Magnesium in PDB 8a78: PCIDS1_F315A in Complex with MG2+/MN2+ and Gpp

All present enzymatic activity of PCIDS1_F315A in Complex with MG2+/MN2+ and Gpp:
2.5.1.1;

The structure of PCIDS1_F315A in Complex with MG2+/MN2+ and Gpp, PDB code: 8a78 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 (°)	59.09, 78.79, 88.48, 90, 102.17, 90
R / Rfree (%)	14.8 / 18.9

The structure of PCIDS1_F315A in Complex with MG2+/MN2+ and Gpp also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the PCIDS1_F315A in Complex with MG2+/MN2+ and Gpp (pdb code 8a78). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the PCIDS1_F315A in Complex with MG2+/MN2+ and Gpp, PDB code: 8a78:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the PCIDS1_F315A in Complex with MG2+/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_F315A in Complex with MG2+/MN2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:16.7 occ:1.00 O1B A:GPP505 2.0 27.4 1.0 O A:HOH648 2.1 22.6 1.0 OD2 A:ASP179 2.1 20.6 1.0 OD2 A:ASP183 2.1 22.2 1.0 O1A A:GPP505 2.1 21.0 1.0 O A:HOH615 2.1 23.8 1.0 CG A:ASP179 3.1 21.6 1.0 CG A:ASP183 3.2 22.2 1.0 PB A:GPP505 3.2 26.5 1.0 MN A:MN501 3.2 25.6 1.0 PA A:GPP505 3.4 23.4 1.0 OD1 A:ASP179 3.4 20.3 1.0 O3A A:GPP505 3.6 27.0 1.0 CB A:ASP183 3.6 22.7 1.0 O3B A:GPP505 3.9 31.2 1.0 NH2 A:ARG188 4.1 27.7 1.0 C1 A:GPP505 4.2 26.0 1.0 O A:ASP179 4.2 21.9 1.0 O A:HOH719 4.3 24.3 1.0 O1 A:GPP505 4.3 24.9 1.0 OD1 A:ASP183 4.3 24.9 1.0 OG A:SER185 4.3 26.2 1.0 CB A:ASP179 4.4 19.9 1.0 O2B A:GPP505 4.4 29.1 1.0 OD1 A:ASP180 4.5 24.1 1.0 OE1 A:GLU340 4.5 40.8 1.0 O2A A:GPP505 4.6 27.3 1.0 C A:ASP179 4.6 20.1 1.0 O A:HOH608 4.6 42.0 1.0 CE A:LYS342 4.9 33.8 1.0 NZ A:LYS342 4.9 35.2 1.0 O A:HOH631 5.0 21.3 1.0

Magnesium binding site 2 out of 3 in the PCIDS1_F315A in Complex with MG2+/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_F315A in Complex with MG2+/MN2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:24.3 occ:1.00 O A:HOH690 2.0 29.3 1.0 OD2 A:ASP319 2.0 27.2 1.0 O A:HOH616 2.1 25.9 1.0 O A:HOH689 2.1 29.4 1.0 O A:HOH709 2.1 31.4 1.0 O A:HOH630 2.1 31.3 1.0 CG A:ASP319 3.1 26.0 1.0 OD1 A:ASP319 3.5 31.9 1.0 O A:HOH679 3.9 35.3 1.0 NE2 A:GLN316 4.1 23.6 1.0 OD1 A:ASP323 4.1 27.3 1.0 OD2 A:ASP337 4.2 26.3 1.0 CB A:ASP319 4.3 23.6 1.0 OD1 A:ASP337 4.3 25.1 1.0 NZ A:LYS342 4.4 35.2 1.0 O A:HOH662 4.4 32.4 1.0 O A:ASP319 4.4 23.1 1.0 OD1 A:ASP320 4.4 22.4 1.0 C A:ASP319 4.6 23.1 1.0 O3B A:GPP505 4.6 31.2 1.0 O A:HOH652 4.7 39.0 1.0 CG A:ASP337 4.7 26.1 1.0 CG A:ASP323 4.8 25.3 1.0 CB A:ASP323 4.9 24.0 1.0 N A:ASP320 4.9 22.0 1.0 CA A:ASP319 5.0 21.5 1.0

Magnesium binding site 3 out of 3 in the PCIDS1_F315A in Complex with MG2+/MN2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PCIDS1_F315A in Complex with MG2+/MN2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:25.6 occ:1.00 OD2 B:ASP319 2.0 27.6 1.0 O B:HOH722 2.0 38.6 1.0 O B:HOH668 2.0 33.4 1.0 O B:HOH695 2.0 31.3 1.0 O B:HOH628 2.1 23.7 1.0 O B:HOH653 2.2 32.3 1.0 CG B:ASP319 3.1 23.1 1.0 OD1 B:ASP319 3.6 31.6 1.0 NE2 B:GLN316 4.1 20.0 1.0 OD2 B:ASP337 4.2 23.7 1.0 OD1 B:ASP323 4.2 28.9 1.0 CB B:ASP319 4.3 20.9 1.0 OD1 B:ASP337 4.3 25.7 1.0 O B:ASP319 4.4 20.8 1.0 O B:HOH646 4.4 32.4 1.0 OD1 B:ASP320 4.4 19.8 1.0 C B:ASP319 4.6 20.0 1.0 CG B:ASP337 4.7 23.3 1.0 CG B:ASP323 4.9 23.7 1.0 CB B:ASP323 4.9 22.1 1.0 N B:ASP320 5.0 18.7 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