Magnesium in PDB 8a73: PCIDS1 in Complex with MN2+ and Gpp

All present enzymatic activity of PCIDS1 in Complex with MN2+ and Gpp:
2.5.1.1;

The structure of PCIDS1 in Complex with MN2+ and Gpp, PDB code: 8a73 was solved by F.Ecker, W.Boland, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.06, 78.41, 87.3, 90, 101.67, 90
R / Rfree (%)	16 / 19.5

The structure of PCIDS1 in Complex with MN2+ and Gpp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the PCIDS1 in Complex with MN2+ and Gpp (pdb code 8a73). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the PCIDS1 in Complex with MN2+ and Gpp, PDB code: 8a73:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the PCIDS1 in Complex with MN2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PCIDS1 in Complex with MN2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:23.6 occ:1.00 O A:HOH643 2.0 33.7 1.0 OD2 A:ASP319 2.0 26.9 1.0 O A:HOH620 2.0 28.4 1.0 O A:HOH725 2.1 35.2 1.0 O A:HOH711 2.1 48.0 1.0 O A:HOH639 2.2 30.2 1.0 CG A:ASP319 3.1 25.4 1.0 OD1 A:ASP319 3.6 29.8 1.0 O A:HOH674 4.0 40.7 1.0 OD2 A:ASP323 4.1 29.2 1.0 NE2 A:GLN316 4.2 25.0 1.0 O2B A:GPP505 4.2 31.2 1.0 OD1 A:ASP337 4.2 27.8 1.0 O A:HOH678 4.3 31.2 1.0 CB A:ASP319 4.4 23.5 1.0 NZ A:LYS342 4.4 40.6 1.0 OD2 A:ASP337 4.4 28.7 1.0 O A:ASP319 4.4 22.9 1.0 OD1 A:ASP320 4.5 23.0 1.0 C A:ASP319 4.6 22.2 1.0 CG A:ASP337 4.8 27.6 1.0 CG A:ASP323 4.8 27.5 1.0 CB A:ASP323 4.9 25.8 1.0 O A:HOH712 4.9 53.0 1.0 O3B A:GPP505 5.0 30.9 1.0

Magnesium binding site 2 out of 2 in the PCIDS1 in Complex with MN2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PCIDS1 in Complex with MN2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:25.1 occ:1.00 O B:HOH666 1.9 33.5 1.0 O B:HOH694 2.0 34.4 1.0 OD2 B:ASP319 2.0 29.9 1.0 O B:HOH734 2.1 36.7 1.0 O B:HOH620 2.1 26.7 1.0 O B:HOH673 2.2 31.6 1.0 CG B:ASP319 3.2 28.7 1.0 OD1 B:ASP319 3.7 31.9 1.0 OD2 B:ASP323 4.1 32.5 1.0 NE2 B:GLN316 4.2 25.3 1.0 OD2 B:ASP337 4.2 27.9 1.0 OD1 B:ASP337 4.3 29.5 1.0 CB B:ASP319 4.4 26.1 1.0 O B:HOH670 4.4 32.9 1.0 O B:ASP319 4.5 24.3 1.0 OD1 B:ASP320 4.6 23.6 1.0 C B:ASP319 4.7 23.7 1.0 CG B:ASP337 4.7 27.2 1.0 CG B:ASP323 4.8 29.2 1.0 O B:HOH635 4.8 50.4 1.0 CB B:ASP323 4.9 27.5 1.0

F.Ecker, W.Boland, M.Groll. Metal-Dependent Enzyme Symmetry Guides the Biosynthetic Flux of Terpene Precursors To Be Published 2023.
DOI: 10.1038/S41557-023-01235-9