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Magnesium in PDB 1n20: (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate

Enzymatic activity of (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate

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

Protein crystallography data

The structure of (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate, PDB code: 1n20 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) 28.77 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.080, 117.540, 120.040, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate (pdb code 1n20). 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 3-Aza- 2,3-Dihydrogeranyl Diphosphate, PDB code: 1n20:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1n20

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Magnesium binding site 1 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex 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: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:29.5
occ:1.00
 OD1 A:ASP351 2.0 34.8 1.0
O5 A:3AG900 2.1 29.2 1.0
O A:HOH978 2.1 27.9 1.0
OD2 A:ASP355 2.2 36.1 1.0
O A:HOH979 2.2 29.7 1.0
O A:HOH977 2.3 26.9 1.0
CG A:ASP351 2.9 34.0 1.0
MG A:MG702 3.1 41.9 1.0
CG A:ASP355 3.2 40.4 1.0
OD2 A:ASP351 3.2 31.6 1.0
P2 A:3AG900 3.3 34.6 1.0
O7 A:3AG900 3.5 37.2 1.0
CB A:ASP355 3.6 35.5 1.0
OE1 A:GLU429 3.8 34.3 1.0
O A:HOH976 4.2 33.8 1.0
OD2 A:ASP509 4.2 49.3 1.0
O A:HOH944 4.3 33.0 1.0
CB A:ASP351 4.3 34.2 1.0
CE2 A:TYR426 4.3 28.8 1.0
OD1 A:ASP355 4.3 39.1 1.0
O A:ASP351 4.3 31.9 1.0
O3 A:3AG900 4.4 38.2 1.0
O6 A:3AG900 4.4 35.4 1.0
CD2 A:TYR426 4.4 29.8 1.0
OD1 A:ASP509 4.4 50.7 1.0
NZ A:LYS512 4.5 39.0 1.0
O A:HOH975 4.6 34.0 1.0
CA A:ASP351 4.8 31.6 1.0
O1 A:3AG900 4.8 25.8 1.0
CG A:ASP509 4.8 51.8 1.0
C A:ASP351 4.9 33.1 1.0
CA A:ASP355 4.9 37.8 1.0
N A:ASP355 4.9 36.6 1.0

Magnesium binding site 2 out of 6 in 1n20

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Magnesium binding site 2 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex 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: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:41.9
occ:1.00
 OD2 A:ASP351 2.0 31.6 1.0
O1 A:3AG900 2.0 25.8 1.0
O A:HOH975 2.0 34.0 1.0
O5 A:3AG900 2.0 29.2 1.0
O A:HOH976 2.1 33.8 1.0
OD2 A:ASP355 2.2 36.1 1.0
CG A:ASP351 3.0 34.0 1.0
CG A:ASP355 3.1 40.4 1.0
MG A:MG701 3.1 29.5 1.0
P1 A:3AG900 3.2 30.3 1.0
P2 A:3AG900 3.2 34.6 1.0
O3 A:3AG900 3.3 38.2 1.0
OD1 A:ASP351 3.3 34.8 1.0
OD1 A:ASP355 3.4 39.1 1.0
O A:HOH1037 3.6 50.3 1.0
NH1 A:ARG507 3.9 55.2 1.0
NH2 A:ARG314 3.9 38.0 1.0
OE2 A:GLU504 4.1 49.8 1.0
O6 A:3AG900 4.1 35.4 1.0
O4 A:3AG900 4.2 38.5 1.0
OD2 A:ASP509 4.2 49.3 1.0
O2 A:3AG900 4.3 41.0 1.0
CB A:ASP351 4.3 34.2 1.0
O7 A:3AG900 4.4 37.2 1.0
CB A:ASP355 4.5 35.5 1.0
O A:HOH977 4.6 26.9 1.0
O A:ASP351 4.6 31.9 1.0
CZ A:ARG314 4.7 40.4 1.0
OD1 A:ASP352 4.7 32.4 1.0
NH1 A:ARG314 4.8 38.6 1.0
C A:ASP351 4.8 33.1 1.0
O A:HOH978 4.9 27.9 1.0
O A:HOH979 4.9 29.7 1.0
CZ A:ARG507 4.9 56.2 1.0
NH2 A:ARG507 4.9 55.7 1.0
CD A:GLU504 5.0 51.8 1.0

Magnesium binding site 3 out of 6 in 1n20

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Magnesium binding site 3 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex 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: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:38.4
occ:1.00
 OD1 A:ASP496 2.0 36.4 1.0
OG1 A:THR500 2.1 32.9 1.0
O6 A:3AG900 2.1 35.4 1.0
O A:HOH980 2.2 37.1 1.0
O4 A:3AG900 2.2 38.5 1.0
OE2 A:GLU504 2.3 49.8 1.0
CD A:GLU504 3.1 51.8 1.0
CG A:ASP496 3.2 41.9 1.0
OE1 A:GLU504 3.2 48.8 1.0
CB A:THR500 3.4 44.1 1.0
P2 A:3AG900 3.5 34.6 1.0
P1 A:3AG900 3.5 30.3 1.0
OD2 A:ASP496 3.7 48.9 1.0
NH1 A:ARG493 3.8 32.2 1.0
O3 A:3AG900 3.8 38.2 1.0
O A:ASP496 3.8 38.5 1.0
CG2 A:THR500 4.0 37.8 1.0
OD1 A:ASP497 4.1 41.6 1.0
C A:ASP496 4.2 37.9 1.0
NZ A:LYS512 4.3 39.0 1.0
O1 A:3AG900 4.4 25.8 1.0
CB A:ASP496 4.4 38.0 1.0
O5 A:3AG900 4.4 29.2 1.0
CG A:GLU504 4.5 49.3 1.0
CA A:THR500 4.5 45.9 1.0
O7 A:3AG900 4.6 37.2 1.0
N A:ASP497 4.6 37.0 1.0
CE A:LYS512 4.6 40.3 1.0
C A:THR500 4.7 48.0 1.0
CA A:ASP497 4.7 40.7 1.0
O2 A:3AG900 4.7 41.0 1.0
O A:HOH976 4.8 33.8 1.0
CA A:ASP496 4.9 38.7 1.0
C8 A:3AG900 4.9 37.4 1.0
N A:SER501 4.9 49.4 1.0
N A:THR500 4.9 45.8 1.0

Magnesium binding site 4 out of 6 in 1n20

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Magnesium binding site 4 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex 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 4 of (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:44.3
occ:1.00
 O6 B:3AG901 2.1 34.6 1.0
O4 B:3AG901 2.1 34.8 1.0
O B:HOH965 2.1 39.6 1.0
OD1 B:ASP496 2.2 38.0 1.0
OE2 B:GLU504 2.3 51.0 1.0
OG1 B:THR500 2.3 36.5 1.0
CD B:GLU504 3.0 55.0 1.0
OE1 B:GLU504 3.1 53.9 1.0
CG B:ASP496 3.4 41.6 1.0
P2 B:3AG901 3.4 32.5 1.0
P1 B:3AG901 3.4 35.4 1.0
CB B:THR500 3.5 44.4 1.0
O3 B:3AG901 3.7 37.5 1.0
NH1 B:ARG493 3.8 27.9 1.0
OD2 B:ASP496 3.9 48.8 1.0
O B:ASP496 3.9 41.3 1.0
CG2 B:THR500 4.2 40.2 1.0
OD1 B:ASP497 4.2 33.7 1.0
O1 B:3AG901 4.3 32.6 1.0
NZ B:LYS512 4.3 35.6 1.0
O5 B:3AG901 4.3 29.7 1.0
C B:ASP496 4.3 39.7 1.0
CG B:GLU504 4.4 58.5 1.0
O B:HOH966 4.4 34.2 1.0
CE B:LYS512 4.6 36.7 1.0
O7 B:3AG901 4.6 39.5 1.0
CB B:ASP496 4.6 39.6 1.0
O2 B:3AG901 4.6 42.4 1.0
CA B:THR500 4.7 46.1 1.0
N B:ASP497 4.7 38.5 1.0
CA B:ASP497 4.8 38.8 1.0
C B:THR500 4.8 47.9 1.0
C8 B:3AG901 4.8 44.1 1.0

Magnesium binding site 5 out of 6 in 1n20

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Magnesium binding site 5 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex 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 5 of (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:33.4
occ:1.00
 OD2 B:ASP351 1.9 30.1 1.0
O B:HOH966 2.0 34.2 1.0
O5 B:3AG901 2.0 29.7 1.0
O B:HOH967 2.1 37.1 1.0
O1 B:3AG901 2.1 32.6 1.0
OD2 B:ASP355 2.2 30.1 1.0
CG B:ASP351 2.9 33.9 1.0
MG B:MG706 3.0 31.9 1.0
CG B:ASP355 3.1 37.5 1.0
P2 B:3AG901 3.1 32.5 1.0
P1 B:3AG901 3.2 35.4 1.0
O3 B:3AG901 3.2 37.5 1.0
OD1 B:ASP351 3.3 34.5 1.0
OD1 B:ASP355 3.3 37.6 1.0
NH2 B:ARG314 3.9 40.5 1.0
NH1 B:ARG507 4.0 71.3 1.0
OE2 B:GLU504 4.0 51.0 1.0
O6 B:3AG901 4.1 34.6 1.0
OD2 B:ASP509 4.2 49.2 1.0
O4 B:3AG901 4.2 34.8 1.0
CB B:ASP351 4.3 30.0 1.0
O7 B:3AG901 4.3 39.5 1.0
O2 B:3AG901 4.4 42.4 1.0
O B:HOH969 4.4 28.0 1.0
CB B:ASP355 4.4 30.0 1.0
OD1 B:ASP352 4.6 32.2 1.0
CZ B:ARG314 4.7 40.4 1.0
O B:HOH968 4.7 34.7 1.0
O B:HOH970 4.8 23.3 1.0
C B:ASP351 4.9 34.3 1.0
O B:ASP351 4.9 35.4 1.0
NH1 B:ARG314 4.9 41.1 1.0

Magnesium binding site 6 out of 6 in 1n20

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Magnesium binding site 6 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex 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 6 of (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-Aza- 2,3-Dihydrogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:31.9
occ:1.00
 OD1 B:ASP351 1.9 34.5 1.0
O B:HOH968 2.0 34.7 1.0
OD2 B:ASP355 2.0 30.1 1.0
O B:HOH969 2.1 28.0 1.0
O5 B:3AG901 2.2 29.7 1.0
O B:HOH970 2.2 23.3 1.0
CG B:ASP351 2.9 33.9 1.0
MG B:MG705 3.0 33.4 1.0
CG B:ASP355 3.1 37.5 1.0
OD2 B:ASP351 3.2 30.1 1.0
P2 B:3AG901 3.4 32.5 1.0
O7 B:3AG901 3.5 39.5 1.0
CB B:ASP355 3.6 30.0 1.0
OE1 B:GLU429 3.9 32.5 1.0
O B:HOH966 4.0 34.2 1.0
OD1 B:ASP355 4.2 37.6 1.0
OD2 B:ASP509 4.2 49.2 1.0
CB B:ASP351 4.3 30.0 1.0
OD1 B:ASP509 4.4 50.0 1.0
O3 B:3AG901 4.4 37.5 1.0
O B:ASP351 4.4 35.4 1.0
CE2 B:TYR426 4.4 25.3 1.0
O B:HOH1006 4.5 34.1 1.0
NZ B:LYS512 4.5 35.6 1.0
CD2 B:TYR426 4.5 25.3 1.0
O6 B:3AG901 4.5 34.6 1.0
O B:HOH967 4.6 37.1 1.0
CA B:ASP351 4.7 31.9 1.0
CG B:ASP509 4.7 51.4 1.0
C B:ASP351 4.8 34.3 1.0
CA B:ASP355 4.9 35.7 1.0
O1 B:3AG901 4.9 32.6 1.0
N B:ASP355 4.9 31.2 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: Tue Aug 13 09:18:40 2024

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