Magnesium in PDB 2ps8: Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate

All present enzymatic activity of Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate:
4.2.3.6;

The structure of Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate, PDB code: 2ps8 was solved by L.S.Vedula, 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 / 2.67
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.272, 122.272, 150.474, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 24.5

The binding sites of Magnesium atom in the Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate (pdb code 2ps8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate, PDB code: 2ps8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:50.7 occ:1.00 OD1 B:ASN225 2.2 47.3 1.0 O1 B:POP700 2.3 47.7 1.0 OG B:SER229 2.4 53.2 1.0 OE2 B:GLU233 2.5 55.5 1.0 O4 B:POP700 2.9 52.7 1.0 CD B:GLU233 2.9 55.7 1.0 OE1 B:GLU233 2.9 54.1 1.0 CG B:ASN225 3.4 43.1 1.0 O B:ASN225 3.6 46.8 1.0 CB B:SER229 3.7 54.5 1.0 P1 B:POP700 3.7 49.4 1.0 NH2 B:ARG182 3.9 36.1 1.0 OD1 B:ASP226 3.9 50.4 1.0 C B:ASN225 4.0 46.7 1.0 O B:POP700 4.0 50.5 1.0 P2 B:POP700 4.0 52.2 1.0 CA B:ASP226 4.0 49.8 1.0 ND2 B:ASN225 4.1 41.1 1.0 O B:HOH883 4.2 32.4 1.0 N B:ASP226 4.2 47.8 1.0 CG B:GLU233 4.2 57.3 1.0 O B:HOH896 4.4 43.5 1.0 CB B:ASN225 4.5 42.9 1.0 CZ B:ARG182 4.6 36.5 1.0 O3 B:POP700 4.6 49.0 1.0 O2 B:POP700 4.7 48.1 1.0 CG B:ASP226 4.7 48.8 1.0 NH1 B:ARG182 4.8 34.1 1.0 O B:HOH830 4.8 32.3 1.0 CA B:SER229 4.8 54.7 1.0 CA B:ASN225 4.9 45.0 1.0 O B:SER229 4.9 53.3 1.0 C B:ASP226 4.9 50.8 1.0 O B:HOH840 4.9 36.0 1.0 C B:SER229 4.9 54.6 1.0 O5 B:POP700 4.9 50.8 1.0 O B:ASP226 5.0 49.9 1.0 CB B:ASP226 5.0 48.5 1.0

Magnesium binding site 2 out of 3 in the Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:45.9 occ:1.00 O B:HOH896 1.8 43.5 1.0 O B:HOH894 2.0 36.1 1.0 O2 B:POP700 2.0 48.1 1.0 O B:HOH895 2.1 41.9 1.0 OD2 B:ASP100 2.2 40.0 1.0 O5 B:POP700 2.4 50.8 1.0 P1 B:POP700 3.0 49.4 1.0 CG B:ASP100 3.0 38.8 1.0 OD1 B:ASP100 3.1 36.1 1.0 O B:HOH898 3.3 38.1 1.0 P2 B:POP700 3.4 52.2 1.0 O B:POP700 3.4 50.5 1.0 MG B:MG703 3.4 51.5 1.0 O1 B:POP700 3.6 47.7 1.0 OD1 B:ASP239 3.9 54.5 1.0 OE2 B:GLU233 4.0 55.5 1.0 O4 B:POP700 4.0 52.7 1.0 O B:HOH883 4.1 32.4 1.0 O B:HOH897 4.2 42.8 1.0 NH2 B:ARG304 4.2 47.5 1.0 NZ B:LYS232 4.2 42.3 1.0 O3 B:POP700 4.2 49.0 1.0 O B:ASP100 4.3 42.0 1.0 CB B:ASP100 4.4 39.3 1.0 OD1 B:ASP101 4.5 47.1 1.0 O6 B:POP700 4.6 53.0 1.0 CG B:ASP239 4.7 55.1 1.0 C B:ASP100 4.8 43.0 1.0

Magnesium binding site 3 out of 3 in the Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Y295F Trichodiene Synthase: Complex with Mg and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:51.5 occ:1.00 O B:HOH897 2.1 42.8 1.0 O2 B:POP700 2.5 48.1 1.0 OD1 B:ASP100 2.5 36.1 1.0 O B:HOH895 2.7 41.9 1.0 OE2 B:GLU164 3.1 47.3 1.0 OE1 B:GLU164 3.3 46.4 1.0 O B:HOH883 3.3 32.4 1.0 MG B:MG702 3.4 45.9 1.0 O B:HOH898 3.6 38.1 1.0 CD B:GLU164 3.6 45.9 1.0 CG B:ASP100 3.6 38.8 1.0 P1 B:POP700 3.9 49.4 1.0 OD2 B:ASP100 4.1 40.0 1.0 CG B:ASN185 4.1 41.9 1.0 O B:HOH896 4.2 43.5 1.0 CB B:ASN185 4.2 39.1 1.0 O3 B:POP700 4.2 49.0 1.0 NH2 B:ARG238 4.3 49.0 1.0 ND2 B:ASN185 4.4 45.8 1.0 OD1 B:ASN185 4.4 42.7 1.0 O1 B:POP700 4.5 47.7 1.0 O B:ASP100 4.6 42.0 1.0 O B:ASN185 4.7 36.9 1.0 O B:HOH814 4.9 31.3 1.0 CB B:ASP100 4.9 39.3 1.0 NH1 B:ARG182 4.9 34.1 1.0 O B:HOH866 4.9 36.2 1.0 CE1 B:PHE157 5.0 26.6 1.0

L.S.Vedula, J.Jiang, T.Zakharian, D.E.Cane, D.W.Christianson. Structural and Mechanistic Analysis of Trichodiene Synthase Using Site-Directed Mutagenesis: Probing the Catalytic Function of Tyrosine-295 and the Asparagine-225/Serine-229/Glutamate-233-MG2+B Motif. Arch.Biochem.Biophys. V. 469 184 2008.
ISSN: ISSN 0003-9861
PubMed: 17996718
DOI: 10.1016/J.ABB.2007.10.015