Magnesium in PDB 1yyt: D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene

All present enzymatic activity of D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene:
4.2.3.6;

The structure of D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene, PDB code: 1yyt was solved by L.S.Vedula, M.J.Rynkiewicz, H.J.Pyun, R.M.Coates, 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)	14.00 / 2.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.703, 122.703, 151.297, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 26.9

The binding sites of Magnesium atom in the D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene (pdb code 1yyt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene, PDB code: 1yyt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:0.8 occ:1.00 O5 B:POP700 2.2 0.4 1.0 O2 B:POP700 2.7 0.2 1.0 OE1 B:GLU100 2.8 49.3 1.0 P2 B:POP700 3.2 0.4 1.0 P1 B:POP700 3.4 0.0 1.0 O B:POP700 3.6 0.9 1.0 O4 B:POP700 3.6 0.8 1.0 CD B:GLU100 3.7 47.1 1.0 OE2 B:GLU100 3.8 47.3 1.0 O1 B:POP700 3.8 0.5 1.0 O6 B:POP700 4.5 0.5 1.0 O3 B:POP700 4.8 0.9 1.0 CD1 B:LEU97 4.8 31.7 1.0 C17 B:SAZ704 4.9 76.9 1.0

Magnesium binding site 2 out of 2 in the D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:33.6 occ:1.00 OD1 B:ASN225 2.9 52.3 1.0 OG B:SER229 2.9 62.6 1.0 O1 B:POP700 3.0 0.5 1.0 O4 B:POP700 3.2 0.8 1.0 CB B:SER229 3.2 63.0 1.0 OE2 B:GLU233 3.3 99.5 1.0 OD1 B:ASP226 3.7 55.9 1.0 O B:POP700 3.7 0.9 1.0 OE1 B:GLU233 3.8 99.4 1.0 CD B:GLU233 4.0 99.8 1.0 P1 B:POP700 4.0 0.0 1.0 P2 B:POP700 4.0 0.4 1.0 CG B:ASN225 4.1 51.9 1.0 CA B:ASP226 4.2 54.6 1.0 NH2 B:ARG182 4.4 40.5 1.0 O B:ASN225 4.4 53.8 1.0 O6 B:POP700 4.5 0.5 1.0 O3 B:POP700 4.5 0.9 1.0 CG B:ASP226 4.5 55.4 1.0 N B:ASP226 4.6 54.1 1.0 C B:ASN225 4.6 53.3 1.0 CA B:SER229 4.7 63.9 1.0 ND2 B:ASN225 4.7 51.1 1.0

L.S.Vedula, M.J.Rynkiewicz, H.J.Pyun, R.M.Coates, D.E.Cane, D.W.Christianson. Molecular Recognition of the Substrate Diphosphate Group Governs Product Diversity in Trichodiene Synthase Mutants. Biochemistry V. 44 6153 2005.
ISSN: ISSN 0006-2960
PubMed: 15835903
DOI: 10.1021/BI050059O