Manganese in PDB 5uv1: Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluorogeranyl Diphosphate

The structure of Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluorogeranyl Diphosphate, PDB code: 5uv1 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)	19.93 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.510, 85.510, 215.420, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.6

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

Fluorine

(F)

1 atom

The binding sites of Manganese atom in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluorogeranyl Diphosphate (pdb code 5uv1). 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- Fluorogeranyl Diphosphate, PDB code: 5uv1:
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- Fluorogeranyl 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- Fluorogeranyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:58.8 occ:1.00 O1A A:0FV704 2.0 54.5 1.0 OD2 A:ASP343 2.1 58.8 1.0 O1B A:0FV704 2.1 64.5 1.0 O A:HOH864 2.2 59.3 1.0 O A:HOH838 2.4 53.2 1.0 OD2 A:ASP347 2.8 63.3 1.0 CG A:ASP343 3.1 54.0 1.0 MN A:MN702 3.2 60.3 1.0 PA A:0FV704 3.2 61.1 1.0 PB A:0FV704 3.3 55.8 1.0 O3A A:0FV704 3.5 61.2 1.0 CG A:ASP347 3.5 61.7 1.0 OD1 A:ASP343 3.6 57.5 1.0 OD1 A:ASP347 3.6 71.4 1.0 O3B A:0FV704 4.1 61.0 1.0 O A:HOH869 4.1 69.8 1.0 O1 A:0FV704 4.2 86.1 1.0 O2A A:0FV704 4.3 61.8 1.0 CB A:ASP343 4.5 51.5 1.0 O2B A:0FV704 4.5 64.6 1.0 O A:HOH868 4.6 67.5 1.0 O A:ASP343 4.6 55.0 1.0 CB A:ASP347 4.8 62.5 1.0 OD1 A:ASP344 4.9 71.9 1.0 C A:ASP343 4.9 56.5 1.0 O A:HOH845 4.9 52.2 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluorogeranyl 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- Fluorogeranyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:60.3 occ:1.00 O A:HOH845 2.1 52.2 1.0 O1B A:0FV704 2.1 64.5 1.0 OD2 A:ASP347 2.2 63.3 1.0 O A:HOH801 2.3 59.2 1.0 O A:HOH868 2.3 67.5 1.0 OD1 A:ASP343 2.4 57.5 1.0 CG A:ASP343 3.2 54.0 1.0 MN A:MN701 3.2 58.8 1.0 PB A:0FV704 3.2 55.8 1.0 O2B A:0FV704 3.3 64.6 1.0 OD2 A:ASP343 3.3 58.8 1.0 CG A:ASP347 3.4 61.7 1.0 OE1 A:GLU422 3.8 76.2 1.0 CB A:ASP347 4.0 62.5 1.0 O A:HOH864 4.1 59.3 1.0 O3A A:0FV704 4.2 61.2 1.0 O3B A:0FV704 4.3 61.0 1.0 OD1 A:ASP347 4.4 71.4 1.0 CE1 A:TYR419 4.4 41.2 1.0 NZ A:LYS504 4.4 68.7 1.0 O A:ASP343 4.5 55.0 1.0 CB A:ASP343 4.5 51.5 1.0 CD1 A:TYR419 4.6 55.1 1.0 O1A A:0FV704 4.6 54.5 1.0 CD A:GLU422 4.9 75.0 1.0 CA A:ASP343 5.0 49.0 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluorogeranyl 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- Fluorogeranyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:65.5 occ:1.00 O3B A:0FV704 2.2 61.0 1.0 OD2 A:ASP488 2.2 56.2 1.0 O A:HOH853 2.3 70.9 1.0 O A:HOH869 2.4 69.8 1.0 O2A A:0FV704 2.4 61.8 1.0 O A:HOH895 2.7 63.5 1.0 CG A:ASP488 3.3 55.8 1.0 O A:HOH826 3.4 71.6 1.0 PB A:0FV704 3.4 55.8 1.0 PA A:0FV704 3.4 61.1 1.0 O3A A:0FV704 3.6 61.2 1.0 OD1 A:ASP488 3.7 66.3 1.0 O1A A:0FV704 3.9 54.5 1.0 O A:ASP488 4.2 54.6 1.0 NH1 A:ARG485 4.2 48.1 1.0 O1B A:0FV704 4.3 64.5 1.0 O A:HOH864 4.3 59.3 1.0 O A:HOH907 4.3 74.8 1.0 OD1 A:ASP489 4.3 52.4 1.0 CB A:ASP488 4.5 53.6 1.0 O2B A:0FV704 4.5 64.6 1.0 NZ A:LYS504 4.6 68.7 1.0 C A:ASP488 4.6 49.8 1.0 CE A:LYS504 4.7 73.5 1.0 O1 A:0FV704 4.9 86.1 1.0

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