Magnesium in PDB 1x83: Y104F Ipp Isomerase Reacted with (S)-Bromohydrine of Ipp

All present enzymatic activity of Y104F Ipp Isomerase Reacted with (S)-Bromohydrine of Ipp:
5.3.3.2;

The structure of Y104F Ipp Isomerase Reacted with (S)-Bromohydrine of Ipp, PDB code: 1x83 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 / 1.80
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 (%)	22.8 / 27.1

The structure of Y104F Ipp Isomerase Reacted with (S)-Bromohydrine of Ipp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Y104F Ipp Isomerase Reacted with (S)-Bromohydrine of Ipp (pdb code 1x83). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Y104F Ipp Isomerase Reacted with (S)-Bromohydrine of Ipp, PDB code: 1x83:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Y104F Ipp Isomerase Reacted with (S)-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 Y104F Ipp Isomerase Reacted with (S)-Bromohydrine of Ipp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:19.6 occ:1.00 OE2 A:GLU87 2.1 20.4 1.0 O3 A:SBH301 2.1 15.5 1.0 O6 A:SBH301 2.1 21.9 1.0 O A:CYS67 2.2 15.7 1.0 O A:HOH503 2.2 17.9 1.0 O A:HOH504 2.3 17.9 1.0 CD A:GLU87 3.0 21.4 1.0 P1 A:SBH301 3.3 22.1 1.0 C A:CYS67 3.3 17.1 1.0 P2 A:SBH301 3.3 19.0 1.0 OE1 A:GLU87 3.4 22.4 1.0 O4 A:SBH301 3.4 17.5 1.0 N A:CYS67 3.9 22.5 1.0 O7 A:SBH301 3.9 23.6 1.0 O1 A:SBH301 4.1 20.3 1.0 CA A:CYS67 4.1 16.6 1.0 OE1 A:GLU135 4.2 20.2 1.0 N A:GLY68 4.2 18.1 1.0 CA A:GLY68 4.2 18.8 1.0 O2 A:SBH301 4.3 21.3 1.0 CG A:GLU87 4.3 19.3 1.0 NH2 A:ARG83 4.3 19.5 1.0 O A:HOH505 4.4 19.0 1.0 O5 A:SBH301 4.4 19.7 1.0 O A:HOH506 4.4 20.2 1.0 NE A:ARG83 4.4 15.6 1.0 NH1 A:ARG51 4.5 16.8 1.0 CB A:CYS67 4.5 21.9 1.0 CZ A:ARG83 4.9 16.1 1.0

Magnesium binding site 2 out of 2 in the Y104F Ipp Isomerase Reacted with (S)-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 Y104F Ipp Isomerase Reacted with (S)-Bromohydrine of Ipp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:22.5 occ:1.00 O6 B:SBH301 1.9 20.3 1.0 OE2 B:GLU87 2.1 24.6 1.0 O3 B:SBH301 2.2 20.0 1.0 O B:HOH515 2.2 21.6 1.0 O B:CYS67 2.3 18.7 1.0 O B:HOH514 2.3 18.1 1.0 CD B:GLU87 3.0 27.1 1.0 P2 B:SBH301 3.2 30.5 1.0 P1 B:SBH301 3.3 28.2 1.0 OE1 B:GLU87 3.3 24.4 1.0 C B:CYS67 3.3 25.8 1.0 O4 B:SBH301 3.4 25.2 1.0 O7 B:SBH301 3.9 66.4 1.0 N B:CYS67 3.9 18.6 1.0 O1 B:SBH301 4.0 30.8 1.0 CA B:CYS67 4.1 25.9 1.0 OE1 B:GLU135 4.2 26.4 1.0 NH2 B:ARG83 4.3 30.1 1.0 NE B:ARG83 4.3 19.6 1.0 O5 B:SBH301 4.3 28.7 1.0 N B:GLY68 4.3 17.7 1.0 NH1 B:ARG51 4.4 20.5 1.0 O B:HOH508 4.4 19.0 1.0 O2 B:SBH301 4.4 22.1 1.0 CA B:GLY68 4.4 19.0 1.0 CG B:GLU87 4.4 22.1 1.0 O B:HOH512 4.4 20.6 1.0 CB B:CYS67 4.5 30.1 1.0 CZ B:ARG83 4.8 26.3 1.0 NZ B:LYS55 4.8 24.4 1.0 CE B:LYS55 4.9 25.3 1.0 CG2 B:VAL66 4.9 24.5 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