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Magnesium in PDB 1n24: (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product

Enzymatic activity of (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product

All present enzymatic activity of (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product:
5.5.1.8;

Protein crystallography data

The structure of (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product, PDB code: 1n24 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) 30.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.200, 117.530, 120.390, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product (pdb code 1n24). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product, PDB code: 1n24:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1n24

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Magnesium binding site 1 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


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: Complex with Mg and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:29.8
occ:1.00
 OD2 A:ASP355 2.0 33.3 1.0
O A:HOH883 2.1 31.1 1.0
OD1 A:ASP351 2.1 31.5 1.0
O5 A:BP2801 2.1 29.6 1.0
O A:HOH884 2.2 26.0 1.0
O A:HOH885 2.2 31.1 1.0
CG A:ASP351 3.0 32.8 1.0
CG A:ASP355 3.0 33.8 1.0
OD2 A:ASP351 3.2 31.4 1.0
MG A:MG703 3.3 38.0 1.0
P2 A:BP2801 3.3 32.8 1.0
CB A:ASP355 3.4 31.7 1.0
O6 A:BP2801 3.5 34.5 1.0
OE1 A:GLU429 3.9 30.2 1.0
OD1 A:ASP355 4.2 31.2 1.0
O A:ASP351 4.2 31.0 1.0
O A:HOH881 4.2 29.9 1.0
OD2 A:ASP509 4.3 41.9 1.0
CE2 A:TYR426 4.3 31.6 1.0
O A:BP2801 4.3 34.1 1.0
O A:HOH816 4.3 30.4 1.0
CB A:ASP351 4.4 30.6 1.0
OD1 A:ASP509 4.4 41.5 1.0
CD2 A:TYR426 4.5 29.9 1.0
O A:HOH882 4.5 39.2 1.0
O4 A:BP2801 4.5 34.5 1.0
NZ A:LYS512 4.6 35.0 1.0
CA A:ASP355 4.7 31.8 1.0
CG A:ASP509 4.7 43.4 1.0
CA A:ASP351 4.7 30.5 1.0
C A:ASP351 4.7 30.7 1.0
N A:ASP355 4.8 31.2 1.0
O1 A:BP2801 4.9 26.4 1.0

Magnesium binding site 2 out of 6 in 1n24

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Magnesium binding site 2 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


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: Complex with Mg and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:28.9
occ:1.00
 OD1 A:ASP496 2.1 29.2 1.0
O4 A:BP2801 2.1 34.5 1.0
O2 A:BP2801 2.1 28.1 1.0
O A:HOH880 2.1 30.4 1.0
OE2 A:GLU504 2.2 46.0 1.0
OG1 A:THR500 2.2 42.1 1.0
CD A:GLU504 3.0 47.3 1.0
CG A:ASP496 3.1 32.5 1.0
OE1 A:GLU504 3.2 46.2 1.0
P1 A:BP2801 3.4 32.2 1.0
P2 A:BP2801 3.4 32.8 1.0
CB A:THR500 3.4 45.9 1.0
OD2 A:ASP496 3.4 34.2 1.0
O A:BP2801 3.6 34.1 1.0
NH1 A:ARG493 3.8 26.1 1.0
O A:ASP496 3.9 33.6 1.0
O1 A:BP2801 4.0 26.4 1.0
OD1 A:ASP497 4.1 36.2 1.0
CG2 A:THR500 4.1 44.8 1.0
NZ A:LYS512 4.2 35.0 1.0
O5 A:BP2801 4.3 29.6 1.0
O A:HOH881 4.3 29.9 1.0
C A:ASP496 4.4 32.7 1.0
CG A:GLU504 4.4 46.8 1.0
CB A:ASP496 4.4 29.5 1.0
O6 A:BP2801 4.5 34.5 1.0
O3 A:BP2801 4.6 34.7 1.0
CA A:THR500 4.6 44.5 1.0
CE A:LYS512 4.7 35.8 1.0
O A:HOH879 4.8 37.3 1.0
C A:THR500 4.8 44.4 1.0
N A:ASP497 4.8 34.3 1.0
MG A:MG703 4.9 38.0 1.0
CA A:ASP497 4.9 35.7 1.0
N A:SER501 4.9 45.2 1.0

Magnesium binding site 3 out of 6 in 1n24

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Magnesium binding site 3 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


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: Complex with Mg and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:38.0
occ:1.00
 O A:HOH882 1.9 39.2 1.0
O1 A:BP2801 2.0 26.4 1.0
OD2 A:ASP351 2.0 31.4 1.0
O A:HOH881 2.1 29.9 1.0
O5 A:BP2801 2.2 29.6 1.0
OD2 A:ASP355 2.5 33.3 1.0
CG A:ASP351 3.1 32.8 1.0
P1 A:BP2801 3.2 32.2 1.0
O A:BP2801 3.2 34.1 1.0
P2 A:BP2801 3.2 32.8 1.0
MG A:MG701 3.3 29.8 1.0
CG A:ASP355 3.3 33.8 1.0
OD1 A:ASP351 3.5 31.5 1.0
O A:HOH879 3.5 37.3 1.0
OD1 A:ASP355 3.6 31.2 1.0
NH2 A:ARG314 3.8 31.1 1.0
OE2 A:GLU504 4.0 46.0 1.0
O4 A:BP2801 4.0 34.5 1.0
O2 A:BP2801 4.2 28.1 1.0
NH1 A:ARG314 4.2 32.1 1.0
NH1 A:ARG507 4.2 50.9 1.0
O3 A:BP2801 4.3 34.7 1.0
CZ A:ARG314 4.3 33.0 1.0
OD2 A:ASP509 4.4 41.9 1.0
CB A:ASP351 4.4 30.6 1.0
O6 A:BP2801 4.5 34.5 1.0
OD1 A:ASP352 4.7 32.7 1.0
CB A:ASP355 4.7 31.7 1.0
O A:HOH885 4.7 31.1 1.0
O A:HOH883 4.8 31.1 1.0
C3 A:BP2801 4.8 33.7 1.0
O A:ASP351 4.8 31.0 1.0
MG A:MG702 4.9 28.9 1.0
CD A:GLU504 4.9 47.3 1.0
C A:ASP351 5.0 30.7 1.0

Magnesium binding site 4 out of 6 in 1n24

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Magnesium binding site 4 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:25.3
occ:1.00
 OD2 B:ASP355 2.0 31.2 1.0
OD1 B:ASP351 2.1 29.3 1.0
O B:HOH865 2.1 18.6 1.0
O5 B:BP2802 2.1 36.2 1.0
O B:HOH866 2.2 35.9 1.0
O B:HOH864 2.2 31.4 1.0
CG B:ASP351 2.9 32.6 1.0
MG B:MG705 3.0 38.6 1.0
CG B:ASP355 3.0 35.7 1.0
OD2 B:ASP351 3.1 31.1 1.0
P2 B:BP2802 3.3 37.5 1.0
CB B:ASP355 3.5 35.0 1.0
O6 B:BP2802 3.5 42.5 1.0
OE1 B:GLU429 4.0 34.6 1.0
O B:HOH862 4.1 51.3 1.0
OD1 B:ASP355 4.1 34.5 1.0
O B:BP2802 4.2 40.5 1.0
CB B:ASP351 4.3 29.7 1.0
O B:ASP351 4.4 32.1 1.0
O B:HOH863 4.4 36.1 1.0
OD2 B:ASP509 4.4 69.5 1.0
NZ B:LYS512 4.5 38.3 1.0
CE2 B:TYR426 4.5 26.5 1.0
O B:HOH932 4.5 32.0 1.0
O4 B:BP2802 4.5 38.3 1.0
CD2 B:TYR426 4.7 28.4 1.0
OD1 B:ASP509 4.7 70.5 1.0
CA B:ASP351 4.7 30.7 1.0
C B:ASP351 4.7 31.9 1.0
CA B:ASP355 4.8 36.3 1.0
O1 B:BP2802 4.8 37.7 1.0
N B:ASP355 4.8 33.4 1.0
CG B:ASP509 5.0 70.9 1.0

Magnesium binding site 5 out of 6 in 1n24

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Magnesium binding site 5 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:38.6
occ:1.00
 O B:HOH863 2.0 36.1 1.0
OD2 B:ASP351 2.0 31.1 1.0
O B:HOH862 2.1 51.3 1.0
O5 B:BP2802 2.1 36.2 1.0
O1 B:BP2802 2.2 37.7 1.0
OD2 B:ASP355 2.2 31.2 1.0
MG B:MG704 3.0 25.3 1.0
CG B:ASP351 3.1 32.6 1.0
CG B:ASP355 3.2 35.7 1.0
O B:BP2802 3.2 40.5 1.0
P2 B:BP2802 3.2 37.5 1.0
P1 B:BP2802 3.3 39.4 1.0
OD1 B:ASP351 3.4 29.3 1.0
OD1 B:ASP355 3.5 34.5 1.0
NH2 B:ARG314 3.9 31.4 1.0
O4 B:BP2802 4.1 38.3 1.0
O2 B:BP2802 4.2 38.4 1.0
CB B:ASP351 4.4 29.7 1.0
NH1 B:ARG507 4.4 90.0 1.0
O6 B:BP2802 4.4 42.5 1.0
O B:HOH864 4.4 31.4 1.0
O3 B:BP2802 4.4 44.5 1.0
CB B:ASP355 4.5 35.0 1.0
NH1 B:ARG314 4.5 29.7 1.0
CZ B:ARG314 4.5 31.8 1.0
OD1 B:ASP352 4.5 30.3 1.0
OD2 B:ASP509 4.6 69.5 1.0
O B:HOH865 4.6 18.6 1.0
MG B:MG706 4.9 45.6 1.0
O B:HOH866 4.9 35.9 1.0
C3 B:BP2802 5.0 46.2 1.0
C B:ASP351 5.0 31.9 1.0

Magnesium binding site 6 out of 6 in 1n24

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Magnesium binding site 6 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:45.6
occ:1.00
 O2 B:BP2802 2.1 38.4 1.0
O4 B:BP2802 2.1 38.3 1.0
OG1 B:THR500 2.3 58.6 1.0
O B:HOH861 2.3 35.4 1.0
OD1 B:ASP496 2.4 42.4 1.0
CG B:ASP496 3.3 42.7 1.0
P1 B:BP2802 3.4 39.4 1.0
P2 B:BP2802 3.4 37.5 1.0
CB B:THR500 3.5 61.6 1.0
OD2 B:ASP496 3.6 43.6 1.0
O B:BP2802 3.7 40.5 1.0
O B:HOH862 4.0 51.3 1.0
O1 B:BP2802 4.0 37.7 1.0
O B:ASP496 4.1 42.9 1.0
O5 B:BP2802 4.2 36.2 1.0
NH1 B:ARG493 4.2 22.7 1.0
CG2 B:THR500 4.2 60.6 1.0
NZ B:LYS512 4.4 38.3 1.0
OD1 B:ASP497 4.4 40.0 1.0
C B:THR500 4.5 62.4 1.0
C B:ASP496 4.6 41.6 1.0
O6 B:BP2802 4.6 42.5 1.0
O3 B:BP2802 4.6 44.5 1.0
CA B:THR500 4.6 61.7 1.0
CE B:LYS512 4.6 39.0 1.0
CB B:ASP496 4.7 40.9 1.0
MG B:MG705 4.9 38.6 1.0

Reference:

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 Cyclase Proc.Natl.Acad.Sci.Usa V. 99 15375 2002.
ISSN: ISSN 0027-8424
PubMed: 12432096
DOI: 10.1073/PNAS.232591099
Page generated: Sun Aug 10 01:16:47 2025

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