Manganese in PDB 8a73: PCIDS1 in Complex with MN2+ and Gpp

All present enzymatic activity of PCIDS1 in Complex with MN2+ and Gpp:
2.5.1.1;

The structure of PCIDS1 in Complex with MN2+ and Gpp, PDB code: 8a73 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 (°)	59.06, 78.41, 87.3, 90, 101.67, 90
R / Rfree (%)	16 / 19.5

The structure of PCIDS1 in Complex with MN2+ and Gpp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the PCIDS1 in Complex with MN2+ and Gpp (pdb code 8a73). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the PCIDS1 in Complex with MN2+ and Gpp, PDB code: 8a73:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the PCIDS1 in Complex with MN2+ and Gpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of PCIDS1 in Complex with MN2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:26.3 occ:1.00 O1B A:GPP505 2.1 26.1 1.0 OD1 A:ASP179 2.1 20.7 1.0 O A:HOH685 2.1 29.1 1.0 O A:HOH621 2.1 22.9 1.0 OD1 A:ASP183 2.2 21.2 1.0 O1A A:GPP505 2.2 21.4 1.0 CG A:ASP179 3.1 20.5 1.0 CG A:ASP183 3.2 23.3 1.0 MN A:MN503 3.3 23.6 1.0 PB A:GPP505 3.3 27.8 1.0 PA A:GPP505 3.4 25.5 1.0 OD2 A:ASP179 3.5 18.6 1.0 O3A A:GPP505 3.6 27.0 1.0 CB A:ASP183 3.7 22.9 1.0 O A:HOH729 3.9 49.3 1.0 O2B A:GPP505 4.0 31.2 1.0 NH1 A:ARG188 4.1 27.4 1.0 C1 A:GPP505 4.2 26.0 1.0 O A:ASP179 4.3 19.2 1.0 O1 A:GPP505 4.3 26.1 1.0 OG A:SER185 4.3 27.6 1.0 OD2 A:ASP183 4.4 23.3 1.0 O A:HOH736 4.4 23.4 1.0 CB A:ASP179 4.4 20.8 1.0 OD1 A:ASP180 4.5 24.3 1.0 O3B A:GPP505 4.5 30.9 1.0 C A:ASP179 4.6 19.1 1.0 OE1 A:GLU340 4.6 40.7 1.0 O2A A:GPP505 4.6 26.6 1.0 NZ A:LYS342 4.8 40.6 1.0 CE A:LYS342 4.8 38.1 1.0 O A:HOH618 4.9 46.9 1.0

Manganese binding site 2 out of 2 in the PCIDS1 in Complex with MN2+ and Gpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of PCIDS1 in Complex with MN2+ and Gpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:23.6 occ:1.00 O A:HOH682 2.1 23.9 1.0 OD2 A:ASP179 2.2 18.6 1.0 OD1 A:ASP183 2.2 21.2 1.0 O1A A:GPP505 2.2 21.4 1.0 O A:HOH736 2.2 23.4 1.0 O A:HOH629 2.2 22.1 1.0 CG A:ASP183 3.0 23.3 1.0 CG A:ASP179 3.1 20.5 1.0 OD2 A:ASP183 3.1 23.3 1.0 MN A:MN502 3.3 26.3 1.0 PA A:GPP505 3.4 25.5 1.0 OD1 A:ASP179 3.4 20.7 1.0 O1 A:GPP505 3.9 26.1 1.0 O2A A:GPP505 3.9 26.6 1.0 O A:HOH614 4.0 36.8 1.0 NE2 A:GLN247 4.0 20.9 1.0 OE1 A:GLN247 4.1 22.1 1.0 OD2 A:ASP250 4.3 31.1 1.0 O A:HOH685 4.4 29.1 1.0 C1 A:GPP505 4.4 26.0 1.0 O A:HOH618 4.4 46.9 1.0 CB A:ASP183 4.4 22.9 1.0 O A:HOH721 4.5 28.5 1.0 CD A:GLN247 4.5 20.7 1.0 CB A:ASP179 4.5 20.8 1.0 C2 A:GPP505 4.6 25.4 1.0 O A:ASP179 4.7 19.2 1.0 O3A A:GPP505 4.7 27.0 1.0 O1B A:GPP505 4.8 26.1 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