Magnesium in PDB 5ily: Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi)

All present enzymatic activity of Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi):
4.2.3.61;

The structure of Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi), PDB code: 5ily was solved by H.J.Koo, G.V.Louie, Y.Xu, M.Bowman, J.P.Noel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.20 / 2.45
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.740, 126.740, 124.760, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.7

The binding sites of Magnesium atom in the Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi) (pdb code 5ily). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi), PDB code: 5ily:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:0.4 occ:1.00 OE2 A:GLU452 2.1 0.9 1.0 OG1 A:THR448 2.1 99.9 1.0 OD1 A:ASP444 2.1 91.1 1.0 O7 A:DPO605 2.1 58.9 0.8 O3 A:DPO605 2.1 78.4 0.8 O A:HOH721 2.3 67.0 1.0 CD A:GLU452 3.1 0.1 1.0 CB A:THR448 3.1 0.6 1.0 CG A:ASP444 3.3 84.9 1.0 P1 A:DPO605 3.4 82.8 0.8 P2 A:DPO605 3.4 70.2 0.8 OE1 A:GLU452 3.5 0.5 1.0 O4 A:DPO605 3.6 0.3 0.8 CG2 A:THR448 3.6 97.2 1.0 OD2 A:ASP444 3.8 92.4 1.0 O A:HOH714 4.1 75.8 1.0 O5 A:DPO605 4.1 82.6 0.8 O A:THR448 4.1 0.7 1.0 O A:ASP444 4.2 71.2 1.0 NH2 A:ARG441 4.2 59.6 1.0 O1 A:DPO605 4.2 85.2 0.8 CG A:GLU452 4.5 0.4 1.0 O2 A:DPO605 4.5 91.7 0.8 CB A:ASP444 4.5 72.4 1.0 CA A:THR448 4.5 0.1 1.0 C A:ASP444 4.5 70.0 1.0 OD1 A:ASP445 4.6 86.1 1.0 O6 A:DPO605 4.6 62.2 0.8 C A:THR448 4.7 1.0 1.0

Magnesium binding site 2 out of 3 in the Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:84.0 occ:1.00 OD2 A:ASP301 2.1 87.5 1.0 O1 A:DPO605 2.1 85.2 0.8 O5 A:DPO605 2.1 82.6 0.8 O A:HOH714 2.4 75.8 1.0 OD1 A:ASP301 2.7 0.1 1.0 CG A:ASP301 2.7 91.5 1.0 MG A:MG603 2.9 88.9 1.0 OD2 A:ASP305 3.3 0.1 1.0 P1 A:DPO605 3.4 82.8 0.8 P2 A:DPO605 3.4 70.2 0.8 O A:HOH705 3.6 72.2 1.0 O4 A:DPO605 3.6 0.3 0.8 CB A:ASP305 4.0 0.8 1.0 CG A:ASP305 4.1 0.5 1.0 O A:ASP301 4.1 0.7 1.0 O3 A:DPO605 4.2 78.4 0.8 CB A:ASP301 4.2 87.7 1.0 O7 A:DPO605 4.2 58.9 0.8 NH2 A:ARG264 4.3 74.5 1.0 O6 A:DPO605 4.5 62.2 0.8 O2 A:DPO605 4.5 91.7 0.8 C A:ASP301 4.6 0.4 1.0 OD1 A:ASP302 4.9 0.3 1.0 O3 A:BTB604 4.9 0.4 1.0 OE2 A:GLU452 4.9 0.9 1.0 CA A:ASP301 5.0 94.0 1.0 NH2 A:ARG455 5.0 0.6 1.0

Magnesium binding site 3 out of 3 in the Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tobacco 5-Epi-Aristolochene Synthase with Bis-Tris Buffer Molecule and Diphosphate (Ppi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:88.9 occ:1.00 O A:HOH705 2.1 72.2 1.0 OD1 A:ASP301 2.1 0.1 1.0 O5 A:DPO605 2.1 82.6 0.8 MG A:MG602 2.9 84.0 1.0 P2 A:DPO605 3.2 70.2 0.8 CG A:ASP301 3.2 91.5 1.0 O6 A:DPO605 3.4 62.2 0.8 OD2 A:ASP301 3.7 87.5 1.0 CE1 A:TYR376 3.8 97.2 1.0 OE2 A:GLU379 3.9 1.0 1.0 O7 A:DPO605 4.2 58.9 0.8 O4 A:DPO605 4.3 0.3 0.8 CD1 A:TYR376 4.4 0.8 1.0 CB A:ASP301 4.4 87.7 1.0 CB A:ASP305 4.4 0.8 1.0 O1 A:DPO605 4.5 85.2 0.8 O A:ASP301 4.5 0.7 1.0 O A:HOH714 4.6 75.8 1.0 CZ A:TYR376 4.7 94.1 1.0 OH A:TYR376 4.9 86.4 1.0 CA A:ASP301 4.9 94.0 1.0 OD2 A:ASP305 4.9 0.1 1.0 CD A:GLU379 4.9 0.1 1.0

H.J.Koo, G.V.Louie, Y.Xu, M.Bowman, J.P.Noel. Small-Molecule Buffer Components Can Directly Affect Terpene-Synthase Activity By Interacting with the Substrate-Binding Site of the Enzyme To Be Published.