Manganese in PDB 5uv2: Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate

The structure of Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate, PDB code: 5uv2 was solved by R.Prem Kumar, K.Malik, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.699, 85.699, 214.880, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23

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

Fluorine

(F)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate (pdb code 5uv2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate, PDB code: 5uv2:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate


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 (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:53.1 occ:1.00 O1A A:LA6704 1.8 51.1 0.5 O2B A:LA6704 1.9 50.9 0.5 OD2 A:ASP343 2.3 47.9 1.0 O A:HOH898 2.4 56.5 1.0 O1A A:LA6704 2.4 51.7 0.5 OD2 A:ASP347 2.4 54.2 1.0 O A:HOH881 2.4 52.8 1.0 O2B A:LA6704 2.5 50.3 0.5 PA A:LA6704 3.1 50.6 0.5 CG A:ASP347 3.2 58.8 1.0 PB A:LA6704 3.3 49.8 0.5 CG A:ASP343 3.3 46.7 1.0 MN A:MN702 3.3 51.4 1.0 OD1 A:ASP347 3.4 70.1 1.0 O3A A:LA6704 3.5 51.0 0.5 PA A:LA6704 3.5 49.4 0.5 PB A:LA6704 3.5 49.8 0.5 O3A A:LA6704 3.6 51.0 0.5 OD1 A:ASP343 3.6 48.5 1.0 O1 A:LA6704 4.0 54.8 0.5 O A:HOH959 4.1 55.2 1.0 O3B A:LA6704 4.1 50.3 0.5 O3B A:LA6704 4.2 50.5 0.5 O2A A:LA6704 4.2 51.1 0.5 O1B A:LA6704 4.3 49.7 0.5 O1 A:LA6704 4.3 54.6 0.5 O A:HOH994 4.4 69.9 1.0 O A:HOH932 4.6 51.5 1.0 CB A:ASP343 4.6 42.6 1.0 CB A:ASP347 4.7 55.7 1.0 O2A A:LA6704 4.7 51.9 0.5 O A:ASP343 4.7 49.4 1.0 O1B A:LA6704 4.8 49.1 0.5 C A:ASP343 5.0 48.4 1.0 OD1 A:ASP344 5.0 52.6 1.0 NZ A:LYS504 5.0 51.1 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate


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 (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:51.4 occ:1.00 O2B A:LA6704 2.0 50.3 0.5 O A:HOH876 2.3 46.6 1.0 OD2 A:ASP347 2.3 54.2 1.0 OD1 A:ASP343 2.3 48.5 1.0 O A:HOH932 2.4 51.5 1.0 O A:HOH813 2.4 48.5 1.0 O2B A:LA6704 2.4 50.9 0.5 O1B A:LA6704 3.0 49.7 0.5 CG A:ASP343 3.2 46.7 1.0 PB A:LA6704 3.3 49.8 0.5 MN A:MN701 3.3 53.1 1.0 PB A:LA6704 3.3 49.8 0.5 CG A:ASP347 3.4 58.8 1.0 OD2 A:ASP343 3.5 47.9 1.0 O1B A:LA6704 3.5 49.1 0.5 OE1 A:GLU422 3.8 51.1 1.0 CB A:ASP347 4.0 55.7 1.0 CE1 A:TYR419 4.2 40.0 1.0 O3A A:LA6704 4.3 51.0 0.5 NZ A:LYS504 4.3 51.1 1.0 O3B A:LA6704 4.3 50.5 0.5 CD1 A:TYR419 4.3 43.8 1.0 O3A A:LA6704 4.4 51.0 0.5 O3B A:LA6704 4.4 50.3 0.5 O A:HOH898 4.4 56.5 1.0 OD1 A:ASP347 4.5 70.1 1.0 O A:HOH829 4.5 52.8 1.0 O1A A:LA6704 4.5 51.1 0.5 CB A:ASP343 4.6 42.6 1.0 O A:ASP343 4.7 49.4 1.0 CZ A:TYR419 4.8 43.2 1.0 O A:HOH851 4.8 45.5 1.0 CD A:GLU422 5.0 51.7 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate


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 (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:55.2 occ:1.00 O3B A:LA6704 2.1 50.3 0.5 OD2 A:ASP488 2.2 47.7 1.0 O A:HOH830 2.3 52.3 1.0 O2A A:LA6704 2.3 51.1 0.5 O3B A:LA6704 2.4 50.5 0.5 O2A A:LA6704 2.4 51.9 0.5 O A:HOH959 2.5 55.2 1.0 O A:HOH966 2.6 57.3 1.0 PA A:LA6704 3.3 49.4 0.5 CG A:ASP488 3.3 41.7 1.0 PB A:LA6704 3.3 49.8 0.5 O A:HOH807 3.3 58.5 1.0 PA A:LA6704 3.4 50.6 0.5 O3A A:LA6704 3.4 51.0 0.5 PB A:LA6704 3.6 49.8 0.5 O1A A:LA6704 3.7 51.7 0.5 O3A A:LA6704 3.7 51.0 0.5 OD1 A:ASP488 3.8 47.7 1.0 O1A A:LA6704 3.9 51.1 0.5 O2B A:LA6704 4.1 50.9 0.5 NH1 A:ARG485 4.1 43.5 1.0 NZ A:LYS504 4.3 51.1 1.0 OD1 A:ASP489 4.4 46.3 1.0 O A:ASP488 4.4 39.9 1.0 O2B A:LA6704 4.4 50.3 0.5 O1B A:LA6704 4.5 49.7 0.5 O A:HOH898 4.5 56.5 1.0 CB A:ASP488 4.5 42.1 1.0 O1B A:LA6704 4.7 49.1 0.5 C A:ASP488 4.7 42.0 1.0 O1 A:LA6704 4.8 54.6 0.5 CE A:LYS504 4.8 56.3 1.0 O1 A:LA6704 4.8 54.8 0.5

R.P.Kumar, B.R.Morehouse, J.O.Matos, K.Malik, H.Lin, I.J.Krauss, D.D.Oprian. Structural Characterization of Early Michaelis Complexes in the Reaction Catalyzed By (+)-Limonene Synthase From Citrus Sinensis Using Fluorinated Substrate Analogues. Biochemistry V. 56 1716 2017.
ISSN: ISSN 1520-4995
PubMed: 28272876
DOI: 10.1021/ACS.BIOCHEM.7B00144