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Magnesium in PDB 1yhm: Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2

Enzymatic activity of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2

All present enzymatic activity of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2:
2.5.1.10;

Protein crystallography data

The structure of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2, PDB code: 1yhm was solved by S.B.Gabelli, J.S.Mclellan, A.Montalvetti, E.Oldfield, R.Docampo, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.71 / 2.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.205, 103.205, 385.236, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 (pdb code 1yhm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2, PDB code: 1yhm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 1yhm

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Magnesium binding site 1 out of 9 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:31.9
occ:1.00
 O10 A:AHD901 1.7 29.8 1.0
O A:HOH905 1.8 38.7 1.0
OD2 A:ASP250 2.1 38.6 1.0
O A:HOH906 2.3 15.0 1.0
O16 A:AHD901 2.6 32.0 1.0
CG A:ASP250 2.8 38.8 1.0
P9 A:AHD901 3.1 32.9 1.0
OD1 A:ASP250 3.2 41.3 1.0
P14 A:AHD901 3.6 26.8 1.0
O13 A:AHD901 3.7 31.3 1.0
C8 A:AHD901 3.7 32.2 1.0
O12 A:AHD901 3.7 31.4 1.0
OD1 A:ASP254 3.8 42.9 1.0
CB A:ASP254 4.0 42.0 1.0
NZ A:LYS264 4.0 40.2 1.0
O A:ASP250 4.0 39.6 1.0
CB A:ASP250 4.1 38.8 1.0
C A:ASP250 4.2 39.4 1.0
O17 A:AHD901 4.2 22.5 1.0
OD2 A:ASP268 4.2 39.4 1.0
O11 A:AHD901 4.2 33.3 1.0
CE A:LYS264 4.3 39.8 1.0
CG A:ASP254 4.3 41.9 1.0
O A:HOH903 4.4 23.8 1.0
OD1 A:ASP268 4.4 31.3 1.0
CA A:ASP250 4.6 38.9 1.0
OD1 A:ASP251 4.6 42.2 1.0
N A:ASP251 4.7 40.0 1.0
CG A:ASP268 4.7 34.3 1.0
NE2 A:GLN247 4.7 30.7 1.0
CA A:ASP254 4.9 42.9 1.0
CA A:ASP251 4.9 40.2 1.0

Magnesium binding site 2 out of 9 in 1yhm

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Magnesium binding site 2 out of 9 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:43.6
occ:1.00
 OD2 A:ASP102 1.9 35.5 1.0
O17 A:AHD901 1.9 22.5 1.0
O A:HOH903 2.0 23.8 1.0
OD2 A:ASP98 2.0 36.0 1.0
O A:HOH902 2.1 18.4 1.0
O12 A:AHD901 2.4 31.4 1.0
CG A:ASP98 2.9 33.6 1.0
MG A:MG403 3.0 26.1 1.0
OD1 A:ASP98 3.0 34.0 1.0
CG A:ASP102 3.1 38.4 1.0
P14 A:AHD901 3.3 26.8 1.0
P9 A:AHD901 3.4 32.9 1.0
C7 A:AHD901 3.6 30.9 1.0
C8 A:AHD901 3.6 32.2 1.0
CB A:ASP102 3.9 37.7 1.0
O15 A:AHD901 4.1 30.1 1.0
O A:HOH907 4.1 30.8 1.0
OD1 A:ASP102 4.1 39.6 1.0
O A:ASP98 4.1 31.0 1.0
O A:HOH904 4.1 23.8 1.0
C2 A:AHD901 4.2 34.2 1.0
O16 A:AHD901 4.2 32.0 1.0
O A:HOH906 4.3 15.0 1.0
NH2 A:ARG107 4.3 37.2 1.0
CB A:ASP98 4.3 30.4 1.0
O11 A:AHD901 4.4 33.3 1.0
O10 A:AHD901 4.5 29.8 1.0
C A:ASP98 4.6 31.9 1.0
OG A:SER104 4.7 34.6 1.0
OD1 A:ASP99 4.8 36.4 1.0
O13 A:AHD901 4.9 31.3 1.0

Magnesium binding site 3 out of 9 in 1yhm

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Magnesium binding site 3 out of 9 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:26.1
occ:1.00
 O A:HOH907 1.8 30.8 1.0
O A:HOH904 1.9 23.8 1.0
OD1 A:ASP98 2.5 34.0 1.0
OD2 A:ASP102 2.5 35.5 1.0
O17 A:AHD901 2.5 22.5 1.0
MG A:MG402 3.0 43.6 1.0
O15 A:AHD901 3.2 30.1 1.0
OD2 A:ASP170 3.2 38.1 1.0
OD1 A:ASP102 3.3 39.6 1.0
CG A:ASP102 3.3 38.4 1.0
P14 A:AHD901 3.4 26.8 1.0
CG A:ASP98 3.5 33.6 1.0
OD2 A:ASP98 3.7 36.0 1.0
O A:HOH903 3.8 23.8 1.0
CG A:ASP170 3.9 38.4 1.0
NZ A:LYS273 3.9 28.4 1.0
OD1 A:ASP170 4.0 41.8 1.0
OE1 A:GLN167 4.3 30.7 1.0
O16 A:AHD901 4.4 32.0 1.0
NE2 A:GLN167 4.4 25.4 1.0
C2 A:AHD901 4.5 34.2 1.0
CE A:LYS273 4.5 27.9 1.0
NZ A:LYS207 4.7 30.7 1.0
C8 A:AHD901 4.7 32.2 1.0
CB A:ASP102 4.8 37.7 1.0
C7 A:AHD901 4.8 30.9 1.0
CD A:GLN167 4.8 29.1 1.0
O A:HOH902 4.8 18.4 1.0
CB A:ASP98 4.9 30.4 1.0
CD A:LYS273 4.9 27.4 1.0
O12 A:AHD901 5.0 31.4 1.0

Magnesium binding site 4 out of 9 in 1yhm

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Magnesium binding site 4 out of 9 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1401

b:27.1
occ:1.00
 O11 B:AHD1901 1.8 25.9 1.0
O17 B:AHD1901 1.8 28.4 1.0
O B:HOH1906 1.9 28.4 1.0
OD2 B:ASP250 2.0 35.4 1.0
O B:HOH1909 2.0 23.3 1.0
O B:HOH1907 2.2 17.4 1.0
P9 B:AHD1901 2.8 27.6 1.0
P14 B:AHD1901 2.8 25.8 1.0
CG B:ASP250 3.0 32.8 1.0
C8 B:AHD1901 3.1 27.7 1.0
O13 B:AHD1901 3.2 28.7 1.0
OD1 B:ASP250 3.3 29.6 1.0
O12 B:AHD1901 3.6 27.4 1.0
O15 B:AHD1901 3.7 23.9 1.0
NZ B:LYS264 4.1 30.3 1.0
O B:ASP250 4.1 35.1 1.0
O10 B:AHD1901 4.2 27.8 1.0
O16 B:AHD1901 4.2 25.4 1.0
NE2 B:GLN247 4.2 28.7 1.0
CB B:ASP250 4.3 33.5 1.0
OD1 B:ASP254 4.3 38.4 1.0
O B:HOH1904 4.3 25.5 1.0
OD1 B:ASP268 4.4 31.2 1.0
C B:ASP250 4.4 34.4 1.0
OD2 B:ASP268 4.5 30.9 1.0
C7 B:AHD1901 4.5 22.4 1.0
CE B:LYS264 4.6 26.4 1.0
OD1 B:ASP251 4.7 33.3 1.0
CB B:ASP254 4.8 34.3 1.0
CG B:ASP268 4.9 31.4 1.0
CG B:ASP254 4.9 35.4 1.0
CA B:ASP250 4.9 34.2 1.0

Magnesium binding site 5 out of 9 in 1yhm

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Magnesium binding site 5 out of 9 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1402

b:41.4
occ:1.00
 O B:HOH1904 1.9 25.5 1.0
O B:HOH1903 2.0 20.3 1.0
OD2 B:ASP98 2.0 29.0 1.0
OD2 B:ASP102 2.0 30.2 1.0
O15 B:AHD1901 2.2 23.9 1.0
O12 B:AHD1901 2.5 27.4 1.0
MG B:MG1403 2.9 24.2 1.0
CG B:ASP98 3.0 29.0 1.0
CG B:ASP102 3.2 30.8 1.0
OD1 B:ASP98 3.3 26.8 1.0
P9 B:AHD1901 3.6 27.6 1.0
P14 B:AHD1901 3.6 25.8 1.0
C7 B:AHD1901 3.7 22.4 1.0
CB B:ASP102 3.7 31.9 1.0
C8 B:AHD1901 3.8 27.7 1.0
NH2 B:ARG107 4.0 30.8 1.0
O B:HOH1902 4.1 25.6 1.0
O B:ASP98 4.2 30.6 1.0
O B:HOH1905 4.2 28.2 1.0
OD1 B:ASP102 4.2 26.6 1.0
O16 B:AHD1901 4.3 25.4 1.0
CB B:ASP98 4.3 28.2 1.0
C2 B:AHD1901 4.4 23.0 1.0
O B:HOH1908 4.4 17.7 1.0
O17 B:AHD1901 4.4 28.4 1.0
C B:ASP98 4.5 29.7 1.0
O10 B:AHD1901 4.5 27.8 1.0
OD1 B:ASP99 4.5 28.6 1.0
O11 B:AHD1901 4.5 25.9 1.0
O B:HOH1907 4.6 17.4 1.0
OG B:SER104 4.6 30.7 1.0
N B:ASP99 4.9 29.1 1.0

Magnesium binding site 6 out of 9 in 1yhm

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Magnesium binding site 6 out of 9 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1403

b:24.2
occ:1.00
 O B:HOH1905 1.7 28.2 1.0
O B:HOH1902 1.8 25.6 1.0
O B:HOH1908 2.0 17.7 1.0
OD2 B:ASP102 2.1 30.2 1.0
OD1 B:ASP98 2.3 26.8 1.0
O15 B:AHD1901 2.4 23.9 1.0
MG B:MG1402 2.9 41.4 1.0
CG B:ASP102 3.0 30.8 1.0
CG B:ASP98 3.1 29.0 1.0
OD1 B:ASP102 3.2 26.6 1.0
O16 B:AHD1901 3.2 25.4 1.0
OD2 B:ASP98 3.3 29.0 1.0
P14 B:AHD1901 3.5 25.8 1.0
O B:HOH1904 3.6 25.5 1.0
OD2 B:ASP170 3.7 29.1 1.0
NZ B:LYS273 3.8 34.4 1.0
C2 B:AHD1901 4.2 23.0 1.0
CB B:ASP102 4.4 31.9 1.0
CG B:ASP170 4.4 31.3 1.0
OE1 B:GLN167 4.4 31.1 1.0
O17 B:AHD1901 4.4 28.4 1.0
C7 B:AHD1901 4.5 22.4 1.0
CB B:ASP98 4.5 28.2 1.0
O B:HOH1903 4.5 20.3 1.0
NE2 B:GLN167 4.6 22.3 1.0
C8 B:AHD1901 4.6 27.7 1.0
OD1 B:ASP170 4.7 26.7 1.0
O B:ASP98 4.8 30.6 1.0
O12 B:AHD1901 4.9 27.4 1.0
NZ B:LYS207 4.9 23.1 1.0
CD B:GLN167 4.9 27.7 1.0

Magnesium binding site 7 out of 9 in 1yhm

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Magnesium binding site 7 out of 9 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2401

b:40.1
occ:1.00
 O17 C:AHD2901 1.7 43.8 1.0
O11 C:AHD2901 2.0 38.3 1.0
O C:HOH2906 2.1 30.4 1.0
O C:HOH2909 2.1 36.1 1.0
OD2 C:ASP250 2.2 41.6 1.0
O C:HOH2907 2.3 35.2 1.0
P14 C:AHD2901 2.8 41.1 1.0
P9 C:AHD2901 2.9 37.4 1.0
O13 C:AHD2901 3.1 34.0 1.0
C8 C:AHD2901 3.1 38.7 1.0
CG C:ASP250 3.3 43.2 1.0
O15 C:AHD2901 3.6 40.3 1.0
O12 C:AHD2901 3.7 37.3 1.0
OD1 C:ASP250 4.0 45.9 1.0
O C:ASP250 4.1 43.5 1.0
NE2 C:GLN247 4.1 36.4 1.0
OD2 C:ASP268 4.1 42.7 1.0
CB C:ASP250 4.1 42.8 1.0
O10 C:AHD2901 4.3 39.9 1.0
O16 C:AHD2901 4.3 39.9 1.0
O C:HOH2904 4.3 33.1 1.0
C C:ASP250 4.4 43.0 1.0
OD1 C:ASP268 4.4 34.8 1.0
CB C:ASP254 4.5 49.3 1.0
OD1 C:ASP254 4.6 49.3 1.0
NZ C:LYS264 4.6 51.4 1.0
C7 C:AHD2901 4.6 37.4 1.0
OD1 C:ASP251 4.6 45.1 1.0
CG C:ASP268 4.7 42.1 1.0
CA C:ASP250 4.9 42.2 1.0
CE C:LYS264 4.9 50.5 1.0
CG C:ASP254 5.0 49.9 1.0
N C:ASP251 5.0 43.1 1.0

Magnesium binding site 8 out of 9 in 1yhm

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Magnesium binding site 8 out of 9 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2402

b:46.9
occ:1.00
 OD2 C:ASP98 1.9 39.3 1.0
O C:HOH2903 2.0 41.3 1.0
O C:HOH2904 2.0 33.1 1.0
OD2 C:ASP102 2.1 39.0 1.0
O15 C:AHD2901 2.4 40.3 1.0
O12 C:AHD2901 2.4 37.3 1.0
MG C:MG2403 2.8 28.8 1.0
CG C:ASP98 2.9 38.9 1.0
CG C:ASP102 3.2 42.2 1.0
OD1 C:ASP98 3.3 41.0 1.0
P9 C:AHD2901 3.6 37.4 1.0
P14 C:AHD2901 3.8 41.1 1.0
CB C:ASP102 3.8 41.0 1.0
C7 C:AHD2901 3.8 37.4 1.0
C8 C:AHD2901 3.8 38.7 1.0
O C:HOH2902 4.1 32.7 1.0
O C:ASP98 4.1 37.9 1.0
CB C:ASP98 4.3 36.6 1.0
OD1 C:ASP102 4.3 42.6 1.0
C C:ASP98 4.4 36.7 1.0
OD1 C:ASP99 4.4 36.4 1.0
OG C:SER104 4.5 39.8 1.0
NH1 C:ARG107 4.5 46.0 1.0
O10 C:AHD2901 4.5 39.9 1.0
O16 C:AHD2901 4.5 39.9 1.0
O C:HOH2908 4.6 25.8 1.0
O C:HOH2905 4.6 23.5 1.0
C2 C:AHD2901 4.6 37.5 1.0
O17 C:AHD2901 4.7 43.8 1.0
O11 C:AHD2901 4.7 38.3 1.0
N C:ASP99 4.8 36.4 1.0
O C:HOH2907 4.9 35.2 1.0
CA C:ASP98 4.9 36.6 1.0

Magnesium binding site 9 out of 9 in 1yhm

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Magnesium binding site 9 out of 9 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Disphosphate Synthase with Alendronate, Isopentenyl Diphosphate and Mg+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2403

b:28.8
occ:1.00
 O C:HOH2902 1.8 32.7 1.0
OD1 C:ASP98 2.0 41.0 1.0
O C:HOH2905 2.0 23.5 1.0
O C:HOH2908 2.1 25.8 1.0
OD2 C:ASP102 2.2 39.0 1.0
O15 C:AHD2901 2.4 40.3 1.0
MG C:MG2402 2.8 46.9 1.0
CG C:ASP98 2.9 38.9 1.0
OD2 C:ASP98 3.1 39.3 1.0
CG C:ASP102 3.1 42.2 1.0
O16 C:AHD2901 3.3 39.9 1.0
OD1 C:ASP102 3.3 42.6 1.0
P14 C:AHD2901 3.6 41.1 1.0
O C:HOH2904 3.8 33.1 1.0
OD2 C:ASP170 4.1 42.9 1.0
NE2 C:GLN167 4.3 38.0 1.0
CB C:ASP98 4.3 36.6 1.0
NZ C:LYS273 4.3 36.7 1.0
OE1 C:GLN167 4.4 33.0 1.0
C7 C:AHD2901 4.4 37.4 1.0
C2 C:AHD2901 4.4 37.5 1.0
C8 C:AHD2901 4.5 38.7 1.0
O C:HOH2903 4.5 41.3 1.0
CG C:ASP170 4.5 41.1 1.0
CB C:ASP102 4.5 41.0 1.0
OD1 C:ASP170 4.6 37.7 1.0
O17 C:AHD2901 4.6 43.8 1.0
O12 C:AHD2901 4.7 37.3 1.0
O C:ASP98 4.8 37.9 1.0
CD C:GLN167 4.8 35.6 1.0
C3 C:AHD2901 4.8 40.6 1.0
NZ C:LYS207 4.9 40.2 1.0

Reference:

S.B.Gabelli, J.S.Mclellan, A.Montalvetti, E.Oldfield, R.Docampo, L.M.Amzel. Structure and Mechanism of the Farnesyl Diphosphate Synthase From Trypanosoma Cruzi: Implications For Drug Design. Proteins V. 62 80 2005.
ISSN: ISSN 0887-3585
PubMed: 16288456
DOI: 10.1002/PROT.20754
Page generated: Tue Aug 13 18:37:48 2024

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