Atomistry » Magnesium » PDB 1mum-1n6i » 1n24
Atomistry »
  Magnesium »
    PDB 1mum-1n6i »
      1n24 »

Magnesium in PDB 1n24: (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product

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

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

Protein crystallography data

The structure of (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product, PDB code: 1n24 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) 30.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.200, 117.530, 120.390, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product (pdb code 1n24). 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 Product, PDB code: 1n24:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1n24

Go back to Magnesium Binding Sites List in 1n24
Magnesium binding site 1 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


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

b:29.8
occ:1.00
 OD2 A:ASP355 2.0 33.3 1.0
O A:HOH883 2.1 31.1 1.0
OD1 A:ASP351 2.1 31.5 1.0
O5 A:BP2801 2.1 29.6 1.0
O A:HOH884 2.2 26.0 1.0
O A:HOH885 2.2 31.1 1.0
CG A:ASP351 3.0 32.8 1.0
CG A:ASP355 3.0 33.8 1.0
OD2 A:ASP351 3.2 31.4 1.0
MG A:MG703 3.3 38.0 1.0
P2 A:BP2801 3.3 32.8 1.0
CB A:ASP355 3.4 31.7 1.0
O6 A:BP2801 3.5 34.5 1.0
OE1 A:GLU429 3.9 30.2 1.0
OD1 A:ASP355 4.2 31.2 1.0
O A:ASP351 4.2 31.0 1.0
O A:HOH881 4.2 29.9 1.0
OD2 A:ASP509 4.3 41.9 1.0
CE2 A:TYR426 4.3 31.6 1.0
O A:BP2801 4.3 34.1 1.0
O A:HOH816 4.3 30.4 1.0
CB A:ASP351 4.4 30.6 1.0
OD1 A:ASP509 4.4 41.5 1.0
CD2 A:TYR426 4.5 29.9 1.0
O A:HOH882 4.5 39.2 1.0
O4 A:BP2801 4.5 34.5 1.0
NZ A:LYS512 4.6 35.0 1.0
CA A:ASP355 4.7 31.8 1.0
CG A:ASP509 4.7 43.4 1.0
CA A:ASP351 4.7 30.5 1.0
C A:ASP351 4.7 30.7 1.0
N A:ASP355 4.8 31.2 1.0
O1 A:BP2801 4.9 26.4 1.0

Magnesium binding site 2 out of 6 in 1n24

Go back to Magnesium Binding Sites List in 1n24
Magnesium binding site 2 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


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

b:28.9
occ:1.00
 OD1 A:ASP496 2.1 29.2 1.0
O4 A:BP2801 2.1 34.5 1.0
O2 A:BP2801 2.1 28.1 1.0
O A:HOH880 2.1 30.4 1.0
OE2 A:GLU504 2.2 46.0 1.0
OG1 A:THR500 2.2 42.1 1.0
CD A:GLU504 3.0 47.3 1.0
CG A:ASP496 3.1 32.5 1.0
OE1 A:GLU504 3.2 46.2 1.0
P1 A:BP2801 3.4 32.2 1.0
P2 A:BP2801 3.4 32.8 1.0
CB A:THR500 3.4 45.9 1.0
OD2 A:ASP496 3.4 34.2 1.0
O A:BP2801 3.6 34.1 1.0
NH1 A:ARG493 3.8 26.1 1.0
O A:ASP496 3.9 33.6 1.0
O1 A:BP2801 4.0 26.4 1.0
OD1 A:ASP497 4.1 36.2 1.0
CG2 A:THR500 4.1 44.8 1.0
NZ A:LYS512 4.2 35.0 1.0
O5 A:BP2801 4.3 29.6 1.0
O A:HOH881 4.3 29.9 1.0
C A:ASP496 4.4 32.7 1.0
CG A:GLU504 4.4 46.8 1.0
CB A:ASP496 4.4 29.5 1.0
O6 A:BP2801 4.5 34.5 1.0
O3 A:BP2801 4.6 34.7 1.0
CA A:THR500 4.6 44.5 1.0
CE A:LYS512 4.7 35.8 1.0
O A:HOH879 4.8 37.3 1.0
C A:THR500 4.8 44.4 1.0
N A:ASP497 4.8 34.3 1.0
MG A:MG703 4.9 38.0 1.0
CA A:ASP497 4.9 35.7 1.0
N A:SER501 4.9 45.2 1.0

Magnesium binding site 3 out of 6 in 1n24

Go back to Magnesium Binding Sites List in 1n24
Magnesium binding site 3 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


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

b:38.0
occ:1.00
 O A:HOH882 1.9 39.2 1.0
O1 A:BP2801 2.0 26.4 1.0
OD2 A:ASP351 2.0 31.4 1.0
O A:HOH881 2.1 29.9 1.0
O5 A:BP2801 2.2 29.6 1.0
OD2 A:ASP355 2.5 33.3 1.0
CG A:ASP351 3.1 32.8 1.0
P1 A:BP2801 3.2 32.2 1.0
O A:BP2801 3.2 34.1 1.0
P2 A:BP2801 3.2 32.8 1.0
MG A:MG701 3.3 29.8 1.0
CG A:ASP355 3.3 33.8 1.0
OD1 A:ASP351 3.5 31.5 1.0
O A:HOH879 3.5 37.3 1.0
OD1 A:ASP355 3.6 31.2 1.0
NH2 A:ARG314 3.8 31.1 1.0
OE2 A:GLU504 4.0 46.0 1.0
O4 A:BP2801 4.0 34.5 1.0
O2 A:BP2801 4.2 28.1 1.0
NH1 A:ARG314 4.2 32.1 1.0
NH1 A:ARG507 4.2 50.9 1.0
O3 A:BP2801 4.3 34.7 1.0
CZ A:ARG314 4.3 33.0 1.0
OD2 A:ASP509 4.4 41.9 1.0
CB A:ASP351 4.4 30.6 1.0
O6 A:BP2801 4.5 34.5 1.0
OD1 A:ASP352 4.7 32.7 1.0
CB A:ASP355 4.7 31.7 1.0
O A:HOH885 4.7 31.1 1.0
O A:HOH883 4.8 31.1 1.0
C3 A:BP2801 4.8 33.7 1.0
O A:ASP351 4.8 31.0 1.0
MG A:MG702 4.9 28.9 1.0
CD A:GLU504 4.9 47.3 1.0
C A:ASP351 5.0 30.7 1.0

Magnesium binding site 4 out of 6 in 1n24

Go back to Magnesium Binding Sites List in 1n24
Magnesium binding site 4 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


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

b:25.3
occ:1.00
 OD2 B:ASP355 2.0 31.2 1.0
OD1 B:ASP351 2.1 29.3 1.0
O B:HOH865 2.1 18.6 1.0
O5 B:BP2802 2.1 36.2 1.0
O B:HOH866 2.2 35.9 1.0
O B:HOH864 2.2 31.4 1.0
CG B:ASP351 2.9 32.6 1.0
MG B:MG705 3.0 38.6 1.0
CG B:ASP355 3.0 35.7 1.0
OD2 B:ASP351 3.1 31.1 1.0
P2 B:BP2802 3.3 37.5 1.0
CB B:ASP355 3.5 35.0 1.0
O6 B:BP2802 3.5 42.5 1.0
OE1 B:GLU429 4.0 34.6 1.0
O B:HOH862 4.1 51.3 1.0
OD1 B:ASP355 4.1 34.5 1.0
O B:BP2802 4.2 40.5 1.0
CB B:ASP351 4.3 29.7 1.0
O B:ASP351 4.4 32.1 1.0
O B:HOH863 4.4 36.1 1.0
OD2 B:ASP509 4.4 69.5 1.0
NZ B:LYS512 4.5 38.3 1.0
CE2 B:TYR426 4.5 26.5 1.0
O B:HOH932 4.5 32.0 1.0
O4 B:BP2802 4.5 38.3 1.0
CD2 B:TYR426 4.7 28.4 1.0
OD1 B:ASP509 4.7 70.5 1.0
CA B:ASP351 4.7 30.7 1.0
C B:ASP351 4.7 31.9 1.0
CA B:ASP355 4.8 36.3 1.0
O1 B:BP2802 4.8 37.7 1.0
N B:ASP355 4.8 33.4 1.0
CG B:ASP509 5.0 70.9 1.0

Magnesium binding site 5 out of 6 in 1n24

Go back to Magnesium Binding Sites List in 1n24
Magnesium binding site 5 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


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

b:38.6
occ:1.00
 O B:HOH863 2.0 36.1 1.0
OD2 B:ASP351 2.0 31.1 1.0
O B:HOH862 2.1 51.3 1.0
O5 B:BP2802 2.1 36.2 1.0
O1 B:BP2802 2.2 37.7 1.0
OD2 B:ASP355 2.2 31.2 1.0
MG B:MG704 3.0 25.3 1.0
CG B:ASP351 3.1 32.6 1.0
CG B:ASP355 3.2 35.7 1.0
O B:BP2802 3.2 40.5 1.0
P2 B:BP2802 3.2 37.5 1.0
P1 B:BP2802 3.3 39.4 1.0
OD1 B:ASP351 3.4 29.3 1.0
OD1 B:ASP355 3.5 34.5 1.0
NH2 B:ARG314 3.9 31.4 1.0
O4 B:BP2802 4.1 38.3 1.0
O2 B:BP2802 4.2 38.4 1.0
CB B:ASP351 4.4 29.7 1.0
NH1 B:ARG507 4.4 90.0 1.0
O6 B:BP2802 4.4 42.5 1.0
O B:HOH864 4.4 31.4 1.0
O3 B:BP2802 4.4 44.5 1.0
CB B:ASP355 4.5 35.0 1.0
NH1 B:ARG314 4.5 29.7 1.0
CZ B:ARG314 4.5 31.8 1.0
OD1 B:ASP352 4.5 30.3 1.0
OD2 B:ASP509 4.6 69.5 1.0
O B:HOH865 4.6 18.6 1.0
MG B:MG706 4.9 45.6 1.0
O B:HOH866 4.9 35.9 1.0
C3 B:BP2802 5.0 46.2 1.0
C B:ASP351 5.0 31.9 1.0

Magnesium binding site 6 out of 6 in 1n24

Go back to Magnesium Binding Sites List in 1n24
Magnesium binding site 6 out of 6 in the (+)-Bornyl Diphosphate Synthase: Complex with Mg and Product


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

b:45.6
occ:1.00
 O2 B:BP2802 2.1 38.4 1.0
O4 B:BP2802 2.1 38.3 1.0
OG1 B:THR500 2.3 58.6 1.0
O B:HOH861 2.3 35.4 1.0
OD1 B:ASP496 2.4 42.4 1.0
CG B:ASP496 3.3 42.7 1.0
P1 B:BP2802 3.4 39.4 1.0
P2 B:BP2802 3.4 37.5 1.0
CB B:THR500 3.5 61.6 1.0
OD2 B:ASP496 3.6 43.6 1.0
O B:BP2802 3.7 40.5 1.0
O B:HOH862 4.0 51.3 1.0
O1 B:BP2802 4.0 37.7 1.0
O B:ASP496 4.1 42.9 1.0
O5 B:BP2802 4.2 36.2 1.0
NH1 B:ARG493 4.2 22.7 1.0
CG2 B:THR500 4.2 60.6 1.0
NZ B:LYS512 4.4 38.3 1.0
OD1 B:ASP497 4.4 40.0 1.0
C B:THR500 4.5 62.4 1.0
C B:ASP496 4.6 41.6 1.0
O6 B:BP2802 4.6 42.5 1.0
O3 B:BP2802 4.6 44.5 1.0
CA B:THR500 4.6 61.7 1.0
CE B:LYS512 4.6 39.0 1.0
CB B:ASP496 4.7 40.9 1.0
MG B:MG705 4.9 38.6 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 09:19:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy