Magnesium in PDB 8a70: PCIDS1 in Complex with MG2+ and Gpp

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

The structure of PCIDS1 in Complex with MG2+ and Gpp, PDB code: 8a70 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 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.32, 77.31, 88.68, 90, 101.43, 90
R / Rfree (%)	17.6 / 22.2

The binding sites of Magnesium atom in the PCIDS1 in Complex with MG2+ and Gpp (pdb code 8a70). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the PCIDS1 in Complex with MG2+ and Gpp, PDB code: 8a70:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the PCIDS1 in Complex with MG2+ 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 MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:44.1 occ:1.00 O A:HOH611 1.9 32.7 1.0 O A:HOH604 2.0 39.2 1.0 O A:HOH629 2.0 37.5 1.0 O A:HOH624 2.0 33.2 1.0 OD2 A:ASP319 2.2 35.0 1.0 O A:HOH650 2.4 41.0 1.0 CG A:ASP319 3.3 36.0 1.0 O A:HOH656 3.8 39.9 1.0 OD1 A:ASP319 3.8 37.2 1.0 OD1 A:ASP337 3.9 45.7 1.0 OD1 A:ASP323 4.0 40.5 1.0 OD2 A:ASP337 4.1 46.0 1.0 O A:ASP319 4.2 37.0 1.0 NE2 A:GLN316 4.3 36.5 1.0 OD1 A:ASP320 4.4 37.1 1.0 O A:HOH644 4.4 41.9 1.0 CG A:ASP337 4.4 44.1 1.0 O A:HOH636 4.5 42.8 1.0 NZ A:LYS342 4.5 51.7 1.0 CB A:ASP319 4.5 35.5 1.0 C A:ASP319 4.5 35.3 1.0 CG A:ASP323 4.7 39.5 1.0 CB A:ASP323 4.8 39.3 1.0 N A:ASP320 4.9 34.8 1.0 O3B A:GPP505 5.0 42.6 1.0

Magnesium binding site 2 out of 5 in the PCIDS1 in Complex with MG2+ 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 MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:41.2 occ:1.00 O1B A:GPP505 1.9 41.2 1.0 O A:HOH602 2.0 40.6 1.0 OD1 A:ASP183 2.1 36.6 1.0 O1A A:GPP505 2.2 43.1 1.0 OD1 A:ASP179 2.2 37.1 1.0 O A:HOH612 2.3 42.8 1.0 PB A:GPP505 3.1 42.6 1.0 CG A:ASP183 3.2 37.9 1.0 CG A:ASP179 3.2 37.0 1.0 PA A:GPP505 3.3 42.8 1.0 O3A A:GPP505 3.3 41.5 1.0 MG A:MG503 3.4 47.5 1.0 OD2 A:ASP179 3.5 36.0 1.0 CB A:ASP183 3.7 38.3 1.0 O3B A:GPP505 3.7 42.6 1.0 NH2 A:ARG188 3.8 43.3 1.0 O A:HOH660 4.0 40.9 1.0 O A:HOH651 4.1 50.5 1.0 C1 A:GPP505 4.2 41.1 1.0 O1 A:GPP505 4.2 41.0 1.0 OD2 A:ASP183 4.3 37.3 1.0 O2B A:GPP505 4.3 41.6 1.0 OG A:SER185 4.3 47.1 1.0 O2A A:GPP505 4.4 44.9 1.0 O A:HOH664 4.4 43.4 1.0 OE1 A:GLU340 4.5 58.2 1.0 O A:ASP179 4.5 36.5 1.0 CB A:ASP179 4.6 36.4 1.0 CE A:LYS342 4.6 49.6 1.0 O A:HOH614 4.7 43.6 1.0 NZ A:LYS342 4.7 51.7 1.0 MG A:MG504 4.8 43.5 1.0 OD1 A:ASP180 4.8 42.0 1.0 C A:ASP179 4.8 36.4 1.0 O A:HOH601 4.9 38.5 1.0 CZ A:ARG188 5.0 45.0 1.0

Magnesium binding site 3 out of 5 in the PCIDS1 in Complex with MG2+ 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 in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:47.5 occ:1.00 O A:HOH601 2.0 38.5 1.0 O A:HOH617 2.1 38.4 1.0 O1A A:GPP505 2.1 43.1 1.0 O A:HOH664 2.2 43.4 1.0 OD2 A:ASP179 2.3 36.0 1.0 OD1 A:ASP183 2.4 36.6 1.0 OD2 A:ASP183 3.1 37.3 1.0 CG A:ASP183 3.1 37.9 1.0 PA A:GPP505 3.3 42.8 1.0 CG A:ASP179 3.3 37.0 1.0 MG A:MG502 3.4 41.2 1.0 OD1 A:ASP179 3.6 37.1 1.0 O2A A:GPP505 3.7 44.9 1.0 OD2 A:ASP250 3.9 45.6 1.0 O1 A:GPP505 3.9 41.0 1.0 OE1 A:GLN247 4.0 36.8 1.0 NE2 A:GLN247 4.1 38.3 1.0 O A:HOH651 4.3 50.5 1.0 O A:HOH602 4.4 40.6 1.0 C1 A:GPP505 4.4 41.1 1.0 CD A:GLN247 4.5 35.8 1.0 CB A:ASP183 4.6 38.3 1.0 O3A A:GPP505 4.6 41.5 1.0 C2 A:GPP505 4.6 41.5 1.0 CB A:ASP179 4.7 36.4 1.0 O1B A:GPP505 4.8 41.2 1.0 O A:ASP179 4.9 36.5 1.0

Magnesium binding site 4 out of 5 in the PCIDS1 in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PCIDS1 in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:43.5 occ:1.00 O3B A:GPP505 2.1 42.6 1.0 O A:HOH648 2.2 46.1 1.0 O A:HOH644 2.2 41.9 1.0 O A:HOH660 2.2 40.9 1.0 O A:HOH669 2.2 47.2 1.0 O A:HOH654 2.3 49.5 1.0 PB A:GPP505 3.3 42.6 1.0 O1B A:GPP505 3.7 41.2 1.0 O A:HOH614 3.8 43.6 1.0 NZ A:LYS342 3.9 51.7 1.0 O A:HOH608 3.9 38.5 1.0 O2B A:GPP505 4.0 41.6 1.0 NZ A:LYS333 4.1 65.6 1.0 O A:HOH636 4.1 42.8 1.0 O A:HOH602 4.1 40.6 1.0 OE2 A:GLU340 4.1 51.2 1.0 O A:HOH624 4.3 33.2 1.0 OG1 A:THR336 4.5 51.2 1.0 O3A A:GPP505 4.6 41.5 1.0 CE A:LYS333 4.7 69.3 1.0 OE1 A:GLU340 4.8 58.2 1.0 MG A:MG502 4.8 41.2 1.0 O A:HOH612 4.8 42.8 1.0 CE A:LYS342 4.9 49.6 1.0 CD A:GLU340 4.9 51.2 1.0

Magnesium binding site 5 out of 5 in the PCIDS1 in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of PCIDS1 in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:45.8 occ:1.00 O B:HOH626 1.9 31.4 1.0 O B:HOH636 2.0 35.1 1.0 O B:HOH653 2.1 43.9 1.0 O B:HOH641 2.2 36.9 1.0 OD2 B:ASP319 2.2 31.5 1.0 O B:HOH630 2.2 43.0 1.0 CG B:ASP319 3.3 34.1 1.0 OD1 B:ASP319 3.9 36.5 1.0 NE2 B:GLN316 4.1 32.4 1.0 OD1 B:ASP337 4.2 44.3 1.0 OD2 B:ASP337 4.2 41.8 1.0 OD2 B:ASP323 4.3 41.9 1.0 OD1 B:ASP320 4.5 34.8 1.0 CB B:ASP319 4.5 33.6 1.0 CG B:ASP337 4.7 40.3 1.0 O B:ASP319 4.7 35.3 1.0 O B:HOH683 4.8 57.0 1.0 C B:ASP319 4.8 33.5 1.0 CG B:ASP323 5.0 37.6 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