1.0 CD2 A:HIS69 3.2 16.7 1.0 CD2 A:HIS32 3.3 22.4 1.0 CG A:GLU116 3.7 20.2 1.0 CG A:GLU114 4.1 20.6 1.0 C10 A:BHI301 4.1 45.0 1.0 ND1 A:HIS32 4.1 20.1 1.0 O A:HOH569 4.2 20.0 1.0 OE1 A:GLU116 4.2 28.6 1.0 ND1 A:HIS69 4.2 17.5 1.0 ND1 A:HIS25 4.2 20.3 1.0 CG A:HIS25 4.2 21.3 1.0 CG A:HIS69 4.3 18.5 1.0 C12 A:BHI301 4.3 30.9 1.0 CG A:HIS32 4.3 18.3 1.0 C13 A:BHI301 4.6 36.5 1.0 CB A:GLU114 4.8 18.4 1.0 C14 A:BHI301 4.9 47.0 1.0 CG1 A:VAL6 5.0 17.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn201 b:18.7 occ:1.00 NE2 B:HIS25 2.0 27.5 1.0 OE2 B:GLU116 2.1 26.5 1.0 NE2 B:HIS69 2.1 22.9 1.0 OE2 B:GLU114 2.1 22.2 1.0 NE2 B:HIS32 2.1 19.9 1.0 OE1 B:GLU114 2.3 22.3 1.0 CD B:GLU114 2.6 24.9 1.0 CE1 B:HIS32 2.9 25.9 1.0 CD2 B:HIS25 3.0 31.3 1.0 CE1 B:HIS25 3.0 29.7 1.0 CE1 B:HIS69 3.0 24.3 1.0 CD2 B:HIS69 3.1 26.4 1.0 CD B:GLU116 3.2 37.0 1.0 CD2 B:HIS32 3.3 24.4 1.0 CG B:GLU116 3.8 23.1 1.0 CG B:GLU114 4.1 19.4 1.0 ND1 B:HIS25 4.1 35.4 1.0 CG B:HIS25 4.1 29.2 1.0 ND1 B:HIS32 4.1 23.1 1.0 ND1 B:HIS69 4.2 20.6 1.0 OE1 B:GLU116 4.2 28.6 1.0 CG B:HIS69 4.3 21.4 1.0 CG B:HIS32 4.3 21.2 1.0 O B:HOH644 4.3 31.4 1.0 C12 B:BHI301 4.4 24.2 0.8 C13 B:BHI301 4.7 30.2 0.8 CG1 B:VAL6 4.8 27.7 1.0 CB B:GLU114 4.9 17.8 1.0 CB B:ALA34 5.0 16.6 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