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

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

The structure of Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene, PDB code: 1yyr 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)	50.00 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.020, 122.020, 150.360, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 25.5

The binding sites of Magnesium atom in the Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene (pdb code 1yyr). 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 (4R)-7-Azabisabolene, PDB code: 1yyr:
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 (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 Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:56.3 occ:1.00 O4 B:POP700 1.9 54.3 1.0 OD1 B:ASN225 2.0 51.6 1.0 OG B:SER229 2.2 60.9 1.0 O B:HOH802 2.2 37.4 1.0 OE1 B:GLU233 2.3 71.5 1.0 O1 B:POP700 2.3 51.6 1.0 CG B:ASN225 3.0 48.3 1.0 P2 B:POP700 3.1 53.6 1.0 CB B:SER229 3.1 62.6 1.0 CD B:GLU233 3.1 70.5 1.0 O B:POP700 3.1 52.9 1.0 ND2 B:ASN225 3.3 43.0 1.0 P1 B:POP700 3.3 51.8 1.0 OE2 B:GLU233 3.5 69.1 1.0 O B:ASN225 3.8 54.5 1.0 O6 B:POP700 3.9 56.7 1.0 NH2 B:ARG182 4.2 52.1 1.0 O5 B:POP700 4.2 55.0 1.0 C B:ASN225 4.2 53.6 1.0 O3 B:POP700 4.3 50.6 1.0 CG B:GLU233 4.3 70.2 1.0 CB B:ASN225 4.4 47.9 1.0 O2 B:POP700 4.4 48.2 1.0 MG B:MG702 4.4 46.8 1.0 CA B:SER229 4.5 63.0 1.0 N B:ASP226 4.7 56.0 1.0 CE B:LYS232 4.7 54.6 1.0 O B:SER229 4.7 62.9 1.0 CA B:ASP226 4.8 58.2 1.0 C B:SER229 4.8 63.4 1.0 OD1 B:ASP226 4.9 60.9 1.0 CA B:ASN225 4.9 51.5 1.0 CZ B:ARG182 4.9 51.4 1.0 NH1 B:ARG182 5.0 49.4 1.0

Magnesium binding site 2 out of 3 in the Y305F 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 Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:46.8 occ:1.00 O2 B:POP700 2.2 48.2 1.0 O B:HOH822 2.3 43.9 1.0 O B:HOH820 2.3 49.8 1.0 O5 B:POP700 2.5 55.0 1.0 OD1 B:ASP100 2.8 50.5 1.0 P1 B:POP700 3.1 51.8 1.0 OD1 B:ASP239 3.3 70.0 1.0 O1 B:POP700 3.4 51.6 1.0 P2 B:POP700 3.4 53.6 1.0 OE1 B:GLU233 3.5 71.5 1.0 NZ B:LYS232 3.5 48.8 1.0 O B:POP700 3.6 52.9 1.0 O4 B:POP700 3.6 54.3 1.0 MG B:MG703 3.6 55.8 1.0 CG B:ASP100 3.8 49.9 1.0 O B:HOH823 3.9 44.0 1.0 OD2 B:ASP100 4.0 49.5 1.0 CG B:ASP239 4.2 68.8 1.0 NH2 B:ARG304 4.3 54.4 1.0 CE B:LYS232 4.4 54.6 1.0 MG B:MG701 4.4 56.3 1.0 O3 B:POP700 4.5 50.6 1.0 OD2 B:ASP239 4.5 70.1 1.0 CD B:GLU233 4.5 70.5 1.0 O B:ASP100 4.6 51.1 1.0 OD1 B:ASP101 4.8 56.0 1.0 O6 B:POP700 4.8 56.7 1.0 CG B:GLU233 4.8 70.2 1.0 O B:HOH821 5.0 49.5 1.0

Magnesium binding site 3 out of 3 in the Y305F 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 3 of Y305F Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:55.8 occ:1.00 OD2 B:ASP100 1.9 49.5 1.0 O B:HOH823 2.1 44.0 1.0 O B:HOH821 2.2 49.5 1.0 O2 B:POP700 2.2 48.2 1.0 O B:HOH820 2.4 49.8 1.0 CG B:ASP100 2.9 49.9 1.0 OD1 B:ASP100 3.3 50.5 1.0 P1 B:POP700 3.5 51.8 1.0 MG B:MG702 3.6 46.8 1.0 OE1 B:GLU164 3.7 59.6 1.0 O3 B:POP700 3.7 50.6 1.0 OE2 B:GLU164 3.8 63.1 1.0 CD B:GLU164 4.2 60.1 1.0 CB B:ASP100 4.2 48.8 1.0 O B:ASP100 4.3 51.1 1.0 CB B:ASN185 4.4 48.3 1.0 O1 B:POP700 4.4 51.6 1.0 CE1 B:PHE157 4.5 35.1 1.0 CA B:ASP100 4.6 51.3 1.0 CG B:ASN185 4.6 50.7 1.0 NH2 B:ARG238 4.7 65.1 1.0 O B:POP700 4.8 52.9 1.0 O B:ASN185 4.8 46.4 1.0 O B:HOH822 4.8 43.9 1.0 C B:ASP100 4.9 52.4 1.0 ND2 B:ASN185 4.9 51.5 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