Magnesium in PDB 1yyu: D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene

All present enzymatic activity of D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene:
4.2.3.6;

The structure of D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene, PDB code: 1yyu 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 / 2.95
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.490, 122.490, 150.610, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 25.5

The binding sites of Magnesium atom in the D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene (pdb code 1yyu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene, PDB code: 1yyu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the D100E 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 D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:41.0 occ:1.00 O1 A:POP701 2.2 83.2 1.0 OD1 A:ASN225 2.5 63.9 1.0 OE1 A:GLU233 2.7 61.9 1.0 OG A:SER229 2.8 70.8 1.0 CB A:SER229 3.1 67.7 1.0 O4 A:POP701 3.1 80.2 1.0 OE2 A:GLU233 3.2 64.2 1.0 CD A:GLU233 3.3 63.4 1.0 OD1 A:ASP226 3.4 67.4 1.0 CA A:ASP226 3.5 65.6 1.0 P1 A:POP701 3.6 83.6 1.0 CG A:ASN225 3.7 62.0 1.0 N A:ASP226 3.8 64.9 1.0 O A:ASN225 3.9 65.2 1.0 C A:ASN225 4.0 64.3 1.0 O A:POP701 4.1 82.2 1.0 P2 A:POP701 4.2 80.4 1.0 O2 A:POP701 4.2 85.0 1.0 CG A:ASP226 4.2 67.3 1.0 NH2 A:ARG182 4.2 47.6 1.0 C A:ASP226 4.4 64.9 1.0 CB A:ASP226 4.4 66.5 1.0 CA A:SER229 4.4 67.3 1.0 O A:ASP226 4.5 64.8 1.0 ND2 A:ASN225 4.6 60.8 1.0 O3 A:POP701 4.7 83.0 1.0 CB A:ASN225 4.7 62.5 1.0 CG A:GLU233 4.7 64.0 1.0 O5 A:POP701 4.7 80.1 1.0 C A:SER229 4.7 67.3 1.0 O A:SER229 5.0 67.8 1.0 CA A:ASN225 5.0 63.3 1.0

Magnesium binding site 2 out of 4 in the D100E 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 D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:54.4 occ:1.00 O2 A:POP701 2.4 85.0 1.0 O A:HOH753 2.4 62.7 1.0 O5 A:POP701 2.6 80.1 1.0 P1 A:POP701 3.5 83.6 1.0 OD1 A:ASP239 3.7 73.7 1.0 P2 A:POP701 3.8 80.4 1.0 O A:POP701 3.8 82.2 1.0 OE1 A:GLU233 4.0 61.9 1.0 NZ A:LYS232 4.3 58.6 1.0 O1 A:POP701 4.4 83.2 1.0 O3 A:POP701 4.6 83.0 1.0 O4 A:POP701 4.6 80.2 1.0 OE1 A:GLU100 4.7 69.9 1.0 CG A:ASP239 4.8 72.0 1.0 CE A:LYS232 4.8 59.1 1.0 O6 A:POP701 4.8 80.1 1.0 NH2 A:ARG304 4.9 84.0 1.0 NH1 A:ARG304 4.9 85.0 1.0

Magnesium binding site 3 out of 4 in the D100E 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 D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg708 b:53.6 occ:1.00 O2 B:POP706 2.1 85.3 1.0 O B:HOH766 2.4 64.0 1.0 P1 B:POP706 2.9 84.0 1.0 O5 B:POP706 3.1 82.3 1.0 OE1 B:GLU100 3.2 68.5 1.0 O B:POP706 3.2 82.9 1.0 O B:HOH757 3.3 43.2 1.0 O3 B:POP706 3.4 83.5 1.0 P2 B:POP706 3.8 83.1 1.0 OE2 B:GLU100 3.9 68.4 1.0 CD B:GLU100 3.9 67.1 1.0 O1 B:POP706 4.3 83.0 1.0 O6 B:POP706 4.6 81.4 1.0 OD2 B:ASP239 4.7 0.2 1.0 O4 B:POP706 5.0 81.1 1.0

Magnesium binding site 4 out of 4 in the D100E 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 4 of D100E Trichodiene Synthase: Complex with Mg, Pyrophosphate, and (4S)-7-Azabisabolene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg707 b:58.6 occ:1.00 OE1 B:GLU233 1.9 97.9 1.0 OD1 B:ASN225 2.2 63.4 1.0 O4 B:POP706 2.5 81.1 1.0 O1 B:POP706 2.6 83.0 1.0 CD B:GLU233 2.7 98.5 1.0 OG B:SER229 2.9 74.0 1.0 OE2 B:GLU233 3.0 97.8 1.0 CB B:SER229 3.2 72.2 1.0 CG B:ASN225 3.4 62.8 1.0 P2 B:POP706 3.7 83.1 1.0 P1 B:POP706 3.7 84.0 1.0 OD1 B:ASP226 4.0 69.1 1.0 CG B:GLU233 4.0 98.8 1.0 O B:POP706 4.0 82.9 1.0 O2 B:POP706 4.0 85.3 1.0 CA B:ASP226 4.1 66.2 1.0 ND2 B:ASN225 4.1 62.2 1.0 O5 B:POP706 4.1 82.3 1.0 NH2 B:ARG182 4.1 50.8 1.0 N B:ASP226 4.1 66.6 1.0 O B:ASN225 4.2 66.9 1.0 C B:ASN225 4.2 65.8 1.0 CB B:ASN225 4.5 62.8 1.0 CA B:SER229 4.6 72.3 1.0 CG B:ASP226 4.7 67.7 1.0 O6 B:POP706 4.9 81.4 1.0 CZ B:ARG182 5.0 49.5 1.0 O3 B:POP706 5.0 83.5 1.0 CB B:ASP226 5.0 66.4 1.0 C B:ASP226 5.0 66.1 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