Magnesium in PDB 2ps5: N225D Trichodiene Synthase: Complex with Mg and Pyrophosphate

All present enzymatic activity of N225D Trichodiene Synthase: Complex with Mg and Pyrophosphate:
4.2.3.6;

The structure of N225D Trichodiene Synthase: Complex with Mg and Pyrophosphate, PDB code: 2ps5 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 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.226, 122.226, 151.300, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 24.8

The binding sites of Magnesium atom in the N225D Trichodiene Synthase: Complex with Mg and Pyrophosphate (pdb code 2ps5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the N225D Trichodiene Synthase: Complex with Mg and Pyrophosphate, PDB code: 2ps5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the N225D 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 N225D Trichodiene Synthase: Complex with Mg and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:49.7 occ:1.00 O B:HOH929 2.1 41.0 1.0 O4 B:POP700 2.2 46.4 1.0 O1 B:POP700 2.2 43.5 1.0 OD1 B:ASP225 2.3 41.1 1.0 OG B:SER229 2.4 48.0 1.0 OE2 B:GLU233 2.5 55.9 1.0 CD B:GLU233 3.0 57.4 1.0 OE1 B:GLU233 3.2 56.3 1.0 P2 B:POP700 3.4 47.2 1.0 CG B:ASP225 3.4 40.6 1.0 P1 B:POP700 3.4 46.4 1.0 CB B:SER229 3.4 49.1 1.0 O B:POP700 3.4 46.5 1.0 OD2 B:ASP225 3.8 38.5 1.0 O B:ASP225 3.9 40.9 1.0 O B:HOH896 4.0 38.4 1.0 CG B:GLU233 4.1 57.1 1.0 NH2 B:ARG182 4.1 35.8 1.0 O B:HOH933 4.2 38.4 1.0 O5 B:POP700 4.2 46.8 1.0 O2 B:POP700 4.3 46.7 1.0 C B:ASP225 4.3 39.8 1.0 O6 B:POP700 4.4 46.5 1.0 O3 B:POP700 4.4 48.7 1.0 OD1 B:ASP226 4.5 40.5 1.0 CB B:ASP225 4.6 38.4 1.0 CA B:ASP226 4.7 43.4 1.0 N B:ASP226 4.7 41.4 1.0 CA B:SER229 4.7 48.7 1.0 CE B:LYS232 4.8 48.4 1.0 CZ B:ARG182 4.8 34.4 1.0 O B:SER229 4.9 49.3 1.0 NH1 B:ARG182 4.9 34.1 1.0 C B:SER229 5.0 48.9 1.0

Magnesium binding site 2 out of 3 in the N225D 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 N225D Trichodiene Synthase: Complex with Mg and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:40.1 occ:1.00 O B:HOH933 2.0 38.4 1.0 O B:HOH934 2.0 42.8 1.0 O2 B:POP700 2.1 46.7 1.0 OD2 B:ASP100 2.2 38.5 1.0 O5 B:POP700 2.4 46.8 1.0 O B:HOH932 2.4 45.7 1.0 CG B:ASP100 3.0 37.1 1.0 P1 B:POP700 3.1 46.4 1.0 MG B:MG703 3.2 45.2 1.0 OD1 B:ASP100 3.2 37.3 1.0 P2 B:POP700 3.5 47.2 1.0 O B:HOH936 3.5 42.5 1.0 O B:POP700 3.5 46.5 1.0 NH2 B:ARG304 3.8 45.3 1.0 O1 B:POP700 3.9 43.5 1.0 O B:HOH930 4.0 39.1 1.0 OD1 B:ASP239 4.1 53.7 1.0 NZ B:LYS232 4.1 46.2 1.0 O B:ASP100 4.2 42.4 1.0 OD1 B:ASP101 4.2 48.6 1.0 O4 B:POP700 4.2 46.4 1.0 OE2 B:GLU233 4.3 55.9 1.0 O3 B:POP700 4.3 48.7 1.0 CB B:ASP100 4.4 37.1 1.0 O B:HOH896 4.6 38.4 1.0 O6 B:POP700 4.7 46.5 1.0 O B:HOH931 4.7 38.6 1.0 CG B:ASP239 4.7 57.0 1.0 O B:HOH935 4.8 32.5 1.0 C B:ASP100 4.8 42.3 1.0 O B:HOH924 4.9 43.4 1.0

Magnesium binding site 3 out of 3 in the N225D 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 N225D Trichodiene Synthase: Complex with Mg and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:45.2 occ:1.00 O2 B:POP700 2.1 46.7 1.0 O B:HOH931 2.1 38.6 1.0 O B:HOH930 2.1 39.1 1.0 O B:HOH935 2.1 32.5 1.0 OD1 B:ASP100 2.2 37.3 1.0 O B:HOH932 2.7 45.7 1.0 MG B:MG702 3.2 40.1 1.0 CG B:ASP100 3.2 37.1 1.0 P1 B:POP700 3.3 46.4 1.0 O3 B:POP700 3.5 48.7 1.0 OD2 B:ASP100 3.6 38.5 1.0 OE2 B:GLU164 3.8 39.0 1.0 OE1 B:GLU164 3.8 34.8 1.0 O B:HOH936 4.1 42.5 1.0 O B:HOH896 4.1 38.4 1.0 O B:HOH933 4.2 38.4 1.0 O B:HOH924 4.2 43.4 1.0 CD B:GLU164 4.2 38.7 1.0 CG B:ASN185 4.3 32.8 1.0 O1 B:POP700 4.3 43.5 1.0 CB B:ASN185 4.3 29.9 1.0 O B:ASN185 4.5 29.4 1.0 CB B:ASP100 4.5 37.1 1.0 ND2 B:ASN185 4.5 31.2 1.0 O B:POP700 4.6 46.5 1.0 OD1 B:ASN185 4.6 30.5 1.0 O B:ASP100 4.7 42.4 1.0 CE1 B:PHE157 4.7 28.2 1.0 O B:HOH934 4.8 42.8 1.0 NH1 B:ARG182 4.9 34.1 1.0 CA B:ASP100 4.9 39.3 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