Magnesium in PDB 8a7a: PCIDS1 in Complex with MG2+ and 3-Br-Gpp

All present enzymatic activity of PCIDS1 in Complex with MG2+ and 3-Br-Gpp:
2.5.1.1;

The structure of PCIDS1 in Complex with MG2+ and 3-Br-Gpp, PDB code: 8a7a 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 (°)	59.46, 78.28, 88.88, 90, 101.54, 90
R / Rfree (%)	15.8 / 19.3

The structure of PCIDS1 in Complex with MG2+ and 3-Br-Gpp also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Magnesium atom in the PCIDS1 in Complex with MG2+ and 3-Br-Gpp (pdb code 8a7a). 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 3-Br-Gpp, PDB code: 8a7a:
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 3-Br-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 3-Br-Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:27.1 occ:1.00 O A:HOH737 2.0 31.7 1.0 O A:HOH613 2.1 29.4 1.0 O A:HOH634 2.1 29.0 1.0 O2A A:L7X505 2.1 28.6 1.0 OD1 A:ASP179 2.1 26.2 1.0 OD2 A:ASP183 2.2 27.5 1.0 CG A:ASP183 3.0 28.6 1.0 CG A:ASP179 3.1 26.6 1.0 OD1 A:ASP183 3.2 28.3 1.0 MG A:MG504 3.2 26.7 1.0 PA A:L7X505 3.4 29.4 1.0 OD2 A:ASP179 3.4 26.5 1.0 O1A A:L7X505 3.7 29.6 1.0 O1 A:L7X505 3.9 28.5 1.0 NE2 A:GLN247 4.0 27.0 1.0 O A:HOH624 4.1 37.3 1.0 OE1 A:GLN247 4.1 25.8 1.0 OD2 A:ASP250 4.2 31.1 1.0 O A:HOH741 4.3 32.0 1.0 C2 A:L7X505 4.3 32.1 1.0 C1 A:L7X505 4.3 29.7 1.0 O A:HOH748 4.4 34.1 1.0 CB A:ASP179 4.4 24.6 1.0 CB A:ASP183 4.4 28.3 1.0 CD A:GLN247 4.5 25.3 1.0 O3A A:L7X505 4.7 30.2 1.0 O3B A:L7X505 4.7 26.9 1.0 O A:ASP179 4.7 25.7 1.0 O A:HOH640 4.9 28.4 1.0 O A:HOH800 5.0 51.5 1.0 CA A:ASP179 5.0 24.1 1.0

Magnesium binding site 2 out of 5 in the PCIDS1 in Complex with MG2+ and 3-Br-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 3-Br-Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:29.3 occ:1.00 O A:HOH698 2.0 26.8 1.0 O A:HOH713 2.0 29.5 1.0 O A:HOH617 2.1 29.0 1.0 OD2 A:ASP319 2.1 28.8 1.0 O A:HOH687 2.1 32.0 1.0 O A:HOH746 2.2 32.6 1.0 CG A:ASP319 3.1 28.6 1.0 OD1 A:ASP319 3.5 32.0 1.0 O A:HOH742 4.0 34.4 1.0 OD1 A:ASP323 4.1 29.8 1.0 OD2 A:ASP337 4.1 31.0 1.0 O A:HOH702 4.2 36.4 1.0 NE2 A:GLN316 4.2 27.4 1.0 OD1 A:ASP337 4.2 31.8 1.0 O A:HOH619 4.3 35.8 1.0 O A:ASP319 4.4 26.7 1.0 CB A:ASP319 4.4 27.2 1.0 OD1 A:ASP320 4.5 26.0 1.0 NZ A:LYS342 4.5 36.5 1.0 O A:HOH657 4.5 36.9 1.0 O A:HOH659 4.5 38.4 1.0 C A:ASP319 4.6 26.2 1.0 CG A:ASP337 4.6 30.7 1.0 CG A:ASP323 4.8 29.2 1.0 O A:HOH610 4.9 51.3 1.0 CB A:ASP323 4.9 27.9 1.0 N A:ASP320 5.0 25.5 1.0

Magnesium binding site 3 out of 5 in the PCIDS1 in Complex with MG2+ and 3-Br-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 3-Br-Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:30.4 occ:1.00 O2B A:L7X505 1.9 30.3 1.0 O A:HOH811 2.0 35.5 1.0 O A:HOH729 2.1 31.9 1.0 O A:HOH666 2.1 33.2 1.0 O A:HOH702 2.1 36.4 1.0 O A:HOH727 2.1 38.3 1.0 PB A:L7X505 3.4 29.8 1.0 NZ A:LYS342 3.8 36.5 1.0 O A:HOH628 3.9 34.0 1.0 O3B A:L7X505 3.9 26.9 1.0 O A:HOH619 4.0 35.8 1.0 O1B A:L7X505 4.0 31.4 1.0 O A:HOH668 4.0 32.3 1.0 O A:HOH713 4.1 29.5 1.0 O A:HOH741 4.1 32.0 1.0 O A:HOH813 4.1 44.0 1.0 OE2 A:GLU340 4.3 39.3 1.0 OE1 A:GLU340 4.4 49.1 1.0 O3A A:L7X505 4.4 30.2 1.0 O A:HOH765 4.6 42.9 1.0 OG1 A:THR336 4.7 39.2 1.0 CD A:GLU340 4.8 40.2 1.0 CE A:LYS342 4.8 36.6 1.0

Magnesium binding site 4 out of 5 in the PCIDS1 in Complex with MG2+ and 3-Br-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 3-Br-Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:26.7 occ:1.00 O3B A:L7X505 2.0 26.9 1.0 OD2 A:ASP179 2.0 26.5 1.0 O A:HOH640 2.0 28.4 1.0 O A:HOH741 2.1 32.0 1.0 O2A A:L7X505 2.1 28.6 1.0 OD2 A:ASP183 2.1 27.5 1.0 CG A:ASP179 3.0 26.6 1.0 PB A:L7X505 3.2 29.8 1.0 CG A:ASP183 3.2 28.6 1.0 MG A:MG501 3.2 27.1 1.0 PA A:L7X505 3.4 29.4 1.0 OD1 A:ASP179 3.4 26.2 1.0 O3A A:L7X505 3.5 30.2 1.0 CB A:ASP183 3.6 28.3 1.0 NH2 A:ARG188 3.9 27.1 1.0 O A:HOH727 4.0 38.3 1.0 O2B A:L7X505 4.0 30.3 1.0 C1 A:L7X505 4.1 29.7 1.0 O1 A:L7X505 4.2 28.5 1.0 O A:HOH737 4.2 31.7 1.0 O A:HOH800 4.2 51.5 1.0 O A:ASP179 4.3 25.7 1.0 OD1 A:ASP183 4.3 28.3 1.0 OG A:SER185 4.3 33.7 1.0 CB A:ASP179 4.3 24.6 1.0 OD1 A:ASP180 4.5 28.3 1.0 O1A A:L7X505 4.5 29.6 1.0 O1B A:L7X505 4.5 31.4 1.0 C A:ASP179 4.6 24.3 1.0 O A:HOH668 4.8 32.3 1.0 O A:HOH613 4.9 29.4 1.0 CE A:LYS342 4.9 36.6 1.0 O A:HOH634 4.9 29.0 1.0 C2 A:L7X505 4.9 32.1 1.0 N A:ASP180 5.0 23.7 1.0

Magnesium binding site 5 out of 5 in the PCIDS1 in Complex with MG2+ and 3-Br-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 3-Br-Gpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:29.4 occ:1.00 O B:HOH634 2.0 27.4 1.0 OD2 B:ASP319 2.1 27.9 1.0 O B:HOH651 2.1 30.8 1.0 O B:HOH706 2.1 30.3 1.0 O B:HOH745 2.1 35.9 1.0 O B:HOH708 2.2 31.8 1.0 CG B:ASP319 3.1 27.8 1.0 OD1 B:ASP319 3.6 32.6 1.0 OD1 B:ASP323 4.0 30.0 1.0 NE2 B:GLN316 4.2 24.8 1.0 OD2 B:ASP337 4.2 26.9 1.0 OD1 B:ASP337 4.3 29.1 1.0 CB B:ASP319 4.4 26.8 1.0 O B:ASP319 4.4 24.8 1.0 OD1 B:ASP320 4.5 22.7 1.0 O B:HOH645 4.5 37.7 1.0 C B:ASP319 4.6 24.5 1.0 CG B:ASP337 4.7 27.1 1.0 CG B:ASP323 4.7 27.8 1.0 CB B:ASP323 4.9 27.0 1.0 N B:ASP320 4.9 22.3 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