Magnesium in PDB 2q9y: Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation

All present enzymatic activity of Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation:
4.2.3.6;

The structure of Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation, PDB code: 2q9y was solved by L.S.Vedula, Y.Zhao, R.M.Coates, T.Koyama, D.E.Cane, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.488, 122.488, 150.494, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 26.5

The binding sites of Magnesium atom in the Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation (pdb code 2q9y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation, PDB code: 2q9y:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:63.0 occ:1.00 OD1 B:ASN225 2.3 75.2 1.0 O1 B:POP700 2.5 98.3 1.0 OE1 B:GLU233 2.6 97.0 1.0 O4 B:POP700 2.7 0.6 1.0 OG B:SER229 2.7 86.3 1.0 OE2 B:GLU233 2.8 96.6 1.0 CD B:GLU233 2.9 97.4 1.0 CG B:ASN225 3.4 74.6 1.0 O B:ASN225 3.6 75.3 1.0 OD1 B:ASP226 3.8 76.2 1.0 P1 B:POP700 3.8 98.9 1.0 CA B:ASP226 3.9 76.3 1.0 P2 B:POP700 3.9 0.7 1.0 C B:ASN225 4.0 74.9 1.0 NH2 B:ARG182 4.0 62.7 1.0 O B:POP700 4.0 0.6 1.0 CB B:SER229 4.1 87.0 1.0 N B:ASP226 4.1 75.8 1.0 ND2 B:ASN225 4.1 73.8 1.0 CG B:GLU233 4.3 98.2 1.0 CB B:ASN225 4.5 73.6 1.0 CZ B:ARG182 4.5 62.4 1.0 CG B:ASP226 4.6 76.4 1.0 C B:ASP226 4.8 76.9 1.0 O2 B:POP700 4.8 98.9 1.0 NH1 B:ARG182 4.8 63.9 1.0 O3 B:POP700 4.8 98.5 1.0 O5 B:POP700 4.8 0.6 1.0 O B:ASP226 4.9 75.9 1.0 CB B:ASP226 4.9 76.1 1.0 O6 B:POP700 4.9 0.2 1.0 CA B:ASN225 4.9 73.8 1.0

Magnesium binding site 2 out of 3 in the Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:59.6 occ:1.00 O5 B:POP700 2.3 0.6 1.0 O2 B:POP700 2.7 98.9 1.0 OD1 B:ASP100 2.9 78.8 1.0 OD2 B:ASP100 3.1 80.5 1.0 OD1 B:ASP239 3.2 20.0 0.0 CG B:ASP100 3.3 78.2 1.0 P2 B:POP700 3.6 0.7 1.0 NH2 B:ARG304 3.6 86.8 1.0 P1 B:POP700 3.7 98.9 1.0 MG B:MG703 3.7 88.7 1.0 O B:POP700 3.9 0.6 1.0 NZ B:LYS232 4.0 81.7 1.0 CG B:ASP239 4.0 20.0 0.0 OD1 B:ASP101 4.0 82.7 1.0 OE2 B:GLU233 4.1 96.6 1.0 O B:ASP100 4.4 75.5 1.0 O4 B:POP700 4.4 0.6 1.0 OD2 B:ASP239 4.4 20.0 0.0 O1 B:POP700 4.5 98.3 1.0 CB B:ASP100 4.7 75.5 1.0 O6 B:POP700 4.7 0.2 1.0 O3 B:POP700 4.9 98.5 1.0 CZ B:ARG304 4.9 86.1 1.0 C B:ASP100 4.9 75.6 1.0

Magnesium binding site 3 out of 3 in the Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trichodiene Synthase: Complex with Mg, Inorganic Pyrophosphate, and Benzyl Triethyl Ammonium Cation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:88.7 occ:1.00 O2 B:POP700 2.2 98.9 1.0 OD2 B:ASP100 2.3 80.5 1.0 CG B:ASP100 2.7 78.2 1.0 OD1 B:ASP100 2.7 78.8 1.0 O3 B:POP700 3.1 98.5 1.0 P1 B:POP700 3.2 98.9 1.0 MG B:MG702 3.7 59.6 1.0 CB B:ASP100 3.9 75.5 1.0 OE1 B:GLU164 3.9 78.0 1.0 O B:POP700 4.1 0.6 1.0 O B:ASN185 4.2 59.3 1.0 CE1 B:PHE157 4.3 45.1 1.0 O1 B:POP700 4.4 98.3 1.0 OE2 B:GLU164 4.5 79.0 1.0 CB B:ASN185 4.6 63.7 1.0 CA B:ASP100 4.6 74.0 1.0 CD B:GLU164 4.6 77.3 1.0 C9 B:BTM704 4.6 96.9 1.0 CG B:ASN185 4.7 66.1 1.0 O5 B:POP700 4.8 0.6 1.0 OD1 B:ASN185 4.8 64.5 1.0 O B:ASP100 4.9 75.5 1.0 NH1 B:ARG182 5.0 63.9 1.0 CZ B:PHE157 5.0 45.0 1.0

L.S.Vedula, Y.Zhao, R.M.Coates, T.Koyama, D.E.Cane, D.W.Christianson. Exploring Biosynthetic Diversity with Trichodiene Synthase. Arch.Biochem.Biophys. V. 466 260 2007.
ISSN: ISSN 0003-9861
PubMed: 17678871
DOI: 10.1016/J.ABB.2007.06.016