Atomistry » Magnesium » PDB 1mum-1n6i » 1n1z
Atomistry »
  Magnesium »
    PDB 1mum-1n6i »
      1n1z »

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

Go back to Magnesium Binding Sites List in 1n1z
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

Go back to Magnesium Binding Sites List in 1n1z
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

Go back to Magnesium Binding Sites List in 1n1z
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

Go back to Magnesium Binding Sites List in 1n1z
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

Go back to Magnesium Binding Sites List in 1n1z
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

Go back to Magnesium Binding Sites List in 1n1z
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy