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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

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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

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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

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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

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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

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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

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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: Tue Aug 13 13:04:37 2024

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