Magnesium in PDB 2b2k: Structure of Y104F Idi-1 Mutant in Complex with Eipp

All present enzymatic activity of Structure of Y104F Idi-1 Mutant in Complex with Eipp:
5.3.3.2;

The structure of Structure of Y104F Idi-1 Mutant in Complex with Eipp, PDB code: 2b2k was solved by J.Wouters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 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 (%)	21.5 / 24.5

The structure of Structure of Y104F Idi-1 Mutant in Complex with Eipp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Structure of Y104F Idi-1 Mutant in Complex with Eipp (pdb code 2b2k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Y104F Idi-1 Mutant in Complex with Eipp, PDB code: 2b2k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Y104F Idi-1 Mutant in 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 Structure of Y104F Idi-1 Mutant in Complex with Eipp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:14.8 occ:1.00 O A:HOH7021 1.8 24.1 1.0 O A:HOH7022 1.9 23.1 1.0 OE2 A:GLU87 2.0 22.8 1.0 O7 A:EIP401 2.0 21.4 1.0 O1 A:EIP401 2.1 22.9 1.0 O A:CYS67 2.1 22.8 1.0 CD A:GLU87 3.0 31.6 1.0 P8 A:EIP401 3.3 28.6 1.0 C A:CYS67 3.3 27.3 1.0 P4 A:EIP401 3.3 27.3 1.0 OE1 A:GLU87 3.4 24.3 1.0 O5 A:EIP401 3.4 21.7 1.0 O9 A:EIP401 3.9 22.7 1.0 O2 A:EIP401 4.0 25.5 1.0 N A:CYS67 4.0 26.4 1.0 CA A:CYS67 4.1 25.4 1.0 N A:GLY68 4.2 20.4 1.0 NH2 A:ARG83 4.2 34.1 1.0 O6 A:EIP401 4.3 25.7 1.0 O3 A:EIP401 4.3 24.7 1.0 NE A:ARG83 4.3 24.5 1.0 CA A:GLY68 4.3 23.9 1.0 CG A:GLU87 4.3 26.1 1.0 O A:HOH7069 4.4 24.7 1.0 OE1 A:GLU135 4.5 20.5 1.0 CB A:CYS67 4.5 32.7 1.0 NH1 A:ARG51 4.6 19.8 1.0 O A:HOH7034 4.6 25.4 1.0 CZ A:ARG83 4.7 26.5 1.0 NZ A:LYS55 4.8 20.4 1.0

Magnesium binding site 2 out of 2 in the Structure of Y104F Idi-1 Mutant in 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 Structure of Y104F Idi-1 Mutant in Complex with Eipp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:16.8 occ:1.00 O7 B:EIP401 1.9 19.1 1.0 O1 B:EIP401 2.0 23.1 1.0 OE2 B:GLU87 2.0 29.4 1.0 O B:HOH7023 2.1 21.9 1.0 O B:CYS67 2.2 21.5 1.0 O B:HOH7024 2.3 32.1 1.0 CD B:GLU87 3.0 26.1 1.0 P8 B:EIP401 3.3 29.5 1.0 P4 B:EIP401 3.3 28.4 1.0 C B:CYS67 3.4 29.5 1.0 OE1 B:GLU87 3.4 22.5 1.0 O5 B:EIP401 3.5 29.2 1.0 O9 B:EIP401 3.9 35.8 1.0 O2 B:EIP401 4.0 28.8 1.0 NH2 B:ARG83 4.1 35.0 1.0 N B:CYS67 4.2 25.7 1.0 CA B:CYS67 4.2 26.6 1.0 O6 B:EIP401 4.2 24.7 1.0 NE B:ARG83 4.2 24.7 1.0 O3 B:EIP401 4.3 31.3 1.0 N B:GLY68 4.3 23.9 1.0 CA B:GLY68 4.3 25.6 1.0 CG B:GLU87 4.4 27.1 1.0 OE1 B:GLU135 4.4 28.8 1.0 NH1 B:ARG51 4.5 15.7 1.0 CB B:CYS67 4.5 36.6 1.0 O B:HOH7039 4.5 21.4 1.0 O B:HOH7032 4.6 23.0 1.0 NZ B:LYS55 4.6 34.1 1.0 CZ B:ARG83 4.6 33.5 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