Manganese in PDB 2onh: Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp)

The structure of Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp), PDB code: 2onh was solved by D.C.Hyatt, B.Youn, R.Croteau, C.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.70
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	198.660, 198.660, 122.670, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.4

The structure of Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp) also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp) (pdb code 2onh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp), PDB code: 2onh:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:61.0 occ:1.00 O3B A:F3P600 2.2 55.9 1.0 OD2 A:ASP352 2.4 51.2 1.0 OD1 A:ASP356 2.7 51.3 1.0 PB A:F3P600 3.5 58.8 1.0 CG A:ASP352 3.6 46.6 1.0 O1B A:F3P600 3.6 55.7 1.0 CG A:ASP356 3.7 52.6 1.0 CE1 A:TYR427 3.7 51.2 1.0 OE2 A:GLU430 3.8 43.7 1.0 MN A:MN602 3.9 52.4 1.0 CD1 A:TYR427 3.9 46.7 1.0 CB A:ASP356 3.9 51.7 1.0 OD1 A:ASP352 4.1 46.2 1.0 O3A A:F3P600 4.5 64.2 1.0 O2B A:F3P600 4.6 49.2 1.0 OD2 A:ASP509 4.6 74.1 1.0 OD1 A:ASP509 4.8 71.2 1.0 CZ A:TYR427 4.8 47.8 1.0 OD2 A:ASP356 4.8 53.2 1.0 CB A:ASP352 4.8 43.4 1.0 O A:ASP352 4.8 52.4 1.0 CD A:GLU430 5.0 44.2 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:52.4 occ:1.00 OD1 A:ASP356 2.2 51.3 1.0 O3B A:F3P600 2.5 55.9 1.0 OD1 A:ASP352 2.6 46.2 1.0 O2A A:F3P600 2.7 60.3 1.0 CG A:ASP356 3.1 52.6 1.0 CG A:ASP352 3.4 46.6 1.0 OD2 A:ASP356 3.4 53.2 1.0 O3A A:F3P600 3.4 64.2 1.0 OD2 A:ASP352 3.5 51.2 1.0 PB A:F3P600 3.5 58.8 1.0 PA A:F3P600 3.6 67.5 1.0 MN A:MN601 3.9 61.0 1.0 NH2 A:ARG315 4.0 49.4 1.0 OD1 A:ASP509 4.0 71.2 1.0 O2B A:F3P600 4.1 49.2 1.0 CB A:ASP356 4.5 51.7 1.0 OD1 A:ASP353 4.5 48.4 1.0 NH1 A:ARG507 4.5 80.9 1.0 O1A A:F3P600 4.7 62.5 1.0 O1 A:F3P600 4.8 61.6 1.0 CB A:ASP352 4.8 43.4 1.0 O1B A:F3P600 4.8 55.7 1.0 CZ A:ARG315 4.8 55.5 1.0 OH A:TYR63 4.9 91.7 1.0 NH2 A:ARG507 5.0 76.9 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:54.1 occ:1.00 O1A A:F3P600 2.3 62.5 1.0 O2B A:F3P600 2.3 49.2 1.0 OD2 A:ASP496 2.6 40.8 1.0 OD1 A:ASP496 3.0 43.1 1.0 CG2 A:THR500 3.1 83.2 1.0 CG A:ASP496 3.2 39.5 1.0 CB A:THR500 3.4 81.7 1.0 PA A:F3P600 3.6 67.5 1.0 O A:THR500 3.6 85.2 1.0 O2A A:F3P600 3.8 60.3 1.0 PB A:F3P600 3.8 58.8 1.0 NH2 A:ARG493 3.9 49.0 1.0 O3A A:F3P600 4.2 64.2 1.0 OD2 A:ASP497 4.2 51.0 1.0 OG1 A:THR500 4.3 79.5 1.0 CE A:LYS512 4.3 47.4 1.0 C A:THR500 4.4 82.8 1.0 CD A:LYS512 4.5 46.3 1.0 NZ A:LYS512 4.5 42.3 1.0 CA A:THR500 4.6 81.1 1.0 CB A:ASP496 4.7 38.2 1.0 O A:ASP496 4.7 39.6 1.0 O3B A:F3P600 4.7 55.9 1.0 C A:ASP496 4.7 38.7 1.0 O1B A:F3P600 4.8 55.7 1.0 O1 A:F3P600 4.8 61.6 1.0 N A:ASP497 4.8 43.7 1.0 CA A:ASP497 4.9 44.7 1.0 C10 A:F3P600 5.0 55.6 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1601 b:49.5 occ:1.00 OD2 B:ASP352 2.5 51.6 1.0 OD1 B:ASP356 2.6 51.9 1.0 O3B B:F3P1600 3.1 50.3 1.0 O1B B:F3P1600 3.2 51.3 1.0 CG B:ASP356 3.6 56.2 1.0 CG B:ASP352 3.7 45.9 1.0 OE2 B:GLU430 3.7 50.6 1.0 PB B:F3P1600 3.8 54.3 1.0 MN B:MN1602 3.8 70.4 1.0 CE1 B:TYR427 3.8 48.7 1.0 CB B:ASP356 3.9 52.8 1.0 CD1 B:TYR427 3.9 43.2 1.0 OD1 B:ASP352 4.1 47.8 1.0 OD1 B:ASP509 4.5 53.5 1.0 OD2 B:ASP356 4.6 58.0 1.0 O3A B:F3P1600 4.7 59.8 1.0 O B:ASP352 4.8 42.6 1.0 OD2 B:ASP509 4.8 54.8 1.0 N B:ASP356 4.9 50.7 1.0 CZ B:TYR427 4.9 44.3 1.0 CD B:GLU430 4.9 49.6 1.0 CB B:ASP352 4.9 42.9 1.0 CA B:ASP356 5.0 51.0 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1602 b:70.4 occ:1.00 O3B B:F3P1600 1.8 50.3 1.0 OD1 B:ASP356 2.1 51.9 1.0 OD1 B:ASP352 2.8 47.8 1.0 CG B:ASP356 3.0 56.2 1.0 PB B:F3P1600 3.2 54.3 1.0 OD2 B:ASP356 3.3 58.0 1.0 O2A B:F3P1600 3.3 63.1 1.0 O3A B:F3P1600 3.4 59.8 1.0 CG B:ASP352 3.6 45.9 1.0 OD2 B:ASP352 3.7 51.6 1.0 MN B:MN1601 3.8 49.5 1.0 OD2 B:ASP509 3.9 54.8 1.0 PA B:F3P1600 4.0 62.6 1.0 O2B B:F3P1600 4.1 49.2 1.0 O1B B:F3P1600 4.2 51.3 1.0 NH2 B:ARG315 4.2 56.7 1.0 CB B:ASP356 4.3 52.8 1.0 OD1 B:ASP353 4.7 44.8 1.0 CZ B:ARG315 4.9 59.4 1.0 CG B:ASP509 4.9 57.9 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of of Limonene Synthase with 2- Fluorolinalyl Diphosphate(Flpp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1603 b:55.0 occ:1.00 O2B B:F3P1600 2.1 49.2 1.0 OD2 B:ASP496 2.6 44.1 1.0 CG2 B:THR500 2.6 74.3 1.0 O1A B:F3P1600 2.9 53.4 1.0 OD1 B:ASP496 3.0 50.4 1.0 CB B:THR500 3.2 72.4 1.0 CG B:ASP496 3.2 45.8 1.0 PB B:F3P1600 3.6 54.3 1.0 O B:THR500 3.7 78.9 1.0 PA B:F3P1600 3.8 62.6 1.0 O2A B:F3P1600 3.9 63.1 1.0 CE B:LYS512 3.9 49.9 1.0 OG1 B:THR500 4.0 66.1 1.0 O3B B:F3P1600 4.1 50.3 1.0 CD B:LYS512 4.1 49.9 1.0 O3A B:F3P1600 4.2 59.8 1.0 NH2 B:ARG493 4.3 43.6 1.0 C B:THR500 4.4 75.0 1.0 CA B:THR500 4.5 72.3 1.0 OD2 B:ASP497 4.5 46.1 1.0 NZ B:LYS512 4.5 41.0 1.0 O B:ASP496 4.6 47.7 1.0 O1B B:F3P1600 4.7 51.3 1.0 CB B:ASP496 4.7 45.4 1.0 C B:ASP496 4.8 47.1 1.0

D.C.Hyatt, B.Youn, Y.Zhao, B.Santhamma, R.M.Coates, R.B.Croteau, C.Kang. Structure of Limonene Synthase, A Simple Model For Terpenoid Cyclase Catalysis. Proc.Natl.Acad.Sci.Usa V. 104 5360 2007.
ISSN: ISSN 0027-8424
PubMed: 17372193
DOI: 10.1073/PNAS.0700915104