Magnesium in PDB 8a7r: PCIDS1_I420A in Complex with MG2+ and Gpp

All present enzymatic activity of PCIDS1_I420A in Complex with MG2+ and Gpp:
2.5.1.1;

The structure of PCIDS1_I420A in Complex with MG2+ and Gpp, PDB code: 8a7r 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 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.01, 78.39, 88.02, 90, 101.85, 90
R / Rfree (%)	18.7 / 23

The binding sites of Magnesium atom in the PCIDS1_I420A in Complex with MG2+ and Gpp (pdb code 8a7r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the PCIDS1_I420A in Complex with MG2+ and Gpp, PDB code: 8a7r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the PCIDS1_I420A 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_I420A in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:29.0 occ:1.00 O A:HOH643 1.8 35.2 1.0 O A:HOH636 2.2 43.9 1.0 O A:HOH637 2.3 40.1 1.0 OD2 A:ASP179 2.4 29.3 1.0 OD2 A:ASP183 2.5 33.0 1.0 OD1 A:ASP183 2.6 35.3 1.0 O1A A:GPP505 2.7 42.0 1.0 CG A:ASP183 2.9 33.3 1.0 CG A:ASP179 3.3 31.5 1.0 MG A:MG502 3.5 22.7 1.0 OD1 A:ASP179 3.6 33.5 1.0 PA A:GPP505 3.8 43.9 1.0 O1 A:GPP505 4.1 45.7 1.0 OE1 A:GLN247 4.2 29.8 1.0 NE2 A:GLN247 4.3 30.3 1.0 O2A A:GPP505 4.3 45.9 1.0 CB A:ASP183 4.3 32.7 1.0 OD2 A:ASP250 4.4 37.9 1.0 NZ A:LYS342 4.5 60.2 1.0 CD A:GLN247 4.6 28.7 1.0 O A:ASP179 4.6 26.1 1.0 CB A:ASP179 4.7 30.9 1.0 O A:HOH620 4.7 34.2 1.0 C1 A:GPP505 4.8 42.1 1.0 CE A:LYS342 4.8 57.8 1.0 NZ A:LYS276 5.0 37.6 1.0

Magnesium binding site 2 out of 4 in the PCIDS1_I420A 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_I420A in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:22.7 occ:1.00 O A:HOH622 2.0 32.0 1.0 OD2 A:ASP183 2.1 33.0 1.0 O1A A:GPP505 2.1 42.0 1.0 O1B A:GPP505 2.1 40.2 1.0 OD1 A:ASP179 2.1 33.5 1.0 O A:HOH620 2.1 34.2 1.0 CG A:ASP179 3.2 31.5 1.0 CG A:ASP183 3.2 33.3 1.0 PA A:GPP505 3.4 43.9 1.0 PB A:GPP505 3.4 44.9 1.0 MG A:MG501 3.5 29.0 1.0 OD2 A:ASP179 3.6 29.3 1.0 NZ A:LYS342 3.6 60.2 1.0 O3A A:GPP505 3.6 43.5 1.0 CB A:ASP183 3.9 32.7 1.0 NH2 A:ARG188 3.9 34.2 1.0 O3B A:GPP505 4.1 47.9 1.0 OD1 A:ASP183 4.2 35.3 1.0 O1 A:GPP505 4.2 45.7 1.0 C1 A:GPP505 4.3 42.1 1.0 OG A:SER185 4.3 36.0 1.0 O A:HOH643 4.4 35.2 1.0 O A:ASP179 4.4 26.1 1.0 CB A:ASP179 4.5 30.9 1.0 OD1 A:ASP180 4.5 29.0 1.0 O2B A:GPP505 4.5 47.0 1.0 O2A A:GPP505 4.5 45.9 1.0 CE A:LYS342 4.7 57.8 1.0 C A:ASP179 4.7 29.4 1.0 OE1 A:GLU340 4.9 53.4 1.0

Magnesium binding site 3 out of 4 in the PCIDS1_I420A 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_I420A in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:37.1 occ:1.00 O A:HOH604 1.8 48.9 1.0 O A:HOH646 1.9 58.0 1.0 O A:HOH626 2.0 37.4 1.0 O A:HOH602 2.2 43.6 1.0 O A:HOH641 2.3 49.2 1.0 OD2 A:ASP319 2.4 41.4 1.0 O A:HOH601 3.1 51.1 1.0 CG A:ASP319 3.4 38.4 1.0 OD1 A:ASP319 3.7 41.0 1.0 O3B A:GPP505 3.9 47.9 1.0 OD1 A:ASP323 4.2 49.7 1.0 OD2 A:ASP337 4.3 43.9 1.0 OD1 A:ASP337 4.4 42.4 1.0 NE2 A:GLN316 4.5 34.7 1.0 O A:ASP319 4.5 35.7 1.0 CB A:ASP319 4.7 36.5 1.0 OD1 A:ASP320 4.8 29.9 1.0 CG A:ASP337 4.8 42.9 1.0 C A:ASP319 4.8 34.1 1.0 CG A:ASP323 4.9 43.4 1.0 CB A:ASP323 4.9 40.0 1.0

Magnesium binding site 4 out of 4 in the PCIDS1_I420A 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_I420A in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:24.5 occ:1.00 O B:HOH675 2.0 46.2 1.0 O B:HOH657 2.2 41.9 1.0 O B:HOH610 2.3 33.1 1.0 O B:HOH669 2.3 41.6 1.0 OD2 B:ASP319 2.3 31.5 1.0 O B:HOH613 2.4 32.1 1.0 O B:HOH630 2.5 42.7 1.0 CG B:ASP319 3.4 30.1 1.0 OD1 B:ASP319 3.8 31.5 1.0 OD2 B:ASP323 4.2 35.8 1.0 OD1 B:ASP337 4.5 36.3 1.0 OD2 B:ASP337 4.5 30.7 1.0 NE2 B:GLN316 4.6 26.8 1.0 CB B:ASP319 4.7 29.1 1.0 O B:ASP319 4.8 26.9 1.0 O B:HOH617 4.9 43.4 1.0 CG B:ASP337 4.9 32.1 1.0 CG B:ASP323 5.0 31.8 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