Magnesium in PDB 2g73: Y104F Mutant Type 1 Ipp Isomerase Complex with Eipp

All present enzymatic activity of Y104F Mutant Type 1 Ipp Isomerase Complex with Eipp:
5.3.3.2;

The structure of Y104F Mutant Type 1 Ipp Isomerase Complex with Eipp, PDB code: 2g73 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 / 1.97
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 (%)	21.3 / 27.6

The structure of Y104F Mutant Type 1 Ipp Isomerase Complex with Eipp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Y104F Mutant Type 1 Ipp Isomerase Complex with Eipp (pdb code 2g73). 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 Type 1 Ipp Isomerase Complex with Eipp, PDB code: 2g73:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Y104F Mutant Type 1 Ipp Isomerase Complex with Eipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Y104F Mutant Type 1 Ipp Isomerase Complex with Eipp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg185 b:4.3 occ:1.00 O A:HOH202 1.8 23.2 1.0 O A:HOH201 1.8 23.4 1.0 O7 A:EIP186 1.9 23.0 0.5 O1 A:EIP186 1.9 21.9 0.5 OE2 A:GLU87 1.9 21.9 1.0 O7 A:EIP186 2.1 19.9 0.5 O A:CYS67 2.2 21.6 1.0 O1 A:EIP186 2.2 17.0 0.5 CD A:GLU87 3.0 31.4 1.0 P8 A:EIP186 3.2 27.2 0.5 O5 A:EIP186 3.3 20.8 0.5 P4 A:EIP186 3.3 25.9 0.5 P8 A:EIP186 3.3 28.1 0.5 P4 A:EIP186 3.3 25.5 0.5 C A:CYS67 3.3 25.8 1.0 OE1 A:GLU87 3.3 24.8 1.0 O5 A:EIP186 3.6 15.7 0.5 O9 A:EIP186 3.8 20.9 0.5 O9 A:EIP186 3.9 22.1 0.5 O2 A:EIP186 4.0 22.6 0.5 O2 A:EIP186 4.0 21.2 0.5 N A:CYS67 4.0 25.2 1.0 CA A:CYS67 4.1 23.4 1.0 O3 A:EIP186 4.2 22.6 0.5 N A:GLY68 4.2 19.3 1.0 O6 A:EIP186 4.2 24.9 0.5 O6 A:EIP186 4.3 23.4 0.5 NH2 A:ARG83 4.3 35.0 1.0 NE A:ARG83 4.3 24.9 1.0 CG A:GLU87 4.3 26.1 1.0 O3 A:EIP186 4.4 21.9 0.5 CA A:GLY68 4.4 21.6 1.0 OE1 A:GLU135 4.4 21.4 1.0 O A:HOH249 4.5 24.5 1.0 CB A:CYS67 4.5 31.4 1.0 O A:HOH214 4.5 25.5 1.0 NH1 A:ARG51 4.6 19.4 1.0 CZ A:ARG83 4.8 26.6 1.0 NZ A:LYS55 4.9 19.1 1.0

Magnesium binding site 2 out of 2 in the Y104F Mutant Type 1 Ipp Isomerase Complex with Eipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Y104F Mutant Type 1 Ipp Isomerase Complex with Eipp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg185 b:6.1 occ:1.00 O7 B:EIP186 1.8 12.1 0.5 O7 B:EIP186 2.0 26.0 0.5 O1 B:EIP186 2.0 19.1 0.5 OE2 B:GLU87 2.0 29.3 1.0 O B:HOH203 2.1 20.6 1.0 O1 B:EIP186 2.1 20.1 0.5 O B:HOH204 2.2 29.3 1.0 O B:CYS67 2.2 22.3 1.0 CD B:GLU87 3.0 27.6 1.0 P8 B:EIP186 3.1 29.7 0.5 P4 B:EIP186 3.2 25.4 0.5 O5 B:EIP186 3.2 21.3 0.5 OE1 B:GLU87 3.4 23.0 1.0 C B:CYS67 3.4 30.3 1.0 P8 B:EIP186 3.4 23.5 0.5 P4 B:EIP186 3.4 28.6 0.5 O5 B:EIP186 3.8 19.3 0.5 O2 B:EIP186 3.9 28.1 0.5 O9 B:EIP186 3.9 32.0 0.5 O6 B:EIP186 3.9 15.8 0.5 O9 B:EIP186 4.0 32.8 0.5 O2 B:EIP186 4.0 24.6 0.5 O3 B:EIP186 4.0 26.8 0.5 NH2 B:ARG83 4.1 33.1 1.0 N B:CYS67 4.1 23.4 1.0 CA B:CYS67 4.2 26.4 1.0 NE B:ARG83 4.3 23.5 1.0 CA B:GLY68 4.4 24.8 1.0 N B:GLY68 4.4 23.7 1.0 OE1 B:GLU135 4.4 31.2 1.0 CG B:GLU87 4.4 25.8 1.0 O6 B:EIP186 4.4 18.1 0.5 CB B:CYS67 4.5 36.7 1.0 O B:HOH219 4.5 21.3 1.0 NH1 B:ARG51 4.5 14.4 1.0 O3 B:EIP186 4.5 22.7 0.5 O B:HOH212 4.6 21.9 1.0 CZ B:ARG83 4.7 33.0 1.0 NZ B:LYS55 4.7 31.1 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