Manganese in PDB 1h48: The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product

All present enzymatic activity of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product:
4.6.1.12;

The structure of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product, PDB code: 1h48 was solved by L.E.Kemp, M.S.Alphey, C.S.Bond, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	198.122, 150.287, 57.559, 90.00, 106.52, 90.00
R / Rfree (%)	20.2 / 23.6

The structure of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Manganese atom in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product (pdb code 1h48). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product, PDB code: 1h48:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:58.4 occ:1.00 OE1 B:GLU149 2.0 48.1 1.0 OE1 C:GLU149 2.0 40.8 1.0 O C:HOH1001 2.1 30.6 1.0 OE1 A:GLU149 2.1 45.4 1.0 OE2 A:GLU149 2.5 49.3 1.0 CD A:GLU149 2.6 45.3 1.0 OE2 B:GLU149 2.6 52.7 1.0 CD B:GLU149 2.6 48.6 1.0 CD C:GLU149 2.8 43.4 1.0 OE2 C:GLU149 2.8 46.8 1.0 NE2 C:HIS5 3.1 44.3 1.0 NE2 A:HIS5 3.4 44.6 1.0 CE1 C:HIS5 3.8 44.2 1.0 NE2 B:HIS5 3.8 41.0 1.0 CG A:GLU149 4.1 41.6 1.0 CG B:GLU149 4.1 44.5 1.0 CD2 C:HIS5 4.1 39.6 1.0 CD2 A:HIS5 4.2 41.2 1.0 CG C:GLU149 4.2 37.9 1.0 CE1 B:HIS5 4.4 39.7 1.0 CE1 A:HIS5 4.4 41.6 1.0 CB A:GLU149 4.6 36.1 1.0 CB C:GLU149 4.8 33.4 1.0 CD2 B:HIS5 4.8 39.9 1.0 C10 C:GPP904 4.9 83.0 0.3 ND1 C:HIS5 4.9 42.4 1.0 C9 C:GPP904 4.9 83.1 0.3 C10 C:GPP904 5.0 81.5 0.3

Manganese binding site 2 out of 2 in the The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase in Complex with Cmp and Product within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn203 b:72.5 occ:1.00 O D:HOH301 2.0 38.5 1.0 OE1 D:GLU149 2.1 52.0 1.0 OE1 E:GLU149 2.2 56.2 1.0 OE1 F:GLU149 2.3 54.6 1.0 OE2 D:GLU149 2.6 53.3 1.0 OE2 E:GLU149 2.7 58.4 1.0 CD D:GLU149 2.7 51.0 1.0 CD E:GLU149 2.7 56.6 1.0 OE2 F:GLU149 2.8 56.9 1.0 CD F:GLU149 2.8 54.2 1.0 NE2 D:HIS5 3.4 46.9 1.0 NE2 F:HIS5 3.5 42.5 1.0 NE2 E:HIS5 3.6 50.7 1.0 CD2 D:HIS5 4.2 45.3 1.0 CG D:GLU149 4.2 45.3 1.0 CE1 F:HIS5 4.2 42.1 1.0 CG E:GLU149 4.2 52.5 1.0 CE1 D:HIS5 4.3 45.0 1.0 CE1 E:HIS5 4.3 49.2 1.0 CG F:GLU149 4.3 49.5 1.0 CD2 F:HIS5 4.4 40.4 1.0 CD2 E:HIS5 4.5 49.2 1.0 C9 E:GPP904 4.8 93.2 0.3 C9 E:GPP904 4.8 91.8 0.3 C9 E:GPP904 4.8 93.2 0.3 CB D:GLU149 4.9 41.0 1.0 CB E:GLU149 4.9 49.0 1.0 CB F:GLU149 5.0 43.4 1.0

L.E.Kemp, M.S.Alphey, C.S.Bond, M.Ferguson, S.Hecht, A.Bacher, W.Eisenreich, F.Rohdich, W.N.Hunter. The Identification of Isoprenoids That Bind in the Intersubunit Cavity of Escherichia Coli 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase By Complementary Biophysical Methods Acta Crystallogr.,Sect.D V. 61 45 2005.
ISSN: ISSN 0907-4449
PubMed: 15608374
DOI: 10.1107/S0907444904025971