Manganese in PDB 2ong: Crystal Structure of of Limonene Synthase with 2- Fluorogeranyl Diphosphate (Fgpp).

The structure of Crystal Structure of of Limonene Synthase with 2- Fluorogeranyl Diphosphate (Fgpp)., PDB code: 2ong 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 (°)	200.480, 200.480, 123.410, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.1

The structure of Crystal Structure of of Limonene Synthase with 2- Fluorogeranyl Diphosphate (Fgpp). 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- Fluorogeranyl Diphosphate (Fgpp). (pdb code 2ong). 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- Fluorogeranyl Diphosphate (Fgpp)., PDB code: 2ong:
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- Fluorogeranyl Diphosphate (Fgpp).


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- Fluorogeranyl Diphosphate (Fgpp). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:52.4 occ:1.00 O2B A:FPG600 2.1 54.6 1.0 OD1 A:ASP352 2.5 32.4 1.0 OD2 A:ASP356 2.6 48.3 1.0 O A:HOH739 3.1 46.8 1.0 PB A:FPG600 3.4 64.1 1.0 O3B A:FPG600 3.6 70.1 1.0 OD1 A:ASP509 3.6 62.1 1.0 CG A:ASP352 3.6 32.4 1.0 CG A:ASP356 3.6 52.2 1.0 MN A:MN602 3.7 42.0 1.0 CB A:ASP356 3.8 47.4 1.0 OE2 A:GLU430 3.9 55.4 1.0 OD2 A:ASP352 3.9 21.4 1.0 OD2 A:ASP509 4.1 68.4 1.0 CE1 A:TYR427 4.2 36.5 1.0 CD1 A:TYR427 4.2 30.7 1.0 CG A:ASP509 4.3 66.2 1.0 O1B A:FPG600 4.3 67.5 1.0 O3A A:FPG600 4.5 68.2 1.0 OD1 A:ASP356 4.7 49.7 1.0 NZ A:LYS512 4.9 32.9 1.0 CB A:ASP352 5.0 25.2 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorogeranyl Diphosphate (Fgpp).


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- Fluorogeranyl Diphosphate (Fgpp). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:42.0 occ:1.00 OD2 A:ASP356 2.2 48.3 1.0 O2B A:FPG600 2.3 54.6 1.0 OD2 A:ASP352 2.4 21.4 1.0 O2A A:FPG600 2.7 72.8 1.0 CG A:ASP356 3.1 52.2 1.0 PB A:FPG600 3.2 64.1 1.0 OD1 A:ASP356 3.3 49.7 1.0 CG A:ASP352 3.4 32.4 1.0 PA A:FPG600 3.4 72.3 1.0 O1B A:FPG600 3.5 67.5 1.0 O3A A:FPG600 3.5 68.2 1.0 OD2 A:ASP509 3.5 68.4 1.0 OD1 A:ASP352 3.6 32.4 1.0 NH2 A:ARG507 3.7 82.6 1.0 MN A:MN601 3.7 52.4 1.0 O1A A:FPG600 3.8 66.6 1.0 NH2 A:ARG315 4.2 52.0 1.0 CB A:ASP356 4.4 47.4 1.0 CG A:ASP509 4.6 66.2 1.0 O3B A:FPG600 4.7 70.1 1.0 CZ A:ARG315 4.7 49.1 1.0 NH1 A:ARG315 4.7 44.5 1.0 CB A:ASP352 4.8 25.2 1.0 CZ A:ARG507 4.9 82.8 1.0 OD1 A:ASP509 5.0 62.1 1.0 MN A:MN603 5.0 43.3 1.0 OD1 A:ASP353 5.0 32.2 1.0 O1 A:FPG600 5.0 74.9 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorogeranyl Diphosphate (Fgpp).


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- Fluorogeranyl Diphosphate (Fgpp). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:43.3 occ:1.00 O1B A:FPG600 2.2 67.5 1.0 O1A A:FPG600 2.2 66.6 1.0 OD2 A:ASP496 2.4 50.2 1.0 OG1 A:THR500 2.7 81.1 1.0 CG2 A:THR500 2.9 72.2 1.0 CB A:THR500 3.3 78.9 1.0 CG A:ASP496 3.5 48.1 1.0 PB A:FPG600 3.5 64.1 1.0 PA A:FPG600 3.6 72.3 1.0 OD1 A:ASP496 3.8 55.9 1.0 O3A A:FPG600 3.8 68.2 1.0 NZ A:LYS512 4.3 32.9 1.0 O3B A:FPG600 4.3 70.1 1.0 O A:ASP496 4.3 40.7 1.0 O1 A:FPG600 4.4 74.9 1.0 CD A:LYS512 4.6 38.8 1.0 OD2 A:ASP497 4.6 38.7 1.0 C A:ASP496 4.7 38.9 1.0 O2A A:FPG600 4.7 72.8 1.0 N A:SER501 4.7 81.6 1.0 O2B A:FPG600 4.7 54.6 1.0 CA A:THR500 4.7 78.9 1.0 CB A:ASP496 4.8 37.5 1.0 NH2 A:ARG493 4.8 38.7 1.0 N A:ASP497 5.0 40.5 1.0 MN A:MN602 5.0 42.0 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorogeranyl Diphosphate (Fgpp).


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- Fluorogeranyl Diphosphate (Fgpp). within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1601 b:52.0 occ:1.00 O2B B:FPG1600 2.4 59.8 1.0 OD2 B:ASP352 2.6 44.5 1.0 OD1 B:ASP356 2.7 65.1 1.0 O3B B:FPG1600 3.5 71.9 1.0 MN B:MN1602 3.5 49.8 1.0 PB B:FPG1600 3.5 69.0 1.0 CG B:ASP352 3.7 40.8 1.0 CG B:ASP356 3.7 60.5 1.0 OE1 B:GLU430 3.7 37.2 1.0 OD1 B:ASP352 4.0 43.7 1.0 CB B:ASP356 4.0 53.7 1.0 CD1 B:TYR427 4.1 28.7 1.0 CE1 B:TYR427 4.1 35.2 1.0 O1B B:FPG1600 4.3 69.3 1.0 O2A B:FPG1600 4.5 88.1 1.0 OD1 B:ASP509 4.5 54.4 1.0 OD2 B:ASP509 4.6 59.0 1.0 O3A B:FPG1600 4.7 73.0 1.0 OD2 B:ASP356 4.8 63.7 1.0 CD B:GLU430 5.0 39.5 1.0 O B:ASP352 5.0 39.0 1.0 CG B:ASP509 5.0 62.0 1.0 CB B:ASP352 5.0 30.6 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorogeranyl Diphosphate (Fgpp).


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- Fluorogeranyl Diphosphate (Fgpp). within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1602 b:49.8 occ:1.00 O2A B:FPG1600 1.9 88.1 1.0 OD1 B:ASP356 2.1 65.1 1.0 OD1 B:ASP352 2.4 43.7 1.0 O2B B:FPG1600 2.4 59.8 1.0 CG B:ASP356 3.1 60.5 1.0 CG B:ASP352 3.3 40.8 1.0 PA B:FPG1600 3.3 83.0 1.0 OD2 B:ASP356 3.4 63.7 1.0 OD2 B:ASP352 3.5 44.5 1.0 MN B:MN1601 3.5 52.0 1.0 PB B:FPG1600 3.8 69.0 1.0 NH2 B:ARG315 3.9 71.0 1.0 O1A B:FPG1600 3.9 78.8 1.0 O3A B:FPG1600 4.0 73.0 1.0 OD2 B:ASP509 4.1 59.0 1.0 CB B:ASP356 4.4 53.7 1.0 O1 B:FPG1600 4.5 82.4 1.0 CB B:ASP352 4.7 30.6 1.0 O1B B:FPG1600 4.7 69.3 1.0 F B:FPG1600 4.8 0.0 1.0 CZ B:ARG315 4.8 69.0 1.0 O3B B:FPG1600 4.8 71.9 1.0 OD1 B:ASP353 4.9 26.2 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of of Limonene Synthase with 2- Fluorogeranyl Diphosphate (Fgpp).


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- Fluorogeranyl Diphosphate (Fgpp). within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1603 b:44.6 occ:1.00 O1A B:FPG1600 1.9 78.8 1.0 OD2 B:ASP496 2.3 52.5 1.0 O1B B:FPG1600 2.7 69.3 1.0 CG2 B:THR500 3.0 89.1 1.0 PA B:FPG1600 3.1 83.0 1.0 OG1 B:THR500 3.2 75.1 1.0 O3A B:FPG1600 3.2 73.0 1.0 CB B:THR500 3.2 83.7 1.0 CG B:ASP496 3.3 56.1 1.0 PB B:FPG1600 3.5 69.0 1.0 OD1 B:ASP496 3.7 61.4 1.0 O1 B:FPG1600 4.1 82.4 1.0 O2A B:FPG1600 4.2 88.1 1.0 NH1 B:ARG493 4.2 39.4 1.0 O2B B:FPG1600 4.2 59.8 1.0 CD B:LYS512 4.5 43.2 1.0 CB B:ASP496 4.7 50.3 1.0 OD2 B:ASP497 4.7 36.1 1.0 NZ B:LYS512 4.8 34.2 1.0 CA B:THR500 4.8 84.8 1.0 O3B B:FPG1600 4.9 71.9 1.0 C B:ASP496 5.0 45.2 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