Atomistry » Magnesium » PDB 1rdd-1rtk » 1rqi
Atomistry »
  Magnesium »
    PDB 1rdd-1rtk »
      1rqi »

Magnesium in PDB 1rqi: Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate

Enzymatic activity of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate

All present enzymatic activity of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate:
2.5.1.10;

Protein crystallography data

The structure of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate, PDB code: 1rqi was solved by D.J.Hosfield, Y.Zhang, D.R.Dougan, A.Brooun, L.W.Tari, R.V.Swanson, J.Finn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.03 / 2.42
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 88.839, 88.839, 174.769, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate (pdb code 1rqi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate, PDB code: 1rqi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1rqi

Go back to Magnesium Binding Sites List in 1rqi
Magnesium binding site 1 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:26.3
occ:1.00
 O A:HOH717 2.0 20.9 1.0
O A:HOH718 2.0 25.5 1.0
O8 A:DST401 2.1 36.9 1.0
O5 A:DST401 2.1 26.2 1.0
O A:HOH734 2.2 20.3 1.0
OD2 A:ASP244 2.2 24.5 1.0
CG A:ASP244 3.3 23.3 1.0
P3 A:DST401 3.3 33.0 1.0
P1 A:DST401 3.4 27.4 1.0
O2 A:DST401 3.5 30.7 1.0
OD1 A:ASP244 3.6 22.8 1.0
O A:HOH835 3.6 34.2 1.0
OD2 A:ASP248 3.8 28.8 1.0
OD2 A:ASP263 4.0 31.8 1.0
O A:ASP244 4.1 22.4 1.0
O A:HOH719 4.1 26.2 1.0
OD1 A:ASP263 4.1 31.0 1.0
NE2 A:GLN241 4.3 23.1 1.0
NZ A:LYS258 4.3 24.6 1.0
O6 A:DST401 4.4 27.7 1.0
O7 A:DST401 4.4 32.4 1.0
O4 A:DST401 4.5 29.8 1.0
CG A:ASP248 4.5 27.0 1.0
CG A:ASP263 4.5 31.6 1.0
CB A:ASP244 4.5 23.1 1.0
S9 A:DST401 4.6 41.7 1.0
C A:ASP244 4.6 23.1 1.0
CB A:ASP248 4.7 25.2 1.0
OD1 A:ASP245 4.7 26.2 1.0
O A:HOH737 4.8 29.5 1.0
CE A:LYS258 4.9 24.5 1.0
C3 A:IPR501 4.9 28.9 1.0

Magnesium binding site 2 out of 6 in 1rqi

Go back to Magnesium Binding Sites List in 1rqi
Magnesium binding site 2 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:34.2
occ:1.00
 O7 A:DST401 2.0 32.4 1.0
O A:HOH721 2.0 26.6 1.0
O A:HOH722 2.0 32.2 1.0
OD1 A:ASP111 2.0 26.4 1.0
O A:HOH738 2.1 32.5 1.0
OD2 A:ASP105 2.3 21.9 1.0
CG A:ASP111 2.9 26.1 1.0
MG A:MG605 3.1 24.8 1.0
CG A:ASP105 3.1 21.8 1.0
OD2 A:ASP111 3.1 25.7 1.0
OD1 A:ASP105 3.2 18.9 1.0
P3 A:DST401 3.3 33.0 1.0
NZ A:LYS268 3.8 33.9 1.0
S9 A:DST401 3.9 41.7 1.0
O A:HOH719 3.9 26.2 1.0
O A:HOH885 4.0 50.1 1.0
OE1 A:GLN179 4.0 26.7 1.0
OD2 A:ASP182 4.0 29.1 1.0
O8 A:DST401 4.2 36.9 1.0
CB A:ASP111 4.3 25.7 1.0
O A:HOH720 4.5 26.0 1.0
O2 A:DST401 4.5 30.7 1.0
NE2 A:GLN179 4.5 27.1 1.0
CE A:LYS268 4.5 32.6 1.0
CB A:ASP105 4.6 21.0 1.0
O6 A:DST401 4.6 27.7 1.0
CG A:ASP182 4.6 25.8 1.0
NZ A:LYS202 4.6 22.7 1.0
O A:HOH835 4.7 34.2 1.0
CD A:GLN179 4.7 25.8 1.0
OD1 A:ASP182 4.7 27.9 1.0
O A:HOH735 4.8 24.3 1.0
O A:ASP105 5.0 20.7 1.0
C10 A:DST401 5.0 41.8 1.0

Magnesium binding site 3 out of 6 in 1rqi

Go back to Magnesium Binding Sites List in 1rqi
Magnesium binding site 3 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:24.8
occ:1.00
 O A:HOH720 1.8 26.0 1.0
O A:HOH719 2.0 26.2 1.0
O6 A:DST401 2.0 27.7 1.0
OD1 A:ASP105 2.2 18.9 1.0
OD1 A:ASP111 2.2 26.4 1.0
O7 A:DST401 2.2 32.4 1.0
MG A:MG604 3.1 34.2 1.0
CG A:ASP111 3.2 26.1 1.0
P1 A:DST401 3.2 27.4 1.0
CG A:ASP105 3.3 21.8 1.0
P3 A:DST401 3.3 33.0 1.0
O2 A:DST401 3.5 30.7 1.0
CB A:ASP111 3.6 25.7 1.0
OD2 A:ASP105 3.6 21.9 1.0
OD2 A:ASP113 3.7 31.3 1.0
O5 A:DST401 3.9 26.2 1.0
O8 A:DST401 4.0 36.9 1.0
O A:HOH735 4.1 24.3 1.0
O A:HOH738 4.3 32.5 1.0
NH1 A:ARG116 4.3 21.6 1.0
O A:HOH718 4.3 25.5 1.0
OD2 A:ASP111 4.3 25.7 1.0
O4 A:DST401 4.4 29.8 1.0
OD2 A:ASP106 4.5 22.8 1.0
CB A:ASP105 4.6 21.0 1.0
O A:ASP105 4.6 20.7 1.0
O A:HOH721 4.6 26.6 1.0
O A:HOH722 4.7 32.2 1.0
CG A:ASP113 4.9 28.7 1.0
S9 A:DST401 4.9 41.7 1.0
C A:ASP105 4.9 20.8 1.0
O A:HOH731 4.9 23.2 1.0
O A:HOH733 5.0 37.6 1.0

Magnesium binding site 4 out of 6 in 1rqi

Go back to Magnesium Binding Sites List in 1rqi
Magnesium binding site 4 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg600

b:20.4
occ:1.00
 O5 B:DST400 2.0 26.4 1.0
OD2 B:ASP244 2.1 23.4 1.0
O8 B:DST400 2.1 34.0 1.0
O B:HOH701 2.2 17.0 1.0
O B:HOH741 2.2 18.7 1.0
O B:HOH700 2.2 24.0 1.0
CG B:ASP244 3.3 20.7 1.0
P1 B:DST400 3.3 26.9 1.0
P3 B:DST400 3.4 31.6 1.0
O2 B:DST400 3.6 31.2 1.0
OD2 B:ASP248 3.7 29.4 1.0
OD1 B:ASP244 3.8 21.4 1.0
OD2 B:ASP263 4.1 30.0 1.0
OD1 B:ASP263 4.1 30.6 1.0
O B:HOH702 4.1 20.1 1.0
NZ B:LYS258 4.2 19.9 1.0
O B:ASP244 4.2 20.6 1.0
O6 B:DST400 4.2 27.4 1.0
O4 B:DST400 4.3 27.2 1.0
CE B:LYS258 4.3 20.7 1.0
O7 B:DST400 4.4 34.0 1.0
CG B:ASP248 4.4 25.9 1.0
NE2 B:GLN241 4.4 15.0 1.0
CB B:ASP244 4.5 20.6 1.0
CG B:ASP263 4.6 29.4 1.0
OD1 B:ASP245 4.6 21.8 1.0
C B:ASP244 4.6 20.9 1.0
S9 B:DST400 4.6 41.4 1.0
CB B:ASP248 4.8 24.1 1.0

Magnesium binding site 5 out of 6 in 1rqi

Go back to Magnesium Binding Sites List in 1rqi
Magnesium binding site 5 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:23.3
occ:1.00
 O B:HOH704 2.0 31.5 1.0
O B:HOH705 2.1 21.9 1.0
O7 B:DST400 2.1 34.0 1.0
OD2 B:ASP105 2.1 20.5 1.0
OD1 B:ASP111 2.1 21.3 1.0
O B:HOH862 2.6 27.0 1.0
CG B:ASP111 2.9 21.0 1.0
OD2 B:ASP111 2.9 19.6 1.0
CG B:ASP105 3.1 20.1 1.0
MG B:MG602 3.3 30.2 1.0
OD1 B:ASP105 3.3 20.0 1.0
P3 B:DST400 3.4 31.6 1.0
O B:HOH702 3.9 20.1 1.0
S9 B:DST400 4.1 41.4 1.0
OD2 B:ASP182 4.1 28.1 1.0
NZ B:LYS268 4.2 28.9 1.0
OE1 B:GLN179 4.3 28.0 1.0
O B:HOH742 4.3 51.9 1.0
O8 B:DST400 4.3 34.0 1.0
NE2 B:GLN179 4.3 26.9 1.0
NZ B:LYS202 4.3 14.7 1.0
CB B:ASP111 4.3 21.4 1.0
CE B:LYS268 4.4 29.0 1.0
CB B:ASP105 4.5 19.0 1.0
O2 B:DST400 4.6 31.2 1.0
CG B:ASP182 4.6 25.2 1.0
OD1 B:ASP182 4.6 26.6 1.0
O B:ASP105 4.7 19.1 1.0
CD B:GLN179 4.7 25.4 1.0
O6 B:DST400 4.8 27.4 1.0
O B:HOH703 4.8 21.3 1.0

Magnesium binding site 6 out of 6 in 1rqi

Go back to Magnesium Binding Sites List in 1rqi
Magnesium binding site 6 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:30.2
occ:1.00
 O B:HOH702 1.9 20.1 1.0
O6 B:DST400 2.0 27.4 1.0
OD1 B:ASP105 2.0 20.0 1.0
O B:HOH703 2.1 21.3 1.0
OD1 B:ASP111 2.2 21.3 1.0
O7 B:DST400 2.4 34.0 1.0
CG B:ASP105 3.1 20.1 1.0
CG B:ASP111 3.3 21.0 1.0
MG B:MG601 3.3 23.3 1.0
P1 B:DST400 3.3 26.9 1.0
P3 B:DST400 3.3 31.6 1.0
O2 B:DST400 3.4 31.2 1.0
OD2 B:ASP105 3.4 20.5 1.0
CB B:ASP111 3.7 21.4 1.0
NH1 B:ARG116 3.8 20.3 1.0
OD2 B:ASP113 4.0 26.0 1.0
O5 B:DST400 4.0 26.4 1.0
O8 B:DST400 4.1 34.0 1.0
O B:ASP105 4.2 19.1 1.0
OD2 B:ASP106 4.2 19.1 1.0
OD2 B:ASP111 4.3 19.6 1.0
O B:HOH701 4.4 17.0 1.0
CB B:ASP105 4.4 19.0 1.0
O4 B:DST400 4.5 27.2 1.0
C B:ASP105 4.6 18.9 1.0
O B:HOH714 4.8 25.6 1.0
O B:HOH862 4.8 27.0 1.0
O B:HOH704 4.8 31.5 1.0
S9 B:DST400 4.9 41.4 1.0
O B:HOH705 5.0 21.9 1.0
CZ B:ARG116 5.0 19.4 1.0

Reference:

D.J.Hosfield, Y.Zhang, D.R.Dougan, A.Brooun, L.W.Tari, R.V.Swanson, J.Finn. Structural Basis For Bisphosphonate-Mediated Inhibition of Isoprenoid Biosynthesis J.Biol.Chem. V. 279 8526 2004.
ISSN: ISSN 0021-9258
PubMed: 14672944
DOI: 10.1074/JBC.C300511200
Page generated: Mon Dec 14 06:42:55 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy