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Magnesium in PDB 3dyf: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate, PDB code: 3dyf was solved by R.Cao, Y.Gao, H.Robinson, A.Goddard, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.939, 117.898, 63.274, 90.00, 111.27, 90.00
R / Rfree (%) 20.1 / 26.8

Other elements in 3dyf:

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate (pdb code 3dyf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate, PDB code: 3dyf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3dyf

Go back to Magnesium Binding Sites List in 3dyf
Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:43.0
occ:1.00
 O A:HOH5225 2.0 31.6 1.0
OD2 A:ASP107 2.1 27.0 1.0
OD2 A:ASP103 2.2 37.5 1.0
O7 A:NI93001 2.4 32.1 1.0
O3 A:NI93001 2.4 53.0 1.0
CG A:ASP103 3.1 38.1 1.0
CG A:ASP107 3.2 32.4 1.0
O1 A:NI93001 3.3 49.5 1.0
P2 A:NI93001 3.3 45.1 1.0
O A:HOH5143 3.5 25.3 1.0
OD1 A:ASP103 3.5 41.0 1.0
P1 A:NI93001 3.5 40.6 1.0
CB A:ASP107 3.6 13.4 1.0
OG A:SER109 3.8 43.7 1.0
C1 A:NI93001 3.9 39.0 1.0
OD1 A:ASP104 3.9 39.1 1.0
MG A:MG3004 4.0 41.2 1.0
NH2 A:ARG112 4.0 19.7 1.0
O A:HOH5001 4.1 20.8 1.0
C2 A:NI93001 4.1 41.4 1.0
O6 A:NI93001 4.2 34.5 1.0
O A:HOH5003 4.2 37.3 1.0
O A:ASP103 4.2 28.0 1.0
OD1 A:ASP107 4.3 12.8 1.0
CB A:ASP103 4.4 33.1 1.0
C A:ASP103 4.5 31.5 1.0
O A:HOH5014 4.6 23.2 1.0
O5 A:NI93001 4.6 62.1 1.0
O A:HOH5048 4.7 39.9 1.0
O4 A:NI93001 4.8 21.1 1.0
N A:ASP104 4.8 20.9 1.0
CA A:ASP104 4.9 25.8 1.0
MG A:MG3003 4.9 21.6 1.0
O A:HOH5002 4.9 33.3 1.0
O A:HOH5027 5.0 39.8 1.0
CB A:SER109 5.0 38.3 1.0
OG1 A:THR272 5.0 23.9 1.0

Magnesium binding site 2 out of 6 in 3dyf

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Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:21.6
occ:1.00
 O A:HOH5001 2.4 20.8 1.0
OD2 A:ASP255 2.4 35.6 1.0
O6 A:NI93001 2.6 34.5 1.0
O3 A:NI93001 2.7 53.0 1.0
O5 A:NI93001 2.7 62.1 1.0
P2 A:NI93001 3.0 45.1 1.0
CG A:ASP255 3.2 41.7 1.0
OD1 A:ASP255 3.5 33.5 1.0
P1 A:NI93001 3.6 40.6 1.0
C1 A:NI93001 3.6 39.0 1.0
O2 A:NI93001 3.6 44.9 1.0
OD1 A:ASP259 3.8 58.7 1.0
CG A:ASP259 4.1 51.1 1.0
O A:ASP255 4.1 20.3 1.0
CB A:ASP259 4.1 39.1 1.0
O A:HOH5225 4.2 31.6 1.0
OD2 A:ASP273 4.4 31.0 1.0
O7 A:NI93001 4.4 32.1 1.0
O A:HOH5060 4.4 51.5 1.0
O A:HOH5143 4.4 25.3 1.0
CB A:ASP255 4.5 42.5 1.0
C A:ASP255 4.5 25.8 1.0
O1 A:NI93001 4.5 49.5 1.0
OD1 A:ASP273 4.6 45.8 1.0
NZ A:LYS269 4.7 25.9 1.0
O4 A:NI93001 4.8 21.1 1.0
CE A:LYS269 4.8 19.7 1.0
CG A:ASP273 4.9 46.4 1.0
MG A:MG3002 4.9 43.0 1.0
OD2 A:ASP259 4.9 35.7 1.0
OE1 A:GLN252 4.9 28.4 1.0

Magnesium binding site 3 out of 6 in 3dyf

Go back to Magnesium Binding Sites List in 3dyf
Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:41.2
occ:1.00
 O A:HOH5002 1.8 33.3 1.0
O7 A:NI93001 2.1 32.1 1.0
O A:HOH5003 2.1 37.3 1.0
OD1 A:ASP103 2.4 41.0 1.0
O4 A:NI93001 2.6 21.1 1.0
P1 A:NI93001 2.9 40.6 1.0
OD2 A:ASP107 3.0 27.0 1.0
CG A:ASP103 3.4 38.1 1.0
OD2 A:ASP175 3.5 37.3 1.0
OD1 A:ASP107 3.6 12.8 1.0
OD2 A:ASP103 3.6 37.5 1.0
CG A:ASP107 3.7 32.4 1.0
O6 A:NI93001 3.8 34.5 1.0
CG A:ASP175 3.9 33.2 1.0
OE1 A:GLN172 3.9 29.8 1.0
NE2 A:GLN172 4.0 36.3 1.0
MG A:MG3002 4.0 43.0 1.0
OD1 A:ASP175 4.1 47.4 1.0
NZ A:LYS212 4.1 15.2 1.0
O A:HOH5060 4.1 51.5 1.0
C1 A:NI93001 4.3 39.0 1.0
C3 A:NI93001 4.3 45.2 1.0
N A:NI93001 4.3 46.3 1.0
O A:HOH5225 4.3 31.6 1.0
NZ A:LYS278 4.4 18.0 1.0
CD A:GLN172 4.4 25.1 1.0
C2 A:NI93001 4.4 41.4 1.0
CB A:ASP103 4.7 33.1 1.0
C7 A:NI93001 4.8 46.2 1.0
C5 A:NI93001 4.9 41.9 1.0
CB A:ASP175 4.9 28.4 1.0

Magnesium binding site 4 out of 6 in 3dyf

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Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4002

b:36.3
occ:1.00
 OD1 B:ASP103 2.1 32.9 1.0
O3 B:NI94001 2.1 58.4 1.0
OD2 B:ASP107 2.2 23.0 1.0
O7 B:NI94001 2.3 45.2 1.0
P2 B:NI94001 3.0 45.6 1.0
CG B:ASP103 3.1 32.3 1.0
O1 B:NI94001 3.1 67.7 1.0
CG B:ASP107 3.2 32.3 1.0
P1 B:NI94001 3.4 42.9 1.0
OD2 B:ASP103 3.4 27.5 1.0
O B:HOH5116 3.5 21.3 1.0
CB B:ASP107 3.6 30.5 1.0
C1 B:NI94001 3.7 45.2 1.0
MG B:MG4004 3.9 27.1 1.0
OG B:SER109 3.9 39.0 1.0
O6 B:NI94001 3.9 36.7 1.0
O B:HOH5161 4.0 25.6 1.0
C2 B:NI94001 4.1 49.7 1.0
OD1 B:ASP107 4.3 28.7 1.0
O5 B:NI94001 4.4 54.5 1.0
O B:HOH5122 4.4 39.0 1.0
O B:ASP103 4.5 15.8 1.0
CB B:ASP103 4.5 32.3 1.0
NH2 B:ARG112 4.5 38.9 1.0
OD1 B:ASP104 4.5 43.2 1.0
O B:HOH5015 4.5 23.0 1.0
MG B:MG4003 4.6 23.4 1.0
C B:ASP103 4.7 24.5 1.0
O4 B:NI94001 4.7 37.5 1.0
O B:HOH5067 4.9 44.3 1.0
O B:HOH5117 4.9 46.5 1.0
N B:ASP104 5.0 14.0 1.0

Magnesium binding site 5 out of 6 in 3dyf

Go back to Magnesium Binding Sites List in 3dyf
Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4003

b:23.4
occ:1.00
 O6 B:NI94001 2.2 36.7 1.0
O B:HOH5264 2.2 29.2 1.0
OD2 B:ASP255 2.4 31.1 1.0
O B:HOH5161 2.4 25.6 1.0
O3 B:NI94001 2.7 58.4 1.0
O5 B:NI94001 2.7 54.5 1.0
P2 B:NI94001 2.9 45.6 1.0
CG B:ASP255 3.1 35.1 1.0
OD1 B:ASP255 3.1 32.5 1.0
P1 B:NI94001 3.2 42.9 1.0
O2 B:NI94001 3.2 45.2 1.0
C1 B:NI94001 3.3 45.2 1.0
OD1 B:ASP259 4.0 54.1 1.0
O7 B:NI94001 4.2 45.2 1.0
O B:HOH5117 4.3 46.5 1.0
OD2 B:ASP273 4.4 39.5 1.0
O4 B:NI94001 4.4 37.5 1.0
O B:ASP255 4.4 22.8 1.0
O B:HOH5116 4.5 21.3 1.0
O1 B:NI94001 4.5 67.7 1.0
NE2 B:GLN252 4.5 27.6 1.0
CB B:ASP255 4.5 36.8 1.0
MG B:MG4002 4.6 36.3 1.0
NZ B:LYS269 4.6 40.5 1.0
CG B:ASP259 4.6 47.4 1.0
OD1 B:ASP273 4.7 36.6 1.0
CB B:ASP259 4.7 40.6 1.0
C B:ASP255 4.7 25.7 1.0
OD1 B:ASP256 4.7 57.4 1.0
CE B:LYS269 4.8 40.8 1.0
C2 B:NI94001 4.8 49.7 1.0
CG B:ASP273 4.9 43.1 1.0

Magnesium binding site 6 out of 6 in 3dyf

Go back to Magnesium Binding Sites List in 3dyf
Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4004

b:27.1
occ:1.00
 O7 B:NI94001 2.3 45.2 1.0
O B:HOH5004 2.3 26.8 1.0
OD2 B:ASP107 2.4 23.0 1.0
OD2 B:ASP103 2.5 27.5 1.0
OD1 B:ASP107 2.9 28.7 1.0
CG B:ASP107 3.0 32.3 1.0
OD1 B:ASP175 3.2 41.8 1.0
O4 B:NI94001 3.3 37.5 1.0
P1 B:NI94001 3.3 42.9 1.0
CG B:ASP103 3.6 32.3 1.0
O B:HOH5117 3.7 46.5 1.0
CG B:ASP175 3.7 40.2 1.0
OD2 B:ASP175 3.8 44.2 1.0
MG B:MG4002 3.9 36.3 1.0
OD1 B:ASP103 4.0 32.9 1.0
O6 B:NI94001 4.1 36.7 1.0
NZ B:LYS278 4.4 65.0 1.0
CE B:LYS278 4.5 55.4 1.0
CB B:ASP107 4.5 30.5 1.0
NZ B:LYS212 4.6 20.9 1.0
OE1 B:GLN172 4.8 42.2 1.0
NE2 B:GLN172 4.8 36.5 1.0
O B:HOH5122 4.8 39.0 1.0
C1 B:NI94001 4.8 45.2 1.0
CB B:ASP103 4.8 32.3 1.0
CB B:ASP175 4.9 38.2 1.0
O3 B:NI94001 5.0 58.4 1.0

Reference:

Y.Zhang, R.Cao, F.Yin, M.P.Hudock, R.T.Guo, K.Krysiak, S.Mukherjee, Y.G.Gao, H.Robinson, Y.Song, J.H.No, K.Bergan, A.Leon, L.Cass, A.Goddard, T.K.Chang, F.Y.Lin, E.Van Beek, S.Papapoulos, A.H.Wang, T.Kubo, M.Ochi, D.Mukkamala, E.Oldfield. Lipophilic Bisphosphonates As Dual Farnesyl/Geranylgeranyl Diphosphate Synthase Inhibitors: An X-Ray and uc(Nmr) Investigation. J.Am.Chem.Soc. V. 131 5153 2009.
ISSN: ISSN 0002-7863
PubMed: 19309137
DOI: 10.1021/JA808285E
Page generated: Wed Aug 14 12:45:28 2024

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