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Magnesium in PDB 1n22: (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene

Enzymatic activity of (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene

All present enzymatic activity of (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene:
5.5.1.8;

Protein crystallography data

The structure of (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene, PDB code: 1n22 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) 29.14 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.670, 117.990, 120.290, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene (pdb code 1n22). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene, PDB code: 1n22:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1n22

Go back to Magnesium Binding Sites List in 1n22
Magnesium binding site 1 out of 7 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene


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 (4R)-7-Aza-7,8-Dihydrolimonene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:38.4
occ:1.00
 OD1 A:ASP351 2.0 42.6 1.0
O A:HOH959 2.1 37.3 1.0
O5 A:POP901 2.1 38.4 1.0
O A:HOH960 2.1 34.9 1.0
OD2 A:ASP355 2.2 44.4 1.0
O A:HOH961 2.3 36.9 1.0
CG A:ASP351 3.0 41.8 1.0
MG A:MG702 3.1 51.0 1.0
CG A:ASP355 3.2 42.8 1.0
OD2 A:ASP351 3.3 42.3 1.0
P2 A:POP901 3.4 41.0 1.0
O6 A:POP901 3.5 42.9 1.0
CB A:ASP355 3.7 41.5 1.0
OE1 A:GLU429 3.8 40.6 1.0
CE2 A:TYR426 4.2 35.2 1.0
O A:ASP351 4.2 41.1 1.0
O A:POP901 4.3 41.7 1.0
CD2 A:TYR426 4.3 35.2 1.0
CB A:ASP351 4.3 40.2 1.0
OD1 A:ASP355 4.3 38.7 1.0
O A:HOH957 4.5 54.5 1.0
O A:HOH934 4.5 33.9 1.0
OD2 A:ASP509 4.5 61.1 1.0
O A:HOH958 4.5 39.0 1.0
O4 A:POP901 4.5 43.6 1.0
NZ A:LYS512 4.6 49.2 1.0
OD1 A:ASP509 4.7 60.7 1.0
CA A:ASP351 4.7 37.8 1.0
C A:ASP351 4.7 39.1 1.0
N A:ASP355 4.9 43.2 1.0
CA A:ASP355 4.9 43.9 1.0
O1 A:POP901 4.9 36.2 1.0
CG A:ASP509 5.0 61.7 1.0

Magnesium binding site 2 out of 7 in 1n22

Go back to Magnesium Binding Sites List in 1n22
Magnesium binding site 2 out of 7 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene


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 (4R)-7-Aza-7,8-Dihydrolimonene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:51.0
occ:1.00
 O5 A:POP901 2.0 38.4 1.0
O A:HOH958 2.1 39.0 1.0
O1 A:POP901 2.1 36.2 1.0
O A:HOH957 2.1 54.5 1.0
OD2 A:ASP351 2.2 42.3 1.0
OD2 A:ASP355 2.3 44.4 1.0
MG A:MG701 3.1 38.4 1.0
P2 A:POP901 3.1 41.0 1.0
O A:POP901 3.1 41.7 1.0
CG A:ASP351 3.1 41.8 1.0
CG A:ASP355 3.2 42.8 1.0
P1 A:POP901 3.2 37.7 1.0
OD1 A:ASP351 3.4 42.6 1.0
OD1 A:ASP355 3.4 38.7 1.0
OE2 A:GLU504 3.9 61.4 1.0
O4 A:POP901 3.9 43.6 1.0
NH1 A:ARG507 3.9 68.5 1.0
O A:HOH956 4.0 51.9 1.0
NH2 A:ARG314 4.1 42.0 1.0
O3 A:POP901 4.2 41.5 1.0
O2 A:POP901 4.3 41.5 1.0
O A:HOH961 4.3 36.9 1.0
OD2 A:ASP509 4.3 61.1 1.0
O6 A:POP901 4.3 42.9 1.0
CB A:ASP355 4.5 41.5 1.0
CB A:ASP351 4.5 40.2 1.0
OD1 A:ASP352 4.7 38.0 1.0
O A:HOH960 4.7 34.9 1.0
CD A:GLU504 4.7 65.7 1.0
OH A:TYR60 4.8 85.8 1.0
O A:HOH959 4.8 37.3 1.0
O A:ASP351 4.8 41.1 1.0
CZ A:ARG314 4.8 43.1 1.0
CZ A:ARG507 4.9 69.2 1.0
NH2 A:ARG507 4.9 69.6 1.0
NZ A:LYS512 5.0 49.2 1.0
MG A:MG703 5.0 40.9 1.0
CG A:GLU504 5.0 68.0 1.0
NH1 A:ARG314 5.0 41.7 1.0

Magnesium binding site 3 out of 7 in 1n22

Go back to Magnesium Binding Sites List in 1n22
Magnesium binding site 3 out of 7 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene


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 (4R)-7-Aza-7,8-Dihydrolimonene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:40.9
occ:1.00
 OD1 A:ASP496 1.9 38.1 1.0
O4 A:POP901 2.0 43.6 1.0
O A:HOH955 2.1 50.0 1.0
OG1 A:THR500 2.2 56.8 1.0
OE2 A:GLU504 2.2 61.4 1.0
O2 A:POP901 2.3 41.5 1.0
CG A:ASP496 2.9 43.0 1.0
CD A:GLU504 3.1 65.7 1.0
OE1 A:GLU504 3.3 64.4 1.0
OD2 A:ASP496 3.3 47.6 1.0
P2 A:POP901 3.4 41.0 1.0
CB A:THR500 3.4 61.9 1.0
P1 A:POP901 3.5 37.7 1.0
O A:POP901 3.5 41.7 1.0
NH1 A:ARG493 3.8 35.5 1.0
O A:ASP496 3.9 42.1 1.0
OD1 A:ASP497 4.0 51.5 1.0
O1 A:POP901 4.1 36.2 1.0
CG2 A:THR500 4.1 61.5 1.0
C A:ASP496 4.2 43.5 1.0
CB A:ASP496 4.2 41.9 1.0
NZ A:LYS512 4.3 49.2 1.0
O5 A:POP901 4.3 38.4 1.0
O6 A:POP901 4.4 42.9 1.0
CG A:GLU504 4.5 68.0 1.0
CE A:LYS512 4.5 50.4 1.0
CA A:THR500 4.6 63.2 1.0
O A:HOH957 4.6 54.5 1.0
N A:ASP497 4.7 46.2 1.0
O3 A:POP901 4.7 41.5 1.0
C A:THR500 4.7 65.8 1.0
CA A:ASP496 4.8 42.7 1.0
CA A:ASP497 4.8 49.1 1.0
CD A:LYS512 5.0 49.6 1.0
N A:SER501 5.0 67.9 1.0
MG A:MG702 5.0 51.0 1.0

Magnesium binding site 4 out of 7 in 1n22

Go back to Magnesium Binding Sites List in 1n22
Magnesium binding site 4 out of 7 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene


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 (4R)-7-Aza-7,8-Dihydrolimonene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:27.0
occ:1.00
 O B:HOH953 2.0 25.4 1.0
O5 B:POP902 2.1 27.0 1.0
OD2 B:ASP351 2.1 33.6 1.0
O1 B:POP902 2.1 30.0 1.0
OD2 B:ASP355 2.3 29.4 1.0
MG B:MG705 2.9 32.3 1.0
CG B:ASP351 3.1 32.2 1.0
CG B:ASP355 3.1 34.7 1.0
OD1 B:ASP355 3.2 34.1 1.0
P2 B:POP902 3.3 28.9 1.0
P1 B:POP902 3.4 30.1 1.0
OD1 B:ASP351 3.4 35.1 1.0
O B:POP902 3.4 31.5 1.0
O B:HOH985 4.0 32.5 1.0
NH2 B:ARG314 4.0 29.9 1.0
O4 B:POP902 4.1 28.3 1.0
O B:HOH950 4.1 24.1 1.0
OE2 B:GLU504 4.3 62.0 1.0
OD2 B:ASP509 4.3 78.1 1.0
OD1 B:ASP352 4.3 28.5 1.0
O3 B:POP902 4.3 34.6 1.0
O2 B:POP902 4.4 31.1 1.0
CB B:ASP351 4.4 31.4 1.0
O6 B:POP902 4.5 30.1 1.0
CB B:ASP355 4.5 33.1 1.0
O B:HOH951 4.6 22.9 1.0
O B:HOH949 4.7 27.9 1.0
O B:ASP351 4.7 33.5 1.0
MG B:MG706 4.8 31.1 1.0
C B:ASP351 4.9 33.0 1.0
CG B:GLU504 5.0 69.2 1.0
CZ B:ARG314 5.0 33.1 1.0

Magnesium binding site 5 out of 7 in 1n22

Go back to Magnesium Binding Sites List in 1n22
Magnesium binding site 5 out of 7 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene


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 (4R)-7-Aza-7,8-Dihydrolimonene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:32.3
occ:1.00
 OD1 B:ASP351 1.9 35.1 1.0
OD2 B:ASP355 2.0 29.4 1.0
O B:HOH950 2.1 24.1 1.0
O5 B:POP902 2.1 27.0 1.0
O B:HOH951 2.1 22.9 1.0
O B:HOH949 2.1 27.9 1.0
CG B:ASP351 2.8 32.2 1.0
MG B:MG704 2.9 27.0 1.0
OD2 B:ASP351 3.0 33.6 1.0
CG B:ASP355 3.2 34.7 1.0
P2 B:POP902 3.3 28.9 1.0
O6 B:POP902 3.5 30.1 1.0
CB B:ASP355 3.8 33.1 1.0
OE1 B:GLU429 4.0 38.0 1.0
OD2 B:ASP509 4.1 78.1 1.0
OD1 B:ASP355 4.1 34.1 1.0
O B:ASP351 4.2 33.5 1.0
CB B:ASP351 4.2 31.4 1.0
CE2 B:TYR426 4.3 26.1 1.0
O B:POP902 4.3 31.5 1.0
CD2 B:TYR426 4.4 28.3 1.0
O4 B:POP902 4.5 28.3 1.0
O B:HOH904 4.5 22.6 1.0
O B:HOH953 4.6 25.4 1.0
CA B:ASP351 4.6 31.9 1.0
C B:ASP351 4.6 33.0 1.0
NZ B:LYS512 4.6 34.1 1.0
O1 B:POP902 4.6 30.0 1.0
N B:ASP355 5.0 32.8 1.0
CG B:ASP509 5.0 79.4 1.0

Magnesium binding site 6 out of 7 in 1n22

Go back to Magnesium Binding Sites List in 1n22
Magnesium binding site 6 out of 7 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene


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 (4R)-7-Aza-7,8-Dihydrolimonene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:31.1
occ:1.00
 O4 B:POP902 2.0 28.3 1.0
O2 B:POP902 2.1 31.1 1.0
OE2 B:GLU504 2.1 62.0 1.0
O B:HOH952 2.2 26.4 1.0
OD1 B:ASP496 2.3 34.1 1.0
CD B:GLU504 2.9 67.4 1.0
OE1 B:GLU504 3.2 69.0 1.0
P1 B:POP902 3.2 30.1 1.0
CG B:ASP496 3.2 34.5 1.0
P2 B:POP902 3.3 28.9 1.0
O B:POP902 3.3 31.5 1.0
MG B:MG707 3.4 43.5 1.0
OD2 B:ASP496 3.5 38.1 1.0
O1 B:POP902 3.7 30.0 1.0
O5 B:POP902 4.1 27.0 1.0
O B:ASP496 4.1 34.9 1.0
NH1 B:ARG493 4.1 31.8 1.0
OG B:SER501 4.1 62.7 1.0
NZ B:LYS512 4.2 34.1 1.0
CG B:GLU504 4.3 69.2 1.0
OD1 B:ASP497 4.4 35.7 1.0
O6 B:POP902 4.4 30.1 1.0
O3 B:POP902 4.5 34.6 1.0
CE B:LYS512 4.5 37.8 1.0
C B:ASP496 4.6 35.1 1.0
CB B:ASP496 4.6 33.7 1.0
O B:HOH985 4.7 32.5 1.0
MG B:MG704 4.8 27.0 1.0

Magnesium binding site 7 out of 7 in 1n22

Go back to Magnesium Binding Sites List in 1n22
Magnesium binding site 7 out of 7 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of (+)-Bornyl Diphosphate Synthase: Complex with Mg, Pyrophosphate, and (4R)-7-Aza-7,8-Dihydrolimonene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg707

b:43.5
occ:1.00
 O2 B:POP902 2.2 31.1 1.0
OD2 B:ASP496 2.3 38.1 1.0
OG B:SER501 2.4 62.7 1.0
CG B:ASP496 3.1 34.5 1.0
CB B:SER501 3.3 65.4 1.0
MG B:MG706 3.4 31.1 1.0
OD1 B:ASP496 3.4 34.1 1.0
P1 B:POP902 3.5 30.1 1.0
O3 B:POP902 3.7 34.6 1.0
O B:ASP496 4.1 34.9 1.0
OE1 B:GLU504 4.1 69.0 1.0
CB B:ASP496 4.3 33.7 1.0
N B:SER501 4.4 66.0 1.0
CA B:SER501 4.4 66.5 1.0
O B:HOH985 4.4 32.5 1.0
O1 B:POP902 4.5 30.0 1.0
CD B:GLU504 4.5 67.4 1.0
OE2 B:GLU504 4.5 62.0 1.0
O B:POP902 4.6 31.5 1.0
CA B:ASP496 4.6 34.4 1.0
C B:ASP496 4.7 35.1 1.0
C B:THR500 4.9 65.1 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 09:18:51 2024

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