Magnesium in PDB 1yys: Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene

All present enzymatic activity of Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene:
4.2.3.6;

The structure of Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene, PDB code: 1yys 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)	75.00 / 2.75
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.138, 121.138, 150.286, 90.00, 90.00, 120.00
R / Rfree (%)	24.8 / 27.4

The binding sites of Magnesium atom in the Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene (pdb code 1yys). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene, PDB code: 1yys:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:71.8 occ:1.00 OE1 B:GLU233 2.0 0.2 1.0 OD1 B:ASN225 2.4 65.7 1.0 O4 B:POP700 3.0 1.0 1.0 O1 B:POP700 3.1 0.0 1.0 CD B:GLU233 3.1 0.2 1.0 OD1 B:ASP226 3.4 64.2 1.0 CB B:SER229 3.4 76.6 1.0 OG B:SER229 3.5 77.2 1.0 OE2 B:GLU233 3.5 0.1 1.0 CG B:ASN225 3.6 64.2 1.0 NH2 B:ARG182 3.7 58.6 1.0 O B:ASN225 3.7 64.3 1.0 CA B:ASP226 3.9 65.0 1.0 O B:POP700 4.0 0.7 1.0 P2 B:POP700 4.0 0.1 1.0 C B:ASN225 4.1 64.1 1.0 N B:ASP226 4.1 64.3 1.0 P1 B:POP700 4.2 0.7 1.0 ND2 B:ASN225 4.2 63.4 1.0 CG B:ASP226 4.3 64.1 1.0 CG B:GLU233 4.3 0.1 1.0 CZ B:ARG182 4.4 59.3 1.0 NH1 B:ARG182 4.6 60.0 1.0 O6 B:POP700 4.7 0.6 1.0 CB B:ASN225 4.7 64.2 1.0 CB B:ASP226 4.7 64.5 1.0 C B:ASP226 4.8 65.9 1.0 CA B:SER229 4.9 77.6 1.0 O B:ASP226 4.9 64.4 1.0 O3 B:POP700 4.9 0.8 1.0

Magnesium binding site 2 out of 3 in the Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:69.2 occ:1.00 O5 B:POP700 2.3 0.3 1.0 O2 B:POP700 2.4 0.9 1.0 OD1 B:ASP100 2.6 77.2 1.0 P1 B:POP700 3.1 0.7 1.0 P2 B:POP700 3.2 0.1 1.0 O B:POP700 3.4 0.7 1.0 O1 B:POP700 3.5 0.0 1.0 O4 B:POP700 3.5 1.0 1.0 CG B:ASP100 3.6 75.1 1.0 MG B:MG703 3.6 79.7 1.0 OD2 B:ASP100 3.8 75.6 1.0 OD1 B:ASP101 4.4 81.5 1.0 NZ B:LYS232 4.5 94.0 1.0 O3 B:POP700 4.5 0.8 1.0 O6 B:POP700 4.6 0.6 1.0 OD1 B:ASP239 4.6 20.0 0.0 O B:ASP100 4.7 75.2 1.0 OE1 B:GLU233 4.9 0.2 1.0 CB B:ASP100 4.9 74.1 1.0

Magnesium binding site 3 out of 3 in the Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:79.7 occ:1.00 O2 B:POP700 2.1 0.9 1.0 OD2 B:ASP100 2.3 75.6 1.0 ND2 B:ASN185 2.5 70.6 1.0 OE1 B:GLU164 2.9 68.8 1.0 CG B:ASP100 3.1 75.1 1.0 OD1 B:ASP100 3.3 77.2 1.0 P1 B:POP700 3.5 0.7 1.0 MG B:MG702 3.6 69.2 1.0 CG B:ASN185 3.6 67.7 1.0 CD B:GLU164 3.7 67.3 1.0 OE2 B:GLU164 3.8 69.6 1.0 O3 B:POP700 4.0 0.8 1.0 CB B:ASN185 4.0 63.2 1.0 O1 B:POP700 4.0 0.0 1.0 O B:ASN185 4.4 57.5 1.0 CB B:ASP100 4.5 74.1 1.0 OD1 B:ASN185 4.6 67.4 1.0 NH1 B:ARG238 4.6 0.1 1.0 O B:ASP100 4.6 75.2 1.0 O B:POP700 4.9 0.7 1.0 CE1 B:PHE157 4.9 44.5 1.0 NH2 B:ARG238 5.0 0.2 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