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Magnesium in PDB 1rqj: Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate

Enzymatic activity of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate

All present enzymatic activity of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate:
2.5.1.10;

Protein crystallography data

The structure of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate, PDB code: 1rqj 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) 20.00 / 1.95
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 88.800, 88.800, 174.988, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate (pdb code 1rqj). 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 Risedronate, PDB code: 1rqj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1rqj

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Magnesium binding site 1 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg907

b:22.0
occ:1.00
 O12 A:RIS901 2.1 21.3 1.0
O15 A:RIS901 2.1 20.3 1.0
O A:HOH945 2.1 19.2 1.0
OD1 A:ASP105 2.1 20.2 1.0
O A:HOH933 2.1 15.2 1.0
OD1 A:ASP111 2.2 22.1 1.0
CG A:ASP105 3.1 19.9 1.0
MG A:MG909 3.2 19.9 1.0
CG A:ASP111 3.2 24.8 1.0
P9 A:RIS901 3.3 21.4 1.0
OD2 A:ASP105 3.3 18.0 1.0
P14 A:RIS901 3.4 21.5 1.0
CB A:ASP111 3.5 25.2 1.0
C8 A:RIS901 3.7 20.6 1.0
C7 A:RIS901 3.9 20.0 1.0
OD2 A:ASP113 4.0 31.9 1.0
O17 A:RIS901 4.0 20.7 1.0
NH1 A:ARG116 4.1 21.6 1.0
O11 A:RIS901 4.1 22.3 1.0
O A:HOH1034 4.2 18.0 1.0
OD2 A:ASP111 4.3 25.6 1.0
O A:HOH941 4.4 25.8 1.0
O A:HOH1032 4.4 21.1 1.0
CB A:ASP105 4.4 20.1 1.0
OD2 A:ASP106 4.5 19.3 1.0
O A:ASP105 4.5 21.3 1.0
O10 A:RIS901 4.6 22.1 1.0
O16 A:RIS901 4.7 16.8 1.0
C A:ASP105 4.8 20.9 1.0
O A:HOH926 4.9 24.4 1.0
O A:HOH1033 4.9 24.5 1.0
MG A:MG908 5.0 25.3 1.0
O A:HOH922 5.0 18.1 1.0
C2 A:RIS901 5.0 20.0 1.0

Magnesium binding site 2 out of 6 in 1rqj

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Magnesium binding site 2 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg908

b:25.3
occ:1.00
 O17 A:RIS901 1.9 20.7 1.0
O11 A:RIS901 1.9 22.3 1.0
OD2 A:ASP244 2.1 23.3 1.0
O A:HOH918 2.1 16.3 1.0
O A:HOH1031 2.2 21.0 1.0
O A:HOH1032 2.2 21.1 1.0
CG A:ASP244 3.2 20.1 1.0
P14 A:RIS901 3.2 21.5 1.0
P9 A:RIS901 3.2 21.4 1.0
O13 A:RIS901 3.4 21.5 1.0
C8 A:RIS901 3.4 20.6 1.0
OD1 A:ASP244 3.6 22.4 1.0
O A:HOH1033 3.8 24.5 1.0
O A:HOH945 4.0 19.2 1.0
OD2 A:ASP248 4.0 31.5 1.0
OD2 A:ASP263 4.1 25.1 1.0
NE2 A:GLN241 4.1 21.0 1.0
O12 A:RIS901 4.1 21.3 1.0
OD1 A:ASP263 4.1 27.1 1.0
O15 A:RIS901 4.2 20.3 1.0
O A:ASP244 4.2 21.9 1.0
O16 A:RIS901 4.3 16.8 1.0
NZ A:LYS258 4.3 21.9 1.0
CB A:ASP244 4.4 20.8 1.0
O10 A:RIS901 4.4 22.1 1.0
C A:ASP244 4.5 21.4 1.0
CG A:ASP263 4.6 28.9 1.0
CE A:LYS258 4.6 22.9 1.0
OD1 A:ASP245 4.6 26.3 1.0
CG A:ASP248 4.7 28.8 1.0
CB A:ASP248 4.8 26.7 1.0
C7 A:RIS901 5.0 20.0 1.0
O A:HOH936 5.0 24.0 1.0
MG A:MG907 5.0 22.0 1.0
N A:ASP245 5.0 21.9 1.0

Magnesium binding site 3 out of 6 in 1rqj

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Magnesium binding site 3 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg909

b:19.9
occ:1.00
 O15 A:RIS901 2.0 20.3 1.0
OD1 A:ASP111 2.0 22.1 1.0
OD2 A:ASP105 2.1 18.0 1.0
O A:HOH1034 2.1 18.0 1.0
O A:HOH926 2.2 24.4 1.0
O A:HOH922 2.2 18.1 1.0
CG A:ASP111 3.0 24.8 1.0
CG A:ASP105 3.1 19.9 1.0
MG A:MG907 3.2 22.0 1.0
OD2 A:ASP111 3.2 25.6 1.0
P14 A:RIS901 3.3 21.5 1.0
OD1 A:ASP105 3.4 20.2 1.0
O16 A:RIS901 3.4 16.8 1.0
OD2 A:ASP182 4.0 28.5 1.0
O A:HOH945 4.2 19.2 1.0
OE1 A:GLN179 4.2 27.1 1.0
NE2 A:GLN179 4.2 22.2 1.0
NZ A:LYS268 4.2 25.7 1.0
O A:HOH1033 4.2 24.5 1.0
O17 A:RIS901 4.2 20.7 1.0
OD1 A:ASP182 4.3 28.6 1.0
CB A:ASP111 4.3 25.2 1.0
CG A:ASP182 4.4 25.6 1.0
C7 A:RIS901 4.4 20.0 1.0
CB A:ASP105 4.5 20.1 1.0
C8 A:RIS901 4.5 20.6 1.0
NZ A:LYS202 4.5 19.1 1.0
C2 A:RIS901 4.6 20.0 1.0
C1 A:RIS901 4.6 22.2 1.0
CD A:GLN179 4.6 23.0 1.0
CE A:LYS268 4.6 26.7 1.0
O12 A:RIS901 4.7 21.3 1.0
O A:HOH933 5.0 15.2 1.0
O A:ASP105 5.0 21.3 1.0

Magnesium binding site 4 out of 6 in 1rqj

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Magnesium binding site 4 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:21.1
occ:1.00
 O11 B:RIS903 1.9 17.8 1.0
O17 B:RIS903 2.0 17.2 1.0
O B:HOH999 2.0 21.4 1.0
OD2 B:ASP244 2.1 19.0 1.0
O B:HOH1000 2.1 19.3 1.0
O B:HOH933 2.2 17.7 1.0
CG B:ASP244 3.2 16.3 1.0
P9 B:RIS903 3.3 18.1 1.0
P14 B:RIS903 3.4 16.1 1.0
O13 B:RIS903 3.4 14.7 1.0
C8 B:RIS903 3.5 16.8 1.0
OD1 B:ASP244 3.5 17.5 1.0
OD2 B:ASP248 3.7 30.4 1.0
O B:HOH927 3.9 18.8 1.0
OD2 B:ASP263 4.0 25.4 1.0
O B:ASP244 4.1 15.6 1.0
O12 B:RIS903 4.1 19.0 1.0
NZ B:LYS258 4.1 18.1 1.0
OD1 B:ASP263 4.2 26.1 1.0
O B:HOH945 4.2 18.9 1.0
NE2 B:GLN241 4.3 15.3 1.0
O16 B:RIS903 4.3 18.1 1.0
CB B:ASP244 4.4 15.9 1.0
O10 B:RIS903 4.4 17.1 1.0
CG B:ASP248 4.4 26.6 1.0
CE B:LYS258 4.4 19.9 1.0
C B:ASP244 4.5 16.3 1.0
CG B:ASP263 4.6 26.4 1.0
O15 B:RIS903 4.6 20.1 1.0
CB B:ASP248 4.7 24.3 1.0
OD1 B:ASP245 4.8 23.5 1.0
O B:HOH1010 4.8 30.6 1.0
N B:ASP245 5.0 17.8 1.0
CA B:ASP244 5.0 16.6 1.0
MG B:MG906 5.0 19.0 1.0

Magnesium binding site 5 out of 6 in 1rqj

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Magnesium binding site 5 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg905

b:17.9
occ:1.00
 O B:HOH1002 2.0 20.5 1.0
O16 B:RIS903 2.0 18.1 1.0
OD2 B:ASP105 2.1 20.6 1.0
O B:HOH1003 2.1 16.8 1.0
O B:HOH913 2.1 15.9 1.0
OD1 B:ASP111 2.2 18.8 1.0
CG B:ASP105 3.1 18.4 1.0
CG B:ASP111 3.1 21.6 1.0
MG B:MG906 3.2 19.0 1.0
P14 B:RIS903 3.2 16.1 1.0
OD2 B:ASP111 3.3 21.2 1.0
OD1 B:ASP105 3.4 16.3 1.0
O15 B:RIS903 3.4 20.1 1.0
OD2 B:ASP182 4.0 25.0 1.0
NE2 B:GLN179 4.1 19.9 1.0
OD1 B:ASP182 4.2 22.9 1.0
OE1 B:GLN179 4.2 21.8 1.0
O B:HOH945 4.3 18.9 1.0
CG B:ASP182 4.3 21.6 1.0
O B:HOH927 4.4 18.8 1.0
O17 B:RIS903 4.4 17.2 1.0
C7 B:RIS903 4.4 15.6 1.0
NZ B:LYS268 4.4 21.9 1.0
C8 B:RIS903 4.4 16.8 1.0
CB B:ASP105 4.4 18.4 1.0
NZ B:LYS202 4.5 15.0 1.0
CB B:ASP111 4.5 22.6 1.0
C2 B:RIS903 4.6 17.9 1.0
CD B:GLN179 4.6 20.9 1.0
C1 B:RIS903 4.8 17.5 1.0
O12 B:RIS903 4.8 19.0 1.0
O B:HOH1001 4.8 16.1 1.0
CE B:LYS268 4.9 23.1 1.0
O B:ASP105 4.9 19.1 1.0

Magnesium binding site 6 out of 6 in 1rqj

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Magnesium binding site 6 out of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate


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 Risedronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg906

b:19.0
occ:1.00
 O B:HOH1001 2.0 16.1 1.0
OD1 B:ASP105 2.0 16.3 1.0
O12 B:RIS903 2.1 19.0 1.0
O B:HOH945 2.1 18.9 1.0
OD1 B:ASP111 2.2 18.8 1.0
O16 B:RIS903 2.2 18.1 1.0
CG B:ASP105 3.1 18.4 1.0
CG B:ASP111 3.2 21.6 1.0
MG B:MG905 3.2 17.9 1.0
P9 B:RIS903 3.3 18.1 1.0
OD2 B:ASP105 3.4 20.6 1.0
P14 B:RIS903 3.4 16.1 1.0
CB B:ASP111 3.6 22.6 1.0
C8 B:RIS903 3.6 16.8 1.0
C7 B:RIS903 3.8 15.6 1.0
O B:HOH983 3.9 24.1 1.0
OD2 B:ASP113 4.0 26.0 1.0
NH1 B:ARG116 4.0 19.2 1.0
O17 B:RIS903 4.1 17.2 1.0
O11 B:RIS903 4.1 17.8 1.0
O B:HOH913 4.2 15.9 1.0
OD2 B:ASP111 4.3 21.2 1.0
CB B:ASP105 4.4 18.4 1.0
O B:HOH975 4.4 25.6 1.0
O B:ASP105 4.4 19.1 1.0
O B:HOH1000 4.5 19.3 1.0
OD2 B:ASP106 4.5 20.6 1.0
O10 B:RIS903 4.6 17.1 1.0
O15 B:RIS903 4.7 20.1 1.0
C B:ASP105 4.7 19.0 1.0
O B:HOH1002 4.8 20.5 1.0
O B:HOH1003 4.9 16.8 1.0
C2 B:RIS903 5.0 17.9 1.0
MG B:MG904 5.0 21.1 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 13:05:02 2024

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