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Magnesium in PDB 1n1z: (+)-Bornyl Diphosphate Synthase: Complex with Mg and Pyrophosphate

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

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

Protein crystallography data

The structure of (+)-Bornyl Diphosphate Synthase: Complex with Mg and Pyrophosphate, PDB code: 1n1z 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) 29.44 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.210, 117.750, 120.620, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Pyrophosphate (pdb code 1n1z). 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 Pyrophosphate, PDB code: 1n1z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1n1z

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


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 Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:31.5
occ:1.00
 OD1 A:ASP496 2.0 28.5 1.0
O A:HOH983 2.0 33.3 1.0
O2 A:POP901 2.1 33.8 1.0
OE2 A:GLU504 2.1 43.2 1.0
O4 A:POP901 2.1 31.4 1.0
OG1 A:THR500 2.2 36.9 1.0
CG A:ASP496 2.9 33.8 1.0
CD A:GLU504 3.0 48.1 1.0
OD2 A:ASP496 3.3 32.3 1.0
OE1 A:GLU504 3.3 44.9 1.0
CB A:THR500 3.4 44.6 1.0
P1 A:POP901 3.4 28.0 1.0
P2 A:POP901 3.5 32.9 1.0
O A:POP901 3.6 35.0 1.0
O A:ASP496 3.9 32.5 1.0
O1 A:POP901 4.0 31.1 1.0
NH1 A:ARG493 4.0 23.5 1.0
CG2 A:THR500 4.0 43.8 1.0
OD1 A:ASP497 4.1 36.8 1.0
NZ A:LYS512 4.3 37.0 1.0
C A:ASP496 4.3 31.1 1.0
CB A:ASP496 4.3 30.5 1.0
CG A:GLU504 4.3 46.5 1.0
O5 A:POP901 4.4 29.2 1.0
O A:HOH984 4.4 33.2 1.0
O6 A:POP901 4.5 33.8 1.0
CA A:THR500 4.6 45.0 1.0
O3 A:POP901 4.6 34.9 1.0
CE A:LYS512 4.6 38.1 1.0
C A:THR500 4.7 48.3 1.0
N A:ASP497 4.7 32.6 1.0
MG A:MG702 4.9 40.9 1.0
CA A:ASP496 4.9 32.1 1.0
CA A:ASP497 4.9 35.9 1.0

Magnesium binding site 2 out of 6 in 1n1z

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


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 Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:40.9
occ:1.00
 O A:HOH985 1.9 29.0 1.0
O5 A:POP901 2.0 29.2 1.0
O1 A:POP901 2.0 31.1 1.0
O A:HOH984 2.1 33.2 1.0
OD2 A:ASP355 2.2 29.0 1.0
OD2 A:ASP351 2.2 28.0 1.0
P2 A:POP901 3.0 32.9 1.0
O A:POP901 3.0 35.0 1.0
CG A:ASP351 3.1 32.5 1.0
MG A:MG703 3.1 29.4 1.0
P1 A:POP901 3.1 28.0 1.0
CG A:ASP355 3.2 32.3 1.0
OD1 A:ASP351 3.3 30.6 1.0
OD1 A:ASP355 3.6 28.4 1.0
O4 A:POP901 3.8 31.4 1.0
OE2 A:GLU504 3.9 43.2 1.0
O A:HOH945 4.0 37.3 1.0
NH1 A:ARG507 4.1 47.2 1.0
O2 A:POP901 4.1 33.8 1.0
O3 A:POP901 4.2 34.9 1.0
NH2 A:ARG314 4.3 31.4 1.0
OD2 A:ASP509 4.3 41.4 1.0
O6 A:POP901 4.3 33.8 1.0
O A:HOH959 4.3 34.5 1.0
CB A:ASP355 4.5 28.7 1.0
CB A:ASP351 4.5 33.6 1.0
O A:HOH987 4.6 28.9 1.0
OD1 A:ASP352 4.7 33.7 1.0
NH1 A:ARG314 4.8 30.9 1.0
CZ A:ARG314 4.8 34.0 1.0
O A:ASP351 4.8 36.0 1.0
MG A:MG701 4.9 31.5 1.0
OH A:TYR60 4.9 54.8 1.0
CD A:GLU504 4.9 48.1 1.0
NZ A:LYS512 5.0 37.0 1.0
O A:HOH986 5.0 28.2 1.0
NH2 A:ARG507 5.0 43.5 1.0
C A:ASP351 5.0 33.6 1.0

Magnesium binding site 3 out of 6 in 1n1z

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


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 Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:29.4
occ:1.00
 OD1 A:ASP351 2.0 30.6 1.0
O A:HOH986 2.1 28.2 1.0
O A:HOH987 2.1 28.9 1.0
O5 A:POP901 2.1 29.2 1.0
OD2 A:ASP355 2.2 29.0 1.0
O A:HOH959 2.3 34.5 1.0
CG A:ASP351 3.0 32.5 1.0
MG A:MG702 3.1 40.9 1.0
CG A:ASP355 3.2 32.3 1.0
OD2 A:ASP351 3.4 28.0 1.0
P2 A:POP901 3.4 32.9 1.0
CB A:ASP355 3.5 28.7 1.0
O6 A:POP901 3.7 33.8 1.0
OE1 A:GLU429 3.8 31.6 1.0
O A:ASP351 4.1 36.0 1.0
O A:HOH958 4.2 29.8 1.0
CE2 A:TYR426 4.3 33.2 1.0
CB A:ASP351 4.3 33.6 1.0
O A:HOH985 4.3 29.0 1.0
CD2 A:TYR426 4.3 32.6 1.0
OD1 A:ASP355 4.3 28.4 1.0
O A:POP901 4.4 35.0 1.0
O A:HOH984 4.4 33.2 1.0
OD2 A:ASP509 4.4 41.4 1.0
O4 A:POP901 4.6 31.4 1.0
NZ A:LYS512 4.6 37.0 1.0
OD1 A:ASP509 4.6 42.5 1.0
CA A:ASP351 4.6 31.9 1.0
C A:ASP351 4.7 33.6 1.0
N A:ASP355 4.7 32.9 1.0
CA A:ASP355 4.8 31.7 1.0
O1 A:POP901 4.9 31.1 1.0
CG A:ASP509 4.9 42.1 1.0

Magnesium binding site 4 out of 6 in 1n1z

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


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 Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:26.2
occ:1.00
 O B:HOH974 1.9 28.7 1.0
OD2 B:ASP351 2.0 31.8 1.0
O5 B:POP902 2.1 28.4 1.0
O B:HOH975 2.1 26.5 1.0
O1 B:POP902 2.2 27.1 1.0
OD2 B:ASP355 2.4 26.0 1.0
MG B:MG705 2.9 24.4 1.0
CG B:ASP351 3.0 28.2 1.0
CG B:ASP355 3.2 34.6 1.0
OD1 B:ASP351 3.3 25.9 1.0
OD1 B:ASP355 3.3 32.4 1.0
P2 B:POP902 3.3 24.7 1.0
P1 B:POP902 3.4 23.2 1.0
O B:POP902 3.4 30.1 1.0
NH2 B:ARG314 3.9 28.4 1.0
OE2 B:GLU504 4.0 70.4 1.0
O B:HOH981 4.1 27.1 1.0
O4 B:POP902 4.2 25.3 1.0
CB B:ASP351 4.3 26.1 1.0
O B:HOH977 4.3 24.8 1.0
OD1 B:ASP352 4.3 26.8 1.0
OD2 B:ASP509 4.4 71.8 1.0
O3 B:POP902 4.4 29.9 1.0
O2 B:POP902 4.4 25.4 1.0
O6 B:POP902 4.4 28.7 1.0
O B:HOH973 4.5 20.3 1.0
O B:ASP351 4.6 29.6 1.0
CB B:ASP355 4.6 32.3 1.0
C B:ASP351 4.7 27.4 1.0
O B:HOH976 4.8 28.9 1.0
CD B:GLU504 4.8 77.0 1.0
CZ B:ARG314 4.9 29.7 1.0
MG B:MG706 4.9 30.0 1.0

Magnesium binding site 5 out of 6 in 1n1z

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


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 Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:24.4
occ:1.00
 OD1 B:ASP351 1.9 25.9 1.0
O B:HOH973 2.0 20.3 1.0
OD2 B:ASP355 2.0 26.0 1.0
O5 B:POP902 2.1 28.4 1.0
O B:HOH976 2.2 28.9 1.0
O B:HOH977 2.2 24.8 1.0
CG B:ASP351 2.8 28.2 1.0
MG B:MG704 2.9 26.2 1.0
OD2 B:ASP351 3.1 31.8 1.0
CG B:ASP355 3.2 34.6 1.0
P2 B:POP902 3.3 24.7 1.0
O6 B:POP902 3.5 28.7 1.0
O B:HOH974 3.9 28.7 1.0
CB B:ASP355 3.9 32.3 1.0
OE1 B:GLU429 4.0 38.5 1.0
OD1 B:ASP355 4.1 32.4 1.0
O B:ASP351 4.1 29.6 1.0
CB B:ASP351 4.2 26.1 1.0
OD2 B:ASP509 4.3 71.8 1.0
O B:POP902 4.3 30.1 1.0
CE2 B:TYR426 4.4 21.2 1.0
O4 B:POP902 4.4 25.3 1.0
O B:HOH908 4.5 23.2 1.0
CD2 B:TYR426 4.5 26.3 1.0
NZ B:LYS512 4.5 28.3 1.0
O B:HOH975 4.6 26.5 1.0
OD1 B:ASP509 4.6 73.4 1.0
CA B:ASP351 4.6 25.5 1.0
C B:ASP351 4.6 27.4 1.0
O1 B:POP902 4.7 27.1 1.0
CG B:ASP509 4.9 74.0 1.0

Magnesium binding site 6 out of 6 in 1n1z

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


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 Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:30.0
occ:1.00
 O2 B:POP902 2.0 25.4 1.0
OE2 B:GLU504 2.0 70.4 1.0
O4 B:POP902 2.1 25.3 1.0
O B:HOH972 2.2 29.3 1.0
OD1 B:ASP496 2.3 33.3 1.0
OG1 B:THR500 2.5 36.3 1.0
CD B:GLU504 2.9 77.0 1.0
OE1 B:GLU504 3.1 82.1 1.0
P1 B:POP902 3.2 23.2 1.0
CG B:ASP496 3.2 30.5 1.0
P2 B:POP902 3.3 24.7 1.0
CB B:THR500 3.3 52.2 1.0
O B:POP902 3.3 30.1 1.0
OD2 B:ASP496 3.4 32.1 1.0
O1 B:POP902 3.8 27.1 1.0
C B:THR500 4.0 52.8 1.0
O5 B:POP902 4.0 28.4 1.0
O B:ASP496 4.1 24.4 1.0
O B:HOH974 4.2 28.7 1.0
NH1 B:ARG493 4.2 21.7 1.0
CG B:GLU504 4.2 79.9 1.0
NZ B:LYS512 4.2 28.3 1.0
CA B:THR500 4.3 53.1 1.0
OD1 B:ASP497 4.4 25.7 1.0
O3 B:POP902 4.5 29.9 1.0
O6 B:POP902 4.5 28.7 1.0
CG2 B:THR500 4.5 51.5 1.0
CB B:ASP496 4.6 30.6 1.0
C B:ASP496 4.6 28.9 1.0
CE B:LYS512 4.6 29.1 1.0
O B:HOH981 4.6 27.1 1.0
O B:THR500 4.8 57.9 1.0
MG B:MG704 4.9 26.2 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 09:18:39 2024

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