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Magnesium in PDB 1n23: (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane

Enzymatic activity of (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane

All present enzymatic activity of (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane:
5.5.1.8;

Protein crystallography data

The structure of (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane, PDB code: 1n23 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) 29.36 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.990, 118.180, 120.070, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane (pdb code 1n23). 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, Pyrophosphate, and (1R,4S)-2-Azabornane, PDB code: 1n23:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1n23

Go back to Magnesium Binding Sites List in 1n23
Magnesium binding site 1 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane


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, Pyrophosphate, and (1R,4S)-2-Azabornane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:39.9
occ:1.00
 O1 A:POP901 2.0 32.2 1.0
O5 A:POP901 2.0 27.6 1.0
OD2 A:ASP351 2.0 36.4 1.0
O A:HOH965 2.0 38.3 1.0
O A:HOH964 2.3 44.8 1.0
OD2 A:ASP355 2.3 38.0 1.0
O A:POP901 2.9 37.7 1.0
CG A:ASP351 3.0 37.5 1.0
P2 A:POP901 3.0 35.3 1.0
MG A:MG702 3.0 28.8 1.0
P1 A:POP901 3.0 36.3 1.0
OD1 A:ASP351 3.3 40.8 1.0
CG A:ASP355 3.4 40.1 1.0
OD1 A:ASP355 3.7 38.5 1.0
O4 A:POP901 3.8 32.5 1.0
OE2 A:GLU504 4.0 52.4 1.0
O A:HOH966 4.0 41.2 1.0
O3 A:POP901 4.1 39.9 1.0
O2 A:POP901 4.1 33.6 1.0
NH1 A:ARG507 4.1 55.2 1.0
NH2 A:ARG314 4.1 34.0 1.0
O6 A:POP901 4.2 37.1 1.0
CB A:ASP351 4.3 37.9 1.0
O A:HOH963 4.4 35.3 1.0
O A:HOH960 4.4 29.5 1.0
OD2 A:ASP509 4.5 51.3 1.0
OD1 A:ASP352 4.6 39.4 1.0
CB A:ASP355 4.7 35.7 1.0
CZ A:ARG314 4.7 33.3 1.0
O A:HOH962 4.8 35.3 1.0
MG A:MG703 4.8 31.1 1.0
NH1 A:ARG314 4.8 31.4 1.0
CD A:GLU504 4.9 53.8 1.0
O A:ASP351 5.0 42.9 1.0
C A:ASP351 5.0 40.1 1.0

Magnesium binding site 2 out of 6 in 1n23

Go back to Magnesium Binding Sites List in 1n23
Magnesium binding site 2 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane


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, Pyrophosphate, and (1R,4S)-2-Azabornane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:28.8
occ:1.00
 OD2 A:ASP355 2.0 38.0 1.0
O A:HOH962 2.0 35.3 1.0
O5 A:POP901 2.2 27.6 1.0
OD1 A:ASP351 2.2 40.8 1.0
O A:HOH960 2.2 29.5 1.0
O A:HOH963 2.3 35.3 1.0
CG A:ASP355 2.9 40.1 1.0
MG A:MG701 3.0 39.9 1.0
CG A:ASP351 3.0 37.5 1.0
OD2 A:ASP351 3.3 36.4 1.0
CB A:ASP355 3.3 35.7 1.0
P2 A:POP901 3.5 35.3 1.0
O6 A:POP901 3.8 37.1 1.0
O A:HOH964 4.0 44.8 1.0
OE1 A:GLU429 4.1 40.8 1.0
OD1 A:ASP355 4.1 38.5 1.0
OD2 A:ASP509 4.1 51.3 1.0
O A:ASP351 4.1 42.9 1.0
O A:HOH965 4.2 38.3 1.0
O A:HOH927 4.3 28.1 1.0
OD1 A:ASP509 4.3 50.9 1.0
CE2 A:TYR426 4.4 36.3 1.0
CB A:ASP351 4.4 37.9 1.0
O A:POP901 4.5 37.7 1.0
CD2 A:TYR426 4.5 33.9 1.0
NZ A:LYS512 4.5 37.6 1.0
CA A:ASP355 4.6 38.5 1.0
O4 A:POP901 4.6 32.5 1.0
CG A:ASP509 4.6 55.1 1.0
N A:ASP355 4.6 36.2 1.0
C A:ASP351 4.7 40.1 1.0
CA A:ASP351 4.7 37.2 1.0
O1 A:POP901 4.9 32.2 1.0

Magnesium binding site 3 out of 6 in 1n23

Go back to Magnesium Binding Sites List in 1n23
Magnesium binding site 3 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane


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, Pyrophosphate, and (1R,4S)-2-Azabornane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:31.1
occ:1.00
 OD1 A:ASP496 2.0 31.6 1.0
OE2 A:GLU504 2.0 52.4 1.0
O4 A:POP901 2.1 32.5 1.0
OG1 A:THR500 2.1 45.0 1.0
O2 A:POP901 2.1 33.6 1.0
O A:HOH961 2.2 30.6 1.0
CD A:GLU504 2.9 53.8 1.0
CG A:ASP496 3.0 34.7 1.0
CB A:THR500 3.1 51.7 1.0
OE1 A:GLU504 3.2 51.4 1.0
OD2 A:ASP496 3.4 42.2 1.0
P1 A:POP901 3.4 36.3 1.0
P2 A:POP901 3.4 35.3 1.0
O A:POP901 3.6 37.7 1.0
CG2 A:THR500 3.8 50.3 1.0
O1 A:POP901 3.9 32.2 1.0
O A:ASP496 3.9 39.4 1.0
NH1 A:ARG493 4.0 30.8 1.0
OD1 A:ASP497 4.2 43.6 1.0
CG A:GLU504 4.3 52.9 1.0
NZ A:LYS512 4.3 37.6 1.0
C A:ASP496 4.3 39.1 1.0
O5 A:POP901 4.3 27.6 1.0
CB A:ASP496 4.3 30.5 1.0
CA A:THR500 4.4 49.5 1.0
O A:HOH964 4.5 44.8 1.0
CE A:LYS512 4.5 41.9 1.0
O6 A:POP901 4.5 37.1 1.0
O3 A:POP901 4.6 39.9 1.0
C A:THR500 4.6 50.6 1.0
N A:ASP497 4.7 40.5 1.0
MG A:MG701 4.8 39.9 1.0
CA A:ASP497 4.8 42.5 1.0
N A:SER501 4.8 51.9 1.0
CA A:ASP496 4.9 36.5 1.0
N A:THR500 5.0 49.0 1.0

Magnesium binding site 4 out of 6 in 1n23

Go back to Magnesium Binding Sites List in 1n23
Magnesium binding site 4 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane


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, Pyrophosphate, and (1R,4S)-2-Azabornane within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:28.9
occ:1.00
 OD1 B:ASP351 1.9 31.4 1.0
OD2 B:ASP355 2.0 26.9 1.0
O B:HOH967 2.1 20.3 1.0
O B:HOH969 2.1 29.1 1.0
O B:HOH968 2.1 27.9 1.0
O5 B:POP902 2.2 27.4 1.0
CG B:ASP351 2.9 33.5 1.0
CG B:ASP355 3.1 33.7 1.0
MG B:MG705 3.2 31.1 1.0
OD2 B:ASP351 3.2 28.7 1.0
P2 B:POP902 3.4 27.7 1.0
O6 B:POP902 3.5 29.0 1.0
CB B:ASP355 3.6 28.3 1.0
OE1 B:GLU429 4.0 38.3 1.0
O B:HOH971 4.0 25.7 1.0
CE2 B:TYR426 4.2 27.3 1.0
OD1 B:ASP355 4.2 31.5 1.0
O B:ASP351 4.2 33.7 1.0
CB B:ASP351 4.3 29.3 1.0
O B:HOH906 4.3 22.5 1.0
CD2 B:TYR426 4.3 29.7 1.0
O B:POP902 4.4 33.0 1.0
OD2 B:ASP509 4.4 43.7 1.0
O4 B:POP902 4.5 30.3 1.0
O B:HOH972 4.5 25.1 1.0
NZ B:LYS512 4.5 27.9 1.0
CA B:ASP351 4.6 31.0 1.0
C B:ASP351 4.7 33.4 1.0
OD1 B:ASP509 4.7 44.5 1.0
N B:ASP355 4.9 33.5 1.0
CA B:ASP355 4.9 34.0 1.0
O1 B:POP902 4.9 31.4 1.0
O B:HOH904 5.0 32.8 1.0

Magnesium binding site 5 out of 6 in 1n23

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Magnesium binding site 5 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane


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, Pyrophosphate, and (1R,4S)-2-Azabornane within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:31.1
occ:1.00
 OD2 B:ASP351 2.0 28.7 1.0
O B:HOH972 2.0 25.1 1.0
O1 B:POP902 2.0 31.4 1.0
O5 B:POP902 2.1 27.4 1.0
O B:HOH971 2.1 25.7 1.0
OD2 B:ASP355 2.4 26.9 1.0
CG B:ASP351 3.0 33.5 1.0
O B:POP902 3.1 33.0 1.0
P2 B:POP902 3.2 27.7 1.0
P1 B:POP902 3.2 30.1 1.0
MG B:MG704 3.2 28.9 1.0
CG B:ASP355 3.3 33.7 1.0
OD1 B:ASP351 3.4 31.4 1.0
OD1 B:ASP355 3.4 31.5 1.0
O B:HOH1002 4.0 36.5 1.0
O4 B:POP902 4.0 30.3 1.0
NH2 B:ARG314 4.0 28.7 1.0
OE2 B:GLU504 4.0 37.5 1.0
NH1 B:ARG507 4.1 57.0 1.0
O2 B:POP902 4.2 32.9 1.0
O3 B:POP902 4.2 33.2 1.0
O B:HOH969 4.3 29.1 1.0
CB B:ASP351 4.3 29.3 1.0
O6 B:POP902 4.3 29.0 1.0
OD1 B:ASP352 4.4 28.8 1.0
OD2 B:ASP509 4.5 43.7 1.0
CZ B:ARG314 4.6 29.4 1.0
CB B:ASP355 4.6 28.3 1.0
O B:HOH967 4.7 20.3 1.0
NH1 B:ARG314 4.7 26.9 1.0
O B:ASP351 4.9 33.7 1.0
C B:ASP351 4.9 33.4 1.0
O B:HOH968 4.9 27.9 1.0
MG B:MG706 5.0 29.1 1.0

Magnesium binding site 6 out of 6 in 1n23

Go back to Magnesium Binding Sites List in 1n23
Magnesium binding site 6 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (1R,4S)-2-Azabornane


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, Pyrophosphate, and (1R,4S)-2-Azabornane within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:29.1
occ:1.00
 OD1 B:ASP496 2.0 33.0 1.0
O2 B:POP902 2.0 32.9 1.0
O B:HOH970 2.1 25.2 1.0
OE2 B:GLU504 2.1 37.5 1.0
OG1 B:THR500 2.2 33.8 1.0
O4 B:POP902 2.2 30.3 1.0
CD B:GLU504 2.9 49.4 1.0
CG B:ASP496 3.0 32.5 1.0
OE1 B:GLU504 3.1 45.9 1.0
OD2 B:ASP496 3.3 31.0 1.0
CB B:THR500 3.3 42.9 1.0
P1 B:POP902 3.4 30.1 1.0
P2 B:POP902 3.5 27.7 1.0
O B:POP902 3.7 33.0 1.0
O B:ASP496 3.9 35.8 1.0
O1 B:POP902 3.9 31.4 1.0
CG2 B:THR500 4.0 40.5 1.0
NH1 B:ARG493 4.1 27.1 1.0
C B:ASP496 4.2 34.0 1.0
OD1 B:ASP497 4.3 29.7 1.0
O5 B:POP902 4.3 27.4 1.0
CG B:GLU504 4.3 50.3 1.0
CB B:ASP496 4.3 31.2 1.0
NZ B:LYS512 4.4 27.9 1.0
O B:HOH971 4.4 25.7 1.0
CE B:LYS512 4.5 25.7 1.0
O3 B:POP902 4.5 33.2 1.0
CA B:THR500 4.6 44.7 1.0
O6 B:POP902 4.6 29.0 1.0
N B:ASP497 4.7 31.9 1.0
C B:THR500 4.7 45.6 1.0
CA B:ASP497 4.8 35.1 1.0
O B:HOH1002 4.8 36.5 1.0
CA B:ASP496 4.8 35.2 1.0
MG B:MG705 5.0 31.1 1.0
N B:SER501 5.0 45.7 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 09:18:53 2024

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