Magnesium in PDB 8a7u: PCIDS1_F315D in Complex with MG2+ and Gpp

All present enzymatic activity of PCIDS1_F315D in Complex with MG2+ and Gpp:
2.5.1.1;

The structure of PCIDS1_F315D in Complex with MG2+ and Gpp, PDB code: 8a7u was solved by F.Ecker, F.Boland, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.97, 78.12, 88.13, 90, 101.44, 90
R / Rfree (%)	14.6 / 18.7

The binding sites of Magnesium atom in the PCIDS1_F315D in Complex with MG2+ and Gpp (pdb code 8a7u). 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_F315D in Complex with MG2+ and Gpp, PDB code: 8a7u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the PCIDS1_F315D 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_F315D in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:20.1 occ:1.00 O A:HOH655 2.1 21.0 1.0 O1A A:GPP506 2.1 19.6 1.0 O A:HOH740 2.1 23.0 1.0 O A:HOH634 2.1 22.3 1.0 OD1 A:ASP179 2.1 19.6 1.0 OD2 A:ASP183 2.1 20.8 1.0 CG A:ASP183 3.0 20.3 1.0 CG A:ASP179 3.0 20.5 1.0 MG A:MG502 3.2 20.4 1.0 OD1 A:ASP183 3.2 21.5 1.0 PA A:GPP506 3.3 21.5 1.0 OD2 A:ASP179 3.4 20.4 1.0 O2A A:GPP506 3.8 21.9 1.0 O1 A:GPP506 3.9 21.4 1.0 NE2 A:GLN247 4.0 21.2 1.0 OE1 A:GLN247 4.1 20.8 1.0 O A:HOH618 4.1 28.9 1.0 O A:HOH722 4.2 21.1 1.0 OD2 A:ASP250 4.3 24.8 1.0 C1 A:GPP506 4.3 24.2 1.0 O A:HOH735 4.3 26.1 1.0 CB A:ASP179 4.4 18.5 1.0 CB A:ASP183 4.4 20.9 1.0 CD A:GLN247 4.4 20.3 1.0 C2 A:GPP506 4.5 22.0 1.0 O3A A:GPP506 4.6 22.7 1.0 O1B A:GPP506 4.6 20.0 1.0 O A:ASP179 4.7 19.4 1.0 O A:HOH643 4.9 21.5 1.0 CA A:ASP179 5.0 18.2 1.0

Magnesium binding site 2 out of 5 in the PCIDS1_F315D 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_F315D in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.4 occ:1.00 O A:HOH722 2.0 21.1 1.0 O1B A:GPP506 2.0 20.0 1.0 O A:HOH643 2.1 21.5 1.0 OD2 A:ASP179 2.1 20.4 1.0 OD2 A:ASP183 2.1 20.8 1.0 O1A A:GPP506 2.2 19.6 1.0 CG A:ASP179 3.0 20.5 1.0 CG A:ASP183 3.1 20.3 1.0 MG A:MG501 3.2 20.1 1.0 PB A:GPP506 3.3 21.5 1.0 PA A:GPP506 3.4 21.5 1.0 OD1 A:ASP179 3.4 19.6 1.0 CB A:ASP183 3.5 20.9 1.0 O3A A:GPP506 3.5 22.7 1.0 NH2 A:ARG188 3.9 21.7 1.0 O3B A:GPP506 3.9 20.8 1.0 O A:HOH708 4.1 25.1 1.0 C1 A:GPP506 4.2 24.2 1.0 O A:ASP179 4.2 19.4 1.0 O A:HOH740 4.2 23.0 1.0 O1 A:GPP506 4.3 21.4 1.0 OD1 A:ASP183 4.3 21.5 1.0 OG A:SER185 4.3 23.5 1.0 OD1 A:ASP180 4.4 21.2 1.0 CB A:ASP179 4.4 18.5 1.0 O2B A:GPP506 4.5 22.6 1.0 O2A A:GPP506 4.5 21.9 1.0 C A:ASP179 4.5 18.7 1.0 O A:HOH657 4.8 23.7 1.0 O A:HOH634 4.8 22.3 1.0 O A:HOH655 4.9 21.0 1.0

Magnesium binding site 3 out of 5 in the PCIDS1_F315D 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_F315D in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:23.3 occ:1.00 OD2 A:ASP319 2.0 22.3 1.0 O A:HOH617 2.0 22.1 1.0 O A:HOH730 2.1 24.5 1.0 O A:HOH715 2.1 21.4 1.0 O A:HOH700 2.1 23.8 1.0 O A:HOH653 2.1 25.5 1.0 CG A:ASP319 3.0 24.3 1.0 OD1 A:ASP319 3.4 30.2 1.0 NE2 A:GLN316 4.0 21.4 1.0 O A:HOH702 4.1 25.9 1.0 OD1 A:ASP323 4.1 24.5 1.0 OD2 A:ASP337 4.2 22.9 1.0 O A:HOH731 4.2 25.6 1.0 O A:ASP319 4.3 22.1 1.0 O A:HOH628 4.3 25.7 1.0 CB A:ASP319 4.3 23.4 1.0 OD1 A:ASP337 4.3 24.3 1.0 OD1 A:ASP320 4.4 21.0 1.0 O A:HOH656 4.5 33.0 1.0 C A:ASP319 4.5 21.7 1.0 NZ A:LYS342 4.6 25.2 1.0 O A:HOH623 4.6 29.7 1.0 CG A:ASP337 4.7 23.4 1.0 CG A:ASP323 4.8 23.7 1.0 N A:ASP320 4.9 21.2 1.0 CA A:ASP319 4.9 20.6 1.0 CB A:ASP323 5.0 22.4 1.0

Magnesium binding site 4 out of 5 in the PCIDS1_F315D 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_F315D in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:23.3 occ:1.00 O3B A:GPP506 2.0 20.8 1.0 O A:HOH708 2.1 25.1 1.0 O A:HOH612 2.1 26.0 1.0 O A:HOH745 2.1 24.8 1.0 O A:HOH772 2.1 29.1 1.0 O A:HOH731 2.2 25.6 1.0 PB A:GPP506 3.3 21.5 1.0 O1B A:GPP506 3.9 20.0 1.0 O A:HOH663 3.9 27.3 1.0 O A:HOH628 3.9 25.7 1.0 O A:HOH700 3.9 23.8 1.0 NZ A:LYS342 4.0 25.2 1.0 O A:HOH657 4.0 23.7 1.0 O2B A:GPP506 4.0 22.6 1.0 O A:HOH777 4.1 39.9 1.0 O A:HOH722 4.1 21.1 1.0 OE2 A:GLU340 4.2 29.3 1.0 OE1 A:GLU340 4.3 45.0 1.0 O3A A:GPP506 4.5 22.7 1.0 O A:HOH757 4.6 34.8 1.0 OG1 A:THR336 4.7 31.5 1.0 CD A:GLU340 4.7 31.7 1.0 CE A:LYS342 4.9 25.7 1.0

Magnesium binding site 5 out of 5 in the PCIDS1_F315D 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_F315D in Complex with MG2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:25.0 occ:1.00 O B:HOH631 2.0 28.7 1.0 OD2 B:ASP319 2.0 25.3 1.0 O B:HOH625 2.0 22.6 1.0 O B:HOH751 2.0 30.3 1.0 O B:HOH722 2.1 26.4 1.0 O B:HOH654 2.1 27.4 1.0 CG B:ASP319 3.1 23.5 1.0 OD1 B:ASP319 3.5 29.8 1.0 OD1 B:ASP323 4.1 27.4 1.0 NE2 B:GLN316 4.1 21.8 1.0 OD2 B:ASP337 4.2 23.7 1.0 OD1 B:ASP337 4.2 25.7 1.0 CB B:ASP319 4.3 19.9 1.0 O B:HOH650 4.4 31.7 1.0 O B:ASP319 4.4 22.4 1.0 OD1 B:ASP320 4.5 20.7 1.0 C B:ASP319 4.6 20.6 1.0 CG B:ASP337 4.6 24.1 1.0 CG B:ASP323 4.7 24.5 1.0 CB B:ASP323 4.9 22.8 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