Manganese 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:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Y104F Mutant of Type 1 Isopentenylpyrophosphate- Dimethylallylpyrophosphate Isomerase, PDB code: 2g74:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn184 b:17.5 occ:1.00 NE2 A:HIS69 2.0 20.1 1.0 OE1 A:GLU114 2.1 24.7 1.0 NE2 A:HIS25 2.1 13.3 1.0 NE2 A:HIS32 2.1 23.3 1.0 OE2 A:GLU116 2.2 19.4 1.0 OE2 A:GLU114 2.3 22.1 1.0 CD A:GLU114 2.5 26.5 1.0 CD2 A:HIS69 2.9 18.5 1.0 CE1 A:HIS69 3.0 17.5 1.0 CD2 A:HIS25 3.1 16.1 1.0 CE1 A:HIS32 3.1 20.4 1.0 CE1 A:HIS25 3.1 16.7 1.0 CD2 A:HIS32 3.1 24.2 1.0 CD A:GLU116 3.3 23.6 1.0 CG A:GLU116 3.8 26.5 1.0 CG A:GLU114 4.0 19.6 1.0 CG A:HIS69 4.1 19.9 1.0 ND1 A:HIS69 4.1 20.2 1.0 O A:HOH210 4.2 22.2 1.0 ND1 A:HIS32 4.2 24.8 1.0 ND1 A:HIS25 4.2 17.3 1.0 CG A:HIS25 4.2 20.6 1.0 CG A:HIS32 4.3 21.8 1.0 OE1 A:GLU116 4.3 21.2 1.0 CG1 A:VAL6 4.8 18.1 1.0 CB A:GLU114 4.9 17.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn184 b:31.1 occ:1.00 NE2 B:HIS25 1.6 84.9 1.0 NE2 B:HIS32 1.9 36.0 1.0 NE2 B:HIS69 2.0 30.8 1.0 CE1 B:HIS25 2.1 86.4 1.0 OE2 B:GLU116 2.2 29.5 1.0 OE2 B:GLU114 2.4 29.9 1.0 OE1 B:GLU114 2.4 25.2 1.0 CD B:GLU114 2.7 29.9 1.0 CE1 B:HIS32 2.9 35.6 1.0 CD2 B:HIS32 2.9 36.6 1.0 CD2 B:HIS25 2.9 81.7 1.0 CD2 B:HIS69 2.9 36.7 1.0 CE1 B:HIS69 3.1 34.0 1.0 CD B:GLU116 3.3 32.7 1.0 ND1 B:HIS25 3.3 86.1 1.0 CG B:HIS25 3.7 80.3 1.0 CG B:GLU116 3.8 26.8 1.0 ND1 B:HIS32 4.0 30.0 1.0 CG B:HIS32 4.1 29.9 1.0 CG B:HIS69 4.1 31.5 1.0 ND1 B:HIS69 4.2 28.7 1.0 CG B:GLU114 4.2 28.6 1.0 OE1 B:GLU116 4.3 32.5 1.0 CG1 B:VAL6 5.0 31.8 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