Magnesium in PDB 8a7l: PCIDS1 in Complex with MG2+, Gpp, and Zol

All present enzymatic activity of PCIDS1 in Complex with MG2+, Gpp, and Zol:
2.5.1.1;

The structure of PCIDS1 in Complex with MG2+, Gpp, and Zol, PDB code: 8a7l 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 / 1.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.17, 86.17, 119.61, 90, 90, 120
R / Rfree (%)	14.7 / 18.2

The binding sites of Magnesium atom in the PCIDS1 in Complex with MG2+, Gpp, and Zol (pdb code 8a7l). 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 in Complex with MG2+, Gpp, and Zol, PDB code: 8a7l:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the PCIDS1 in Complex with MG2+, Gpp, and Zol


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 MG2+, Gpp, and Zol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:30.6 occ:1.00 O12 A:ZOL505 2.0 28.4 1.0 O15 A:ZOL505 2.1 28.7 1.0 O A:HOH613 2.2 25.8 1.0 OD2 A:ASP319 2.2 29.8 1.0 O A:HOH616 2.2 27.2 1.0 O A:HOH692 2.2 27.2 1.0 CG A:ASP319 3.1 27.9 1.0 P9 A:ZOL505 3.2 29.0 1.0 P14 A:ZOL505 3.4 29.1 1.0 O13 A:ZOL505 3.5 27.4 1.0 C8 A:ZOL505 3.6 28.0 1.0 OD1 A:ASP319 3.6 29.9 1.0 O A:HOH623 4.0 28.2 1.0 O A:HOH725 4.0 38.6 1.0 O11 A:ZOL505 4.0 26.6 1.0 O A:HOH737 4.1 30.8 1.0 O A:ASP319 4.1 27.6 1.0 OD2 A:ASP337 4.2 30.8 1.0 O16 A:ZOL505 4.2 29.1 1.0 OD1 A:ASP323 4.2 35.9 1.0 NE2 A:GLN316 4.3 26.9 1.0 O10 A:ZOL505 4.4 26.2 1.0 OD1 A:ASP337 4.4 33.5 1.0 NZ A:LYS333 4.4 30.4 1.0 CB A:ASP319 4.4 26.5 1.0 C A:ASP319 4.4 28.0 1.0 O17 A:ZOL505 4.5 28.5 1.0 OD1 A:ASP320 4.5 30.2 1.0 CB A:ASP323 4.6 32.2 1.0 CG A:ASP337 4.7 31.8 1.0 CG A:ASP323 4.8 35.1 1.0 MG A:MG502 4.8 29.9 1.0 N A:ASP320 4.9 27.9 1.0 O A:HOH717 4.9 30.8 1.0 CE A:LYS333 4.9 29.8 1.0 CA A:ASP319 5.0 27.0 1.0

Magnesium binding site 2 out of 3 in the PCIDS1 in Complex with MG2+, Gpp, and Zol


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 MG2+, Gpp, and Zol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:29.9 occ:1.00 O11 A:ZOL505 2.0 26.6 1.0 O A:HOH737 2.1 30.8 1.0 OD2 A:ASP179 2.1 28.5 1.0 O A:HOH618 2.1 26.7 1.0 O16 A:ZOL505 2.1 29.1 1.0 OD2 A:ASP183 2.2 31.8 1.0 CG A:ASP179 3.1 27.7 1.0 MG A:MG503 3.2 30.4 1.0 P9 A:ZOL505 3.2 29.0 1.0 CG A:ASP183 3.3 30.6 1.0 P14 A:ZOL505 3.3 29.1 1.0 OD1 A:ASP179 3.5 28.7 1.0 C8 A:ZOL505 3.7 28.0 1.0 CB A:ASP183 3.8 30.8 1.0 O A:HOH717 3.8 30.8 1.0 O15 A:ZOL505 3.9 28.7 1.0 O12 A:ZOL505 4.0 28.4 1.0 NH2 A:ARG188 4.0 28.4 1.0 C7 A:ZOL505 4.0 28.2 1.0 O A:ASP179 4.3 29.0 1.0 O A:HOH616 4.3 27.2 1.0 O A:HOH693 4.3 29.7 1.0 O10 A:ZOL505 4.4 26.2 1.0 CB A:ASP179 4.4 27.1 1.0 OD1 A:ASP183 4.4 30.2 1.0 OG A:SER185 4.5 33.8 1.0 O A:HOH651 4.5 33.6 1.0 O17 A:ZOL505 4.6 28.5 1.0 OD1 A:ASP180 4.6 31.4 1.0 O A:HOH654 4.6 33.9 1.0 C A:ASP179 4.6 28.8 1.0 MG A:MG501 4.8 30.6 1.0 O A:HOH607 4.9 31.7 1.0 O A:HOH606 4.9 29.3 1.0

Magnesium binding site 3 out of 3 in the PCIDS1 in Complex with MG2+, Gpp, and Zol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PCIDS1 in Complex with MG2+, Gpp, and Zol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:30.4 occ:1.00 O16 A:ZOL505 2.1 29.1 1.0 O A:HOH606 2.1 29.3 1.0 OD1 A:ASP179 2.1 28.7 1.0 O A:HOH693 2.1 29.7 1.0 O A:HOH607 2.1 31.7 1.0 OD2 A:ASP183 2.2 31.8 1.0 CG A:ASP179 3.0 27.7 1.0 CG A:ASP183 3.0 30.6 1.0 MG A:MG502 3.2 29.9 1.0 OD1 A:ASP183 3.2 30.2 1.0 P14 A:ZOL505 3.3 29.1 1.0 OD2 A:ASP179 3.3 28.5 1.0 O17 A:ZOL505 3.4 28.5 1.0 OD2 A:ASP250 3.9 32.3 1.0 OE1 A:GLN247 4.2 34.5 1.0 O A:HOH737 4.2 30.8 1.0 NE2 A:GLN247 4.2 35.9 1.0 O A:HOH623 4.2 28.2 1.0 NZ A:LYS342 4.2 37.6 1.0 O15 A:ZOL505 4.2 28.7 1.0 C19 A:ZOL505 4.3 28.4 1.0 CB A:ASP179 4.4 27.1 1.0 O A:HOH630 4.5 37.1 1.0 CB A:ASP183 4.5 30.8 1.0 CG A:ASP250 4.5 30.8 1.0 C8 A:ZOL505 4.6 28.0 1.0 O A:ASP179 4.6 29.0 1.0 C7 A:ZOL505 4.6 28.2 1.0 OD1 A:ASP250 4.6 32.7 1.0 CD A:GLN247 4.6 36.3 1.0 N15 A:ZOL505 4.7 29.2 1.0 O11 A:ZOL505 4.7 26.6 1.0 CA A:ASP179 4.9 27.5 1.0 NZ A:LYS276 4.9 28.7 1.0 O A:HOH618 4.9 26.7 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