Magnesium in PDB 5ik6: Tobacco 5-Epi-Aristolochene Synthase with Germacrene A and Ppi

All present enzymatic activity of Tobacco 5-Epi-Aristolochene Synthase with Germacrene A and Ppi:
4.2.3.61;

The structure of Tobacco 5-Epi-Aristolochene Synthase with Germacrene A and Ppi, PDB code: 5ik6 was solved by H.J.Koo, Y.Xu, G.V.Louie, M.Bowman, J.P.Noel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.13 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.510, 126.510, 123.210, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20

The binding sites of Magnesium atom in the Tobacco 5-Epi-Aristolochene Synthase with Germacrene A and Ppi (pdb code 5ik6). 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 Germacrene A and Ppi, PDB code: 5ik6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tobacco 5-Epi-Aristolochene Synthase with Germacrene A and 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 Germacrene A and Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:69.7 occ:1.00 OE1 A:GLU452 2.1 98.0 1.0 O5 A:DPO605 2.1 0.5 1.0 O A:HOH732 2.4 48.6 1.0 OD1 A:ASP444 2.5 64.2 1.0 O A:HOH701 2.9 63.2 1.0 OG1 A:THR448 2.9 63.5 1.0 O1 A:DPO605 3.0 0.3 1.0 CD A:GLU452 3.2 0.4 1.0 CG A:ASP444 3.5 56.4 1.0 P2 A:DPO605 3.6 0.6 1.0 OE2 A:GLU452 3.7 0.2 1.0 OD2 A:ASP444 3.8 70.1 1.0 CB A:THR448 3.9 63.6 1.0 NH2 A:ARG441 4.0 40.0 1.0 O4 A:DPO605 4.1 0.4 1.0 CG2 A:THR448 4.2 54.5 1.0 P1 A:DPO605 4.2 0.6 1.0 O6 A:DPO605 4.3 0.1 1.0 CG A:GLU452 4.5 98.0 1.0 O7 A:DPO605 4.6 0.1 1.0 O A:ASP444 4.7 44.3 1.0 OD1 A:ASP445 4.7 49.4 1.0 CB A:ASP444 4.8 45.1 1.0 O2 A:DPO605 4.9 0.5 1.0 C A:ASP444 5.0 42.7 1.0

Magnesium binding site 2 out of 3 in the Tobacco 5-Epi-Aristolochene Synthase with Germacrene A and 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 Germacrene A and Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:0.3 occ:1.00 O A:HOH702 2.1 73.6 1.0 O A:HOH706 2.1 55.8 1.0 OD1 A:ASP301 2.1 63.4 1.0 O A:HOH723 2.1 59.0 1.0 O2 A:DPO605 2.1 0.5 1.0 O6 A:DPO605 2.7 0.1 1.0 MG A:MG603 2.9 92.8 1.0 CG A:ASP301 3.0 65.0 1.0 OD2 A:ASP301 3.2 74.1 1.0 P1 A:DPO605 3.5 0.6 1.0 OD2 A:ASP305 3.7 0.9 1.0 CB A:ASP305 3.7 86.9 1.0 CG A:ASP305 3.8 95.8 1.0 O4 A:DPO605 3.8 0.4 1.0 OE2 A:GLU379 3.8 82.8 1.0 P2 A:DPO605 3.9 0.6 1.0 O A:ASP301 4.2 66.9 1.0 CB A:ASP301 4.4 55.6 1.0 O1 A:DPO605 4.4 0.3 1.0 OD1 A:ASP305 4.5 94.0 1.0 O3 A:DPO605 4.5 0.1 1.0 C A:ASP301 4.8 65.8 1.0 CD A:GLU379 4.8 73.8 1.0 OE1 A:GLU379 4.8 69.8 1.0 CA A:ASP301 4.9 59.5 1.0 CE1 A:TYR376 4.9 46.3 1.0 O5 A:DPO605 4.9 0.5 1.0 O A:HOH789 4.9 0.6 1.0 CA A:ASP305 4.9 80.8 1.0 O7 A:DPO605 4.9 0.1 1.0

Magnesium binding site 3 out of 3 in the Tobacco 5-Epi-Aristolochene Synthase with Germacrene A and 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 Germacrene A and Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:92.8 occ:1.00 O A:HOH789 2.1 0.6 1.0 OD2 A:ASP301 2.1 74.1 1.0 O2 A:DPO605 2.1 0.5 1.0 OD2 A:ASP305 2.9 0.9 1.0 MG A:MG602 2.9 0.3 1.0 CG A:ASP301 3.0 65.0 1.0 P1 A:DPO605 3.0 0.6 1.0 O3 A:DPO605 3.2 0.1 1.0 OD1 A:ASP301 3.3 63.4 1.0 CB A:ASP305 3.6 86.9 1.0 CG A:ASP305 3.6 95.8 1.0 OD1 A:ASP302 3.7 82.8 1.0 NH2 A:ARG264 3.8 73.4 1.0 O1 A:DPO605 4.0 0.3 1.0 O A:ASP301 4.1 66.9 1.0 O A:HOH723 4.2 59.0 1.0 O4 A:DPO605 4.3 0.4 1.0 CB A:ASP301 4.4 55.6 1.0 O A:HOH706 4.4 55.8 1.0 CZ A:ARG264 4.4 72.5 1.0 C A:ASP301 4.4 65.8 1.0 N A:ASP302 4.7 62.8 1.0 NH1 A:ARG264 4.7 74.2 1.0 O6 A:DPO605 4.7 0.1 1.0 CA A:ASP302 4.8 66.7 1.0 OD1 A:ASP305 4.8 94.0 1.0 O A:HOH702 4.8 73.6 1.0 CG A:ASP302 4.9 78.3 1.0

H.J.Koo, C.R.Vickery, Y.Xu, G.V.Louie, P.E.O'maille, M.Bowman, C.M.Nartey, M.D.Burkart, J.P.Noel. Biosynthetic Potential of Sesquiterpene Synthases: Product Profiles of Egyptian Henbane Premnaspirodiene Synthase and Related Mutants. J.Antibiot. V. 69 524 2016.
ISSN: ISSN 0021-8820
PubMed: 27328867
DOI: 10.1038/JA.2016.68