Magnesium in PDB 1pvf: E.Coli Ipp Isomerase in Complex with Diphosphate

All present enzymatic activity of E.Coli Ipp Isomerase in Complex with Diphosphate:
5.3.3.2;

The structure of E.Coli Ipp Isomerase in Complex with Diphosphate, PDB code: 1pvf was solved by J.Wouters, V.Durisotti, Y.Oudjama, V.Stalon, L.Droogmans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.78
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 (%)	19.7 / 23.6

The structure of E.Coli Ipp Isomerase in Complex with Diphosphate also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

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

Magnesium binding site 1 out of 2 in the E.Coli Ipp Isomerase in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E.Coli Ipp Isomerase in Complex with Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.6 occ:1.00 O2 A:DPO301 1.9 18.6 1.0 O A:HOH502 2.0 18.0 1.0 O6 A:DPO301 2.0 17.2 1.0 OE2 A:GLU87 2.1 11.7 1.0 O A:CYS67 2.2 16.4 1.0 O A:HOH501 2.2 12.1 1.0 CD A:GLU87 3.1 15.3 1.0 P1 A:DPO301 3.2 18.7 1.0 C A:CYS67 3.3 17.6 1.0 P2 A:DPO301 3.3 21.8 1.0 OE1 A:GLU87 3.3 17.8 1.0 O4 A:DPO301 3.5 20.4 1.0 N A:CYS67 4.0 13.2 1.0 O3 A:DPO301 4.1 16.8 1.0 CA A:CYS67 4.1 14.7 1.0 O7 A:DPO301 4.1 28.9 1.0 O1 A:DPO301 4.2 19.0 1.0 N A:GLY68 4.2 12.7 1.0 O5 A:DPO301 4.2 27.4 1.0 O A:HOH505 4.3 16.6 1.0 CA A:GLY68 4.3 12.4 1.0 OE1 A:GLU135 4.4 14.8 1.0 NH2 A:ARG83 4.4 17.9 1.0 O A:HOH504 4.4 16.8 1.0 CG A:GLU87 4.4 15.6 1.0 NE A:ARG83 4.4 19.1 1.0 NH1 A:ARG51 4.5 18.0 1.0 CB A:CYS67 4.5 20.4 1.0 NZ A:LYS55 4.7 17.6 1.0 CZ A:ARG83 4.9 19.8 1.0 CG2 A:VAL66 4.9 21.2 1.0 CE A:LYS55 5.0 13.8 1.0

Magnesium binding site 2 out of 2 in the E.Coli Ipp Isomerase in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E.Coli Ipp Isomerase in Complex with Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:16.4 occ:1.00 O6 B:DPO301 2.0 18.1 1.0 OE2 B:GLU87 2.0 15.0 1.0 O2 B:DPO301 2.1 14.6 1.0 O B:CYS67 2.2 13.1 1.0 O B:HOH513 2.3 16.2 1.0 O B:HOH514 2.3 13.5 1.0 CD B:GLU87 3.0 28.6 1.0 OE1 B:GLU87 3.3 23.9 1.0 P1 B:DPO301 3.3 21.7 1.0 P2 B:DPO301 3.3 23.1 1.0 C B:CYS67 3.4 18.5 1.0 O4 B:DPO301 3.5 23.0 1.0 N B:CYS67 3.9 12.8 1.0 O7 B:DPO301 4.0 23.1 1.0 O3 B:DPO301 4.1 17.3 1.0 CA B:CYS67 4.1 19.6 1.0 NE B:ARG83 4.2 19.0 1.0 NH2 B:ARG83 4.2 22.1 1.0 O5 B:DPO301 4.3 28.2 1.0 OE1 B:GLU135 4.3 19.4 1.0 CA B:GLY68 4.3 11.1 1.0 N B:GLY68 4.3 13.6 1.0 O1 B:DPO301 4.3 22.0 1.0 CG B:GLU87 4.3 16.2 1.0 O B:HOH507 4.4 13.0 1.0 NH1 B:ARG51 4.5 19.6 1.0 O B:HOH511 4.5 12.7 1.0 CB B:CYS67 4.5 23.6 1.0 CZ B:ARG83 4.7 19.7 1.0 NZ B:LYS55 4.7 19.8 1.0 CG2 B:VAL66 4.9 23.8 1.0 CE B:LYS55 5.0 27.2 1.0

J.Wouters, V.Durisotti, Y.Oudjama, V.Stalon, L.Droogmans. E.Coli Isopentenyl Diphosphate: Dimethylallyl Diphosphate Isomerase in Complex with Diphosphate To Be Published.