Manganese 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:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Y104F Idi-1 Mutant in Complex with Eipp, PDB code: 2b2k:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn201 b:21.6 occ:1.00 NE2 A:HIS69 1.9 18.4 1.0 NE2 A:HIS25 2.1 19.0 1.0 OE1 A:GLU114 2.1 28.8 1.0 NE2 A:HIS32 2.2 23.6 1.0 OE2 A:GLU114 2.2 25.1 1.0 OE2 A:GLU116 2.3 24.3 1.0 CD A:GLU114 2.5 31.0 1.0 CE1 A:HIS69 2.8 24.6 1.0 CE1 A:HIS32 3.0 20.8 1.0 CE1 A:HIS25 3.0 22.5 1.0 CD2 A:HIS69 3.0 19.6 1.0 CD2 A:HIS25 3.1 18.4 1.0 CD2 A:HIS32 3.3 25.8 1.0 CD A:GLU116 3.4 26.1 1.0 ND1 A:HIS69 4.0 21.4 1.0 CG A:GLU116 4.0 30.9 1.0 CG A:GLU114 4.0 22.8 1.0 CG A:HIS69 4.1 25.6 1.0 ND1 A:HIS25 4.1 22.8 1.0 O A:HOH7030 4.2 28.3 1.0 ND1 A:HIS32 4.2 26.9 1.0 O15 A:EIP401 4.2 52.7 1.0 CG A:HIS25 4.2 23.9 1.0 OE1 A:GLU116 4.3 36.1 1.0 CG A:HIS32 4.4 25.3 1.0 C10 A:EIP401 4.4 26.3 1.0 C11 A:EIP401 4.8 30.2 1.0 C12 A:EIP401 4.8 39.1 1.0 CG1 A:VAL6 4.9 20.6 1.0 CB A:GLU114 4.9 22.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn201 b:29.9 occ:1.00 NE2 B:HIS25 1.9 38.6 1.0 NE2 B:HIS32 1.9 32.7 1.0 NE2 B:HIS69 2.0 31.5 1.0 OE2 B:GLU114 2.3 27.0 1.0 OE1 B:GLU114 2.4 29.7 1.0 OE2 B:GLU116 2.5 33.2 1.0 CE1 B:HIS25 2.7 36.3 1.0 CD B:GLU114 2.7 34.6 1.0 CD2 B:HIS32 2.9 37.0 1.0 CE1 B:HIS32 3.0 38.9 1.0 CD2 B:HIS69 3.0 35.2 1.0 CE1 B:HIS69 3.0 35.1 1.0 CD2 B:HIS25 3.1 39.6 1.0 CD B:GLU116 3.6 43.9 1.0 ND1 B:HIS25 3.9 40.5 1.0 ND1 B:HIS32 4.1 38.9 1.0 CG B:HIS32 4.1 37.0 1.0 CG B:HIS25 4.1 42.0 1.0 ND1 B:HIS69 4.1 35.3 1.0 CG B:HIS69 4.1 32.3 1.0 CG B:GLU114 4.2 36.4 1.0 OE1 B:GLU116 4.4 43.9 1.0 C10 B:EIP401 4.4 38.6 1.0 CG B:GLU116 4.5 37.8 1.0 C11 B:EIP401 4.6 44.7 1.0 CG1 B:VAL6 4.8 39.9 1.0 C12 B:EIP401 4.8 51.5 1.0 CB B:ALA34 4.9 19.7 1.0 C13 B:EIP401 4.9 48.5 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