Magnesium in PDB 1n21: (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate

All present enzymatic activity of (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate:
5.5.1.8;

The structure of (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate, PDB code: 1n21 was solved by D.A.Whittington, M.L.Wise, M.Urbansky, R.M.Coates, R.B.Croteau, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.93 / 3.10
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	198.380, 198.380, 122.840, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 23.3

The binding sites of Magnesium atom in the (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate (pdb code 1n21). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate, PDB code: 1n21:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:10.6 occ:1.00 O A:HOH921 2.0 48.0 1.0 OD1 A:ASP351 2.2 29.2 1.0 O A:HOH922 2.2 20.7 1.0 O5 A:3AG900 2.5 19.6 1.0 OD2 A:ASP355 2.8 26.3 1.0 MG A:MG703 3.3 3.0 1.0 CG A:ASP351 3.3 28.6 1.0 CB A:ASP355 3.4 26.4 1.0 CG A:ASP355 3.4 31.5 1.0 OE1 A:GLU429 3.6 30.5 1.0 OD2 A:ASP351 3.8 26.1 1.0 CD2 A:TYR426 3.9 17.9 1.0 P2 A:3AG900 4.0 24.6 1.0 CE2 A:TYR426 4.0 16.5 1.0 OD1 A:ASP509 4.4 31.9 1.0 O7 A:3AG900 4.4 27.4 1.0 O A:ASP351 4.5 26.6 1.0 OD1 A:ASP355 4.6 30.2 1.0 CB A:ASP351 4.6 28.9 1.0 CA A:ASP355 4.6 13.3 1.0 N A:ASP355 4.6 12.1 1.0 OD2 A:ASP509 4.7 30.7 1.0 CA A:ASP351 4.8 26.6 1.0 CD A:GLU429 4.8 33.3 1.0 NZ A:LYS512 4.9 27.3 1.0 O6 A:3AG900 4.9 25.2 1.0 C A:ASP351 4.9 28.1 1.0 O3 A:3AG900 4.9 28.2 1.0 O A:HOH920 5.0 18.2 1.0 CG A:ASP509 5.0 33.1 1.0 O A:HOH925 5.0 17.1 1.0

Magnesium binding site 2 out of 3 in the (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:26.1 occ:1.00 O4 A:3AG900 1.8 28.7 1.0 O6 A:3AG900 2.1 25.2 1.0 O A:HOH919 2.1 19.8 1.0 OG1 A:THR500 2.1 17.1 1.0 OD1 A:ASP496 2.2 22.9 1.0 OE2 A:GLU504 2.2 17.2 1.0 CD A:GLU504 3.1 19.4 1.0 CG A:ASP496 3.1 28.4 1.0 P1 A:3AG900 3.1 20.8 1.0 CB A:THR500 3.2 28.3 1.0 OE1 A:GLU504 3.3 16.9 1.0 P2 A:3AG900 3.4 24.6 1.0 OD2 A:ASP496 3.4 35.4 1.0 O3 A:3AG900 3.6 28.2 1.0 CG2 A:THR500 3.7 21.6 1.0 O1 A:3AG900 3.9 16.3 1.0 O A:ASP496 3.9 18.9 1.0 NH1 A:ARG493 4.1 18.1 1.0 O7 A:3AG900 4.2 27.4 1.0 C A:ASP496 4.3 18.2 1.0 O2 A:3AG900 4.4 31.2 1.0 CG A:GLU504 4.4 16.7 1.0 O A:HOH923 4.5 13.0 1.0 NZ A:LYS512 4.5 27.3 1.0 OD1 A:ASP497 4.5 31.8 1.0 O5 A:3AG900 4.5 19.6 1.0 CB A:ASP496 4.5 24.3 1.0 CA A:THR500 4.5 23.3 1.0 C8 A:3AG900 4.6 27.5 1.0 C A:THR500 4.7 25.5 1.0 N A:ASP497 4.7 34.1 1.0 MG A:MG703 4.8 3.0 1.0 CA A:ASP497 4.8 37.9 1.0 CE A:LYS512 4.9 29.2 1.0 N A:SER501 5.0 40.6 1.0 CA A:ASP496 5.0 19.3 1.0

Magnesium binding site 3 out of 3 in the (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3- Aza-2,3-Dihydrogeranyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:3.0 occ:1.00 O5 A:3AG900 1.9 19.6 1.0 OD2 A:ASP351 2.1 26.1 1.0 O A:HOH920 2.3 18.2 1.0 O1 A:3AG900 2.3 16.3 1.0 OD2 A:ASP355 2.3 26.3 1.0 O A:HOH923 2.4 13.0 1.0 P2 A:3AG900 2.9 24.6 1.0 O A:HOH921 2.9 48.0 1.0 CG A:ASP351 3.0 28.6 1.0 O3 A:3AG900 3.0 28.2 1.0 OD1 A:ASP351 3.1 29.2 1.0 CG A:ASP355 3.2 31.5 1.0 P1 A:3AG900 3.2 20.8 1.0 MG A:MG701 3.3 10.6 1.0 O6 A:3AG900 3.5 25.2 1.0 OD1 A:ASP355 3.5 30.2 1.0 OE2 A:GLU504 3.9 17.2 1.0 OD2 A:ASP509 4.2 30.7 1.0 O4 A:3AG900 4.2 28.7 1.0 O7 A:3AG900 4.3 27.4 1.0 CB A:ASP355 4.3 26.4 1.0 O A:HOH922 4.4 20.7 1.0 CB A:ASP351 4.4 28.9 1.0 O2 A:3AG900 4.4 31.2 1.0 NH2 A:ARG314 4.5 25.2 1.0 MG A:MG702 4.8 26.1 1.0 NH1 A:ARG507 4.8 42.0 1.0 CD A:GLU504 4.8 19.4 1.0

D.A.Whittington, M.L.Wise, M.Urbansky, R.M.Coates, R.B.Croteau, D.W.Christianson. Bornyl Diphosphate Synthase: Structure and Strategy For Carbocation Manipulation By A Terpenoid Synthase Proc.Natl.Acad.Sci.Usa V. 99 15375 2002.
ISSN: ISSN 0027-8424
PubMed: 12432096
DOI: 10.1073/PNAS.232591099