Magnesium in PDB 1yyq: Y305F Trichodiene Synthase Complexed with Pyrophosphate

All present enzymatic activity of Y305F Trichodiene Synthase Complexed with Pyrophosphate:
4.2.3.6;

The structure of Y305F Trichodiene Synthase Complexed with Pyrophosphate, PDB code: 1yyq 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 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.060, 122.060, 150.340, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 26.1

The binding sites of Magnesium atom in the Y305F Trichodiene Synthase Complexed with Pyrophosphate (pdb code 1yyq). 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 Complexed with Pyrophosphate, PDB code: 1yyq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Y305F Trichodiene Synthase Complexed with Pyrophosphate


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 Complexed with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:47.4 occ:1.00 O1 B:POP700 2.1 39.6 1.0 OE1 B:GLU233 2.1 56.5 1.0 O B:HOH800 2.2 40.7 1.0 O4 B:POP700 2.2 43.1 1.0 OD1 B:ASN225 2.2 45.6 1.0 OG B:SER229 2.5 47.2 1.0 CD B:GLU233 3.0 55.5 1.0 P1 B:POP700 3.3 42.0 1.0 CG B:ASN225 3.3 43.8 1.0 OE2 B:GLU233 3.3 53.4 1.0 P2 B:POP700 3.3 43.4 1.0 O B:POP700 3.4 41.0 1.0 CB B:SER229 3.5 50.8 1.0 O B:HOH772 3.7 43.8 1.0 ND2 B:ASN225 3.9 42.4 1.0 O B:ASN225 3.9 47.1 1.0 O B:HOH804 4.0 41.6 1.0 O5 B:POP700 4.1 40.9 1.0 NH2 B:ARG182 4.1 41.9 1.0 O2 B:POP700 4.2 41.5 1.0 CG B:GLU233 4.2 55.9 1.0 C B:ASN225 4.3 45.7 1.0 O3 B:POP700 4.4 43.5 1.0 OD1 B:ASP226 4.4 45.1 1.0 O6 B:POP700 4.4 44.1 1.0 CB B:ASN225 4.6 43.5 1.0 CA B:ASP226 4.6 48.3 1.0 N B:ASP226 4.7 46.4 1.0 NH1 B:ARG182 4.7 39.1 1.0 CZ B:ARG182 4.8 40.7 1.0 O B:HOH759 4.8 41.0 1.0 CE B:LYS232 4.9 45.0 1.0 CA B:SER229 4.9 51.4 1.0 MG B:MG702 4.9 41.8 1.0

Magnesium binding site 2 out of 3 in the Y305F Trichodiene Synthase Complexed with Pyrophosphate


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 Complexed with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:41.8 occ:1.00 O B:HOH805 2.0 40.0 1.0 O B:HOH804 2.1 41.6 1.0 OD1 B:ASP100 2.1 40.1 1.0 O2 B:POP700 2.2 41.5 1.0 O B:HOH803 2.2 41.8 1.0 O5 B:POP700 2.3 40.9 1.0 CG B:ASP100 3.0 38.4 1.0 MG B:MG703 3.0 45.7 1.0 OD2 B:ASP100 3.2 35.2 1.0 P1 B:POP700 3.2 42.0 1.0 P2 B:POP700 3.5 43.4 1.0 O B:POP700 3.5 41.0 1.0 NH2 B:ARG304 3.7 48.3 1.0 NZ B:LYS232 3.9 43.0 1.0 O1 B:POP700 3.9 39.6 1.0 O B:HOH801 3.9 38.2 1.0 O B:ASP100 4.0 44.1 1.0 OD1 B:ASP239 4.1 48.6 1.0 OD1 B:ASP101 4.2 49.7 1.0 OE1 B:GLU233 4.2 56.5 1.0 O4 B:POP700 4.3 43.1 1.0 CB B:ASP100 4.4 39.1 1.0 O3 B:POP700 4.4 43.5 1.0 O B:HOH772 4.4 43.8 1.0 O B:HOH802 4.6 40.4 1.0 O6 B:POP700 4.6 44.1 1.0 C B:ASP100 4.6 43.1 1.0 O B:HOH806 4.8 35.3 1.0 CG B:ASP239 4.8 54.0 1.0 MG B:MG701 4.9 47.4 1.0 OD2 B:ASP239 4.9 53.1 1.0 CE B:LYS232 4.9 45.0 1.0 CZ B:ARG304 5.0 49.1 1.0

Magnesium binding site 3 out of 3 in the Y305F Trichodiene Synthase Complexed with Pyrophosphate


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 Complexed with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:45.7 occ:1.00 OD2 B:ASP100 1.9 35.2 1.0 O2 B:POP700 2.0 41.5 1.0 O B:HOH806 2.0 35.3 1.0 O B:HOH801 2.0 38.2 1.0 O B:HOH802 2.1 40.4 1.0 O B:HOH803 2.3 41.8 1.0 CG B:ASP100 3.0 38.4 1.0 MG B:MG702 3.0 41.8 1.0 P1 B:POP700 3.3 42.0 1.0 OD1 B:ASP100 3.4 40.1 1.0 O3 B:POP700 3.6 43.5 1.0 OE2 B:GLU164 3.9 44.1 1.0 OE1 B:GLU164 4.0 40.3 1.0 O B:HOH772 4.1 43.8 1.0 O B:HOH804 4.2 41.6 1.0 CB B:ASP100 4.2 39.1 1.0 O1 B:POP700 4.3 39.6 1.0 O B:ASP100 4.3 44.1 1.0 CD B:GLU164 4.4 44.1 1.0 O B:POP700 4.5 41.0 1.0 CE1 B:PHE157 4.5 35.6 1.0 CB B:ASN185 4.5 35.6 1.0 O B:ASN185 4.6 37.4 1.0 O B:HOH805 4.6 40.0 1.0 CG B:ASN185 4.6 37.2 1.0 CA B:ASP100 4.7 41.2 1.0 O5 B:POP700 4.9 40.9 1.0 C B:ASP100 4.9 43.1 1.0 ND2 B:ASN185 4.9 38.8 1.0 OD1 B:ASN185 4.9 34.4 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