Magnesium in PDB 2g74: Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase

All present enzymatic activity of Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase:
5.3.3.2;

The structure of Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase, PDB code: 2g74 was solved by J.De Ruyck, J.Wouters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.935, 71.477, 91.955, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 27

The structure of Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase (pdb code 2g74). 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 Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase, PDB code: 2g74:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg185 b:8.0 occ:1.00 O A:HOH201 1.9 17.8 1.0 OE2 A:GLU87 2.0 20.4 1.0 O A:CYS67 2.2 20.1 1.0 O A:HOH202 2.2 26.1 1.0 CD A:GLU87 3.0 28.7 1.0 O A:HOH362 3.3 12.9 1.0 C A:CYS67 3.3 23.3 1.0 O A:HOH363 3.3 22.7 1.0 OE1 A:GLU87 3.5 21.6 1.0 N A:CYS67 4.0 21.9 1.0 CA A:CYS67 4.1 22.3 1.0 NH2 A:ARG83 4.2 26.8 1.0 N A:GLY68 4.2 18.9 1.0 NE A:ARG83 4.2 18.4 1.0 CA A:GLY68 4.3 18.8 1.0 CG A:GLU87 4.3 23.6 1.0 CB A:CYS67 4.4 24.1 0.3 O A:HOH249 4.4 19.6 1.0 CB A:CYS67 4.4 24.4 0.7 O A:HOH214 4.4 16.6 1.0 OE1 A:GLU135 4.4 21.1 1.0 NH1 A:ARG51 4.5 18.9 1.0 CZ A:ARG83 4.7 24.7 1.0 NZ A:LYS55 4.8 15.4 1.0 CG2 A:VAL66 5.0 23.6 1.0

Magnesium binding site 2 out of 2 in the Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg185 b:42.1 occ:1.00 OE2 B:GLU87 2.0 39.7 1.0 O B:HOH203 2.4 16.2 1.0 O B:CYS67 2.5 26.2 1.0 CD B:GLU87 3.1 34.1 1.0 O B:HOH204 3.2 45.4 1.0 NH2 B:ARG83 3.3 64.9 1.0 OE1 B:GLU87 3.4 28.1 1.0 NE B:ARG83 3.4 35.0 1.0 C B:CYS67 3.6 30.1 1.0 CZ B:ARG83 3.8 37.0 1.0 NZ B:LYS55 4.3 51.5 1.0 N B:CYS67 4.3 20.3 1.0 CG B:GLU87 4.4 23.2 1.0 CA B:GLY68 4.4 28.8 1.0 N B:GLY68 4.5 27.2 1.0 O B:HOH219 4.5 18.1 1.0 CA B:CYS67 4.5 23.4 1.0 NH1 B:ARG51 4.6 11.5 1.0 O B:HOH212 4.6 18.1 1.0 CD B:ARG83 4.7 34.1 1.0 CG2 B:VAL66 4.8 31.1 1.0 CE B:LYS55 4.9 48.7 1.0

J.De Ruyck, V.Durisotti, Y.Oudjama, J.Wouters. Structural Role For Tyr-104 in Escherichia Coli Isopentenyl-Diphosphate Isomerase: Site-Directed Mutagenesis, Enzymology, and Protein Crystallography. J.Biol.Chem. V. 281 17864 2006.
ISSN: ISSN 0021-9258
PubMed: 16617181
DOI: 10.1074/JBC.M601851200