Manganese in PDB 8a6z: PCIDS1 in Complex with MN2+ and Ipp

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

The structure of PCIDS1 in Complex with MN2+ and Ipp, PDB code: 8a6z 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 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.94, 186.74, 213.29, 90, 90, 90
R / Rfree (%)	22.4 / 26.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Manganese atom in the PCIDS1 in Complex with MN2+ and Ipp (pdb code 8a6z). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 18 binding sites of Manganese where determined in the PCIDS1 in Complex with MN2+ and Ipp, PDB code: 8a6z:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


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 Ipp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:36.7 occ:1.00 O1B A:IPE505 2.1 30.1 1.0 OD2 A:ASP319 2.1 28.1 1.0 O A:HOH601 2.3 27.6 1.0 O A:HOH607 2.4 28.0 1.0 O2A A:IPE505 2.8 23.3 1.0 CG A:ASP319 3.3 27.6 1.0 PB A:IPE505 3.4 28.5 1.0 O3A A:IPE505 3.6 26.6 1.0 PA A:IPE505 3.6 25.7 1.0 OD1 A:ASP319 4.0 27.4 1.0 NE2 A:GLN316 4.0 23.4 1.0 OD2 A:ASP337 4.1 28.0 1.0 OD1 A:ASP337 4.1 26.3 1.0 OD1 A:ASP323 4.2 26.1 1.0 O1A A:IPE505 4.2 25.2 1.0 O A:ASP319 4.3 30.9 1.0 CB A:ASP319 4.3 26.8 1.0 O3B A:IPE505 4.3 29.3 1.0 OD1 A:ASP320 4.3 24.9 1.0 O A:HOH637 4.3 41.8 1.0 O2B A:IPE505 4.4 29.5 1.0 C A:ASP319 4.4 26.1 1.0 CG A:ASP337 4.5 27.6 1.0 CB A:ASP323 4.6 27.3 1.0 CG A:ASP323 4.8 27.5 1.0 N A:ASP320 4.8 24.8 1.0 NZ A:LYS333 4.9 29.0 1.0 CA A:ASP319 5.0 27.7 1.0 C5 A:IPE504 5.0 24.1 1.0 O1 A:IPE505 5.0 29.2 1.0

Manganese binding site 2 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


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 Ipp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:35.7 occ:1.00 OD2 A:ASP179 2.0 30.2 1.0 O A:HOH605 2.0 31.4 1.0 O A:HOH637 2.1 41.8 1.0 O1A A:IPE505 2.1 25.2 1.0 O3B A:IPE505 2.1 29.3 1.0 OD2 A:ASP183 2.3 23.8 1.0 CG A:ASP179 3.0 28.6 1.0 PB A:IPE505 3.2 28.5 1.0 MN A:MN503 3.3 30.0 1.0 PA A:IPE505 3.3 25.7 1.0 O3A A:IPE505 3.4 26.6 1.0 CG A:ASP183 3.4 25.0 1.0 OD1 A:ASP179 3.5 26.4 1.0 CB A:ASP183 3.8 25.9 1.0 O1B A:IPE505 3.9 30.1 1.0 O A:HOH607 4.1 28.0 1.0 NH2 A:ARG188 4.3 27.4 1.0 CB A:ASP179 4.3 28.8 1.0 O1 A:IPE505 4.3 29.2 1.0 O2A A:IPE505 4.3 23.3 1.0 O A:ASP179 4.4 30.0 1.0 O2B A:IPE505 4.5 29.5 1.0 OG A:SER185 4.5 27.1 1.0 OD1 A:ASP183 4.5 25.6 1.0 OD1 A:ASP180 4.6 36.4 1.0 C A:ASP179 4.6 28.4 1.0 O A:HOH644 4.7 38.1 1.0 O A:HOH618 4.9 37.9 1.0

Manganese binding site 3 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of PCIDS1 in Complex with MN2+ and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:30.0 occ:1.00 OD2 A:ASP183 2.1 23.8 1.0 O A:HOH618 2.3 37.9 1.0 O1A A:IPE505 2.3 25.2 1.0 OD1 A:ASP179 2.3 26.4 1.0 O A:HOH606 2.3 27.9 1.0 O A:HOH644 2.4 38.1 1.0 CG A:ASP183 2.9 25.0 1.0 CG A:ASP179 3.1 28.6 1.0 OD1 A:ASP183 3.1 25.6 1.0 MN A:MN502 3.3 35.7 1.0 OD2 A:ASP179 3.3 30.2 1.0 PA A:IPE505 3.3 25.7 1.0 O1 A:IPE505 3.5 29.2 1.0 O A:HOH637 3.9 41.8 1.0 O2A A:IPE505 4.0 23.3 1.0 OD2 A:ASP250 4.1 29.5 1.0 NZ A:LYS276 4.1 27.1 1.0 NZ A:LYS342 4.2 37.0 1.0 NE2 A:GLN247 4.2 27.5 1.0 OE1 A:GLN247 4.3 24.2 1.0 CB A:ASP183 4.3 25.9 1.0 O3A A:IPE505 4.5 26.6 1.0 CE A:LYS342 4.5 34.2 1.0 CB A:ASP179 4.5 28.8 1.0 CG A:ASP250 4.7 28.5 1.0 CD A:GLN247 4.7 27.9 1.0 O A:HOH605 4.8 31.4 1.0 C1 A:IPE505 4.8 35.9 1.0 OD1 A:ASP250 4.8 30.3 1.0 O A:ASP179 4.8 30.0 1.0 O3B A:IPE505 4.9 29.3 1.0

Manganese binding site 4 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of PCIDS1 in Complex with MN2+ and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:36.8 occ:1.00 O1B B:IPE506 2.0 30.1 1.0 OD2 B:ASP319 2.2 31.2 1.0 O B:HOH604 2.4 36.3 1.0 O B:HOH612 2.6 35.6 1.0 O2A B:IPE506 2.9 29.4 1.0 O B:HOH610 3.2 29.4 1.0 CG B:ASP319 3.3 31.7 1.0 PB B:IPE506 3.4 27.7 1.0 O3A B:IPE506 3.6 29.3 1.0 PA B:IPE506 3.7 28.8 1.0 O B:HOH626 3.8 41.7 1.0 OD1 B:ASP319 3.9 32.7 1.0 O B:ASP319 3.9 30.0 1.0 OD1 B:ASP323 3.9 39.9 1.0 OD2 B:ASP337 4.0 35.1 1.0 NZ B:LYS333 4.1 32.0 1.0 OD1 B:ASP337 4.2 36.5 1.0 CE B:LYS333 4.3 32.9 1.0 NE2 B:GLN316 4.3 26.7 1.0 O1A B:IPE506 4.3 28.4 1.0 O2B B:IPE506 4.3 28.5 1.0 CB B:ASP319 4.4 30.3 1.0 O3B B:IPE506 4.4 31.3 1.0 O B:HOH644 4.4 30.1 1.0 C B:ASP319 4.4 27.4 1.0 CG B:ASP337 4.5 34.3 1.0 CB B:ASP323 4.5 32.2 1.0 OD1 B:ASP320 4.6 25.8 1.0 CG B:ASP323 4.6 34.2 1.0 C5 B:IPE505 4.9 25.5 1.0 N B:ASP320 4.9 26.4 1.0 CA B:ASP319 5.0 30.0 1.0

Manganese binding site 5 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of PCIDS1 in Complex with MN2+ and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:40.6 occ:1.00 O B:HOH602 2.0 27.4 1.0 O1A B:IPE506 2.0 28.4 1.0 OD2 B:ASP179 2.1 27.2 1.0 O3B B:IPE506 2.2 31.3 1.0 OD2 B:ASP183 2.3 29.0 1.0 O B:HOH644 2.6 30.1 1.0 CG B:ASP179 3.1 27.1 1.0 PA B:IPE506 3.3 28.8 1.0 PB B:IPE506 3.3 27.7 1.0 CG B:ASP183 3.4 30.4 1.0 O3A B:IPE506 3.5 29.3 1.0 OD1 B:ASP179 3.6 24.8 1.0 MN B:MN503 3.7 42.1 1.0 CB B:ASP183 3.7 30.6 1.0 O1B B:IPE506 4.0 30.1 1.0 O B:ASP179 4.1 24.3 1.0 O B:HOH626 4.2 41.7 1.0 NH2 B:ARG188 4.2 32.5 1.0 OG B:SER185 4.2 33.5 1.0 O1 B:IPE506 4.3 29.2 1.0 OD1 B:ASP180 4.3 23.6 1.0 CB B:ASP179 4.4 26.7 1.0 O2A B:IPE506 4.4 29.4 1.0 OD1 B:ASP183 4.5 32.0 1.0 C B:ASP179 4.5 24.1 1.0 O2B B:IPE506 4.6 28.5 1.0 O B:HOH617 4.7 34.1 1.0 O B:HOH610 4.9 29.4 1.0 O B:HOH605 5.0 36.1 1.0

Manganese binding site 6 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of PCIDS1 in Complex with MN2+ and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:42.1 occ:1.00 O B:HOH616 2.1 51.5 1.0 OD1 B:ASP179 2.3 24.8 1.0 O1A B:IPE506 2.5 28.4 1.0 O B:HOH601 2.5 29.0 1.0 O B:HOH629 2.6 38.4 1.0 OD2 B:ASP183 2.6 29.0 1.0 O1 B:IPE506 3.2 29.2 1.0 PA B:IPE506 3.3 28.8 1.0 CG B:ASP179 3.3 27.1 1.0 CG B:ASP183 3.5 30.4 1.0 OD1 B:ASP183 3.6 32.0 1.0 OD2 B:ASP179 3.6 27.2 1.0 MN B:MN502 3.7 40.6 1.0 O2A B:IPE506 3.9 29.4 1.0 OD2 B:ASP250 3.9 37.6 1.0 OE1 B:GLN247 4.0 31.2 1.0 NE2 B:GLN247 4.1 26.4 1.0 NZ B:LYS276 4.3 31.0 1.0 O B:HOH610 4.3 29.4 1.0 CD B:GLN247 4.4 29.2 1.0 CG B:ASP250 4.5 33.6 1.0 C1 B:IPE506 4.5 30.3 1.0 O B:HOH644 4.6 30.1 1.0 NZ B:LYS342 4.6 40.3 1.0 OD1 B:ASP250 4.6 34.6 1.0 O3A B:IPE506 4.6 29.3 1.0 CB B:ASP179 4.6 26.7 1.0 CE B:LYS342 4.7 37.4 1.0 CB B:ASP183 4.9 30.6 1.0 O B:ASP179 5.0 24.3 1.0

Manganese binding site 7 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of PCIDS1 in Complex with MN2+ and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn501 b:60.5 occ:1.00 O C:HOH618 2.1 47.6 1.0 O C:HOH602 2.1 54.3 1.0 O2B C:IPE506 2.1 33.5 1.0 OD2 C:ASP319 2.1 53.4 1.0 O1A C:IPE506 2.3 43.1 1.0 O C:HOH615 2.4 81.2 1.0 CG C:ASP319 3.3 48.9 1.0 PB C:IPE506 3.5 34.5 1.0 PA C:IPE506 3.6 37.8 1.0 O3A C:IPE506 3.9 35.0 1.0 OD1 C:ASP323 3.9 40.3 1.0 OD1 C:ASP319 4.0 48.9 1.0 OD2 C:ASP337 4.0 34.6 1.0 O C:ASP319 4.1 38.9 1.0 O1B C:IPE506 4.2 33.9 1.0 NE2 C:GLN316 4.2 37.2 1.0 OD1 C:ASP337 4.3 32.0 1.0 CB C:ASP319 4.4 47.3 1.0 C C:ASP319 4.4 41.3 1.0 O1 C:IPE506 4.5 43.5 1.0 OD1 C:ASP320 4.5 38.3 1.0 CB C:ASP323 4.5 44.2 1.0 CG C:ASP337 4.6 35.8 1.0 NZ C:LYS333 4.6 30.1 1.0 O3B C:IPE506 4.6 36.7 1.0 CG C:ASP323 4.6 42.1 1.0 O2A C:IPE506 4.7 42.9 1.0 N C:ASP320 4.9 39.2 1.0 C5 C:IPE505 5.0 35.0 1.0

Manganese binding site 8 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of PCIDS1 in Complex with MN2+ and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn502 b:54.8 occ:1.00 OD2 C:ASP183 2.2 35.0 1.0 OD2 C:ASP179 2.3 37.4 1.0 O C:HOH603 2.5 43.5 1.0 O2A C:IPE506 2.5 42.9 1.0 O1B C:IPE506 2.6 33.9 1.0 O3A C:IPE506 3.1 35.0 1.0 PA C:IPE506 3.2 37.8 1.0 CG C:ASP179 3.3 35.0 1.0 CG C:ASP183 3.3 34.5 1.0 MN C:MN503 3.4 55.8 1.0 PB C:IPE506 3.4 34.5 1.0 O C:HOH627 3.5 50.8 1.0 OD1 C:ASP179 3.7 36.0 1.0 CB C:ASP183 3.8 35.5 1.0 O1A C:IPE506 3.8 43.1 1.0 O C:HOH618 3.9 47.6 1.0 O C:HOH619 3.9 37.1 1.0 O2B C:IPE506 4.1 33.5 1.0 OG C:SER185 4.3 38.6 1.0 OD1 C:ASP183 4.4 34.4 1.0 NH2 C:ARG188 4.4 24.9 1.0 OD1 C:ASP180 4.5 27.6 1.0 CB C:ASP179 4.5 36.4 1.0 O C:ASP179 4.6 35.6 1.0 O3B C:IPE506 4.6 36.7 1.0 O1 C:IPE506 4.7 43.5 1.0 O C:HOH610 4.7 52.6 1.0 C C:ASP179 4.8 34.7 1.0

Manganese binding site 9 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of PCIDS1 in Complex with MN2+ and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn503 b:55.8 occ:1.00 O2A C:IPE506 2.0 42.9 1.0 OD1 C:ASP179 2.1 36.0 1.0 OD2 C:ASP183 2.2 35.0 1.0 O C:HOH610 2.2 52.6 1.0 O C:HOH604 2.3 55.5 1.0 O C:HOH605 2.3 52.8 1.0 CG C:ASP179 3.0 35.0 1.0 CG C:ASP183 3.0 34.5 1.0 OD1 C:ASP183 3.1 34.4 1.0 OD2 C:ASP179 3.2 37.4 1.0 MN C:MN502 3.4 54.8 1.0 PA C:IPE506 3.4 37.8 1.0 C1 C:IPE506 3.8 44.7 1.0 O1 C:IPE506 4.0 43.5 1.0 O C:HOH627 4.1 50.8 1.0 NE2 C:GLN247 4.2 36.0 1.0 OD2 C:ASP250 4.2 41.7 1.0 O1A C:IPE506 4.3 43.1 1.0 CB C:ASP179 4.4 36.4 1.0 O3A C:IPE506 4.4 35.0 1.0 CB C:ASP183 4.4 35.5 1.0 OE1 C:GLN247 4.5 32.9 1.0 NZ C:LYS342 4.6 36.6 1.0 CG C:ASP250 4.7 38.9 1.0 CE C:LYS342 4.7 38.0 1.0 OD1 C:ASP250 4.7 38.9 1.0 CD C:GLN247 4.7 35.0 1.0 O C:ASP179 4.8 35.6 1.0 NZ C:LYS276 4.8 42.8 1.0 CA C:ASP179 5.0 35.2 1.0

Manganese binding site 10 out of 18 in the PCIDS1 in Complex with MN2+ and Ipp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of PCIDS1 in Complex with MN2+ and Ipp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:36.4 occ:1.00 O2B D:IPE505 1.9 31.3 1.0 OD2 D:ASP319 2.2 32.9 1.0 O D:HOH615 2.3 29.1 1.0 O D:HOH605 2.4 39.8 1.0 O D:HOH626 2.4 35.7 1.0 O1A D:IPE505 2.4 37.8 1.0 PB D:IPE505 3.1 31.7 1.0 O3A D:IPE505 3.2 32.0 1.0 CG D:ASP319 3.2 31.7 1.0 PA D:IPE505 3.4 34.7 1.0 OD1 D:ASP319 3.8 33.9 1.0 O1B D:IPE505 3.9 31.2 1.0 OD2 D:ASP337 4.2 23.0 1.0 NZ D:LYS333 4.3 27.0 1.0 O3B D:IPE505 4.3 31.3 1.0 NE2 D:GLN316 4.3 24.9 1.0 O D:ASP319 4.4 32.5 1.0 O2A D:IPE505 4.4 35.7 1.0 CB D:ASP319 4.4 30.8 1.0 OD1 D:ASP337 4.5 30.9 1.0 OD1 D:ASP323 4.5 28.1 1.0 O1 D:IPE505 4.5 33.7 1.0 O D:HOH641 4.5 46.3 1.0 C D:ASP319 4.6 29.1 1.0 OD1 D:ASP320 4.7 25.1 1.0 O D:HOH624 4.7 49.9 1.0 CE D:LYS333 4.7 27.8 1.0 MN D:MN502 4.8 30.8 1.0 C5 D:IPE504 4.8 23.5 1.0 CB D:ASP323 4.8 27.2 1.0 CG D:ASP337 4.8 27.2 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