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Magnesium in PDB 3dyh: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721, PDB code: 3dyh 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) 28.83 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.915, 118.733, 63.036, 90.00, 112.29, 90.00
R / Rfree (%) 24 / 28.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721 (pdb code 3dyh). 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-721, PDB code: 3dyh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3dyh

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Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721


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-721 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:29.9
occ:1.00
 O3 A:7213001 2.0 32.1 1.0
OD2 A:ASP103 2.0 29.8 1.0
O6 A:7213001 2.1 30.9 1.0
O A:HOH3022 2.1 29.6 1.0
OD2 A:ASP107 2.2 30.7 1.0
CG A:ASP103 2.9 29.1 1.0
MG A:MG3004 3.2 30.9 1.0
OD1 A:ASP103 3.2 29.0 1.0
CG A:ASP107 3.3 32.8 1.0
P2 A:7213001 3.3 31.5 1.0
P1 A:7213001 3.3 35.1 1.0
O A:HOH3024 3.5 34.8 1.0
C1 A:7213001 3.6 32.4 1.0
CB A:ASP107 3.8 34.5 1.0
O4 A:7213001 3.8 33.1 1.0
C2 A:7213001 3.9 29.7 1.0
O1 A:7213001 4.1 32.9 1.0
NH2 A:ARG112 4.1 26.8 1.0
CB A:ASP103 4.3 27.5 1.0
OD1 A:ASP107 4.3 34.8 1.0
O A:HOH3017 4.4 28.6 1.0
O A:HOH3016 4.4 39.0 1.0
O A:ASP103 4.4 28.5 1.0
O2 A:7213001 4.4 32.7 1.0
O A:HOH3005 4.5 29.9 1.0
OG A:SER109 4.5 36.2 1.0
O5 A:7213001 4.5 31.6 1.0
C A:ASP103 4.6 28.6 1.0
OD1 A:ASP104 4.6 30.4 1.0
N1 A:7213001 4.8 28.0 1.0
O A:HOH3035 4.8 36.7 1.0
C7 A:7213001 4.9 28.3 1.0
O A:HOH3006 4.9 26.9 1.0
N A:ASP104 4.9 28.0 1.0

Magnesium binding site 2 out of 6 in 3dyh

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Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721


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-721 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:33.1
occ:1.00
 O A:HOH3005 2.1 29.9 1.0
OD2 A:ASP255 2.1 29.3 1.0
O4 A:7213001 2.1 33.1 1.0
O1 A:7213001 2.1 32.9 1.0
O A:HOH3048 2.2 29.5 1.0
O A:HOH3026 2.2 35.2 1.0
CG A:ASP255 3.2 31.0 1.0
P1 A:7213001 3.4 35.1 1.0
P2 A:7213001 3.4 31.5 1.0
C1 A:7213001 3.6 32.4 1.0
OD1 A:ASP255 3.6 31.6 1.0
O A:HOH3047 4.0 35.3 1.0
OD2 A:ASP273 4.0 43.2 1.0
NZ A:LYS269 4.1 52.4 1.0
OD1 A:ASP259 4.1 41.5 1.0
NE2 A:GLN252 4.1 29.9 1.0
OD1 A:ASP273 4.1 42.0 1.0
O3 A:7213001 4.2 32.1 1.0
O A:ASP255 4.3 34.3 1.0
O A:HOH3022 4.4 29.6 1.0
O6 A:7213001 4.4 30.9 1.0
CB A:ASP255 4.4 32.9 1.0
O5 A:7213001 4.4 31.6 1.0
CE A:LYS269 4.5 52.6 1.0
O2 A:7213001 4.5 32.7 1.0
CG A:ASP273 4.5 43.6 1.0
OD1 A:ASP256 4.5 36.0 1.0
C A:ASP255 4.6 33.7 1.0
CG A:ASP259 4.7 44.0 1.0
CB A:ASP259 4.8 42.3 1.0
O A:HOH3024 4.9 34.8 1.0
N A:ASP256 5.0 34.3 1.0

Magnesium binding site 3 out of 6 in 3dyh

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Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721


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-721 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:30.9
occ:1.00
 OD1 A:ASP103 2.0 29.0 1.0
O6 A:7213001 2.1 30.9 1.0
OD2 A:ASP107 2.2 30.7 1.0
O A:HOH3017 2.2 28.6 1.0
O A:HOH3006 2.3 26.9 1.0
O A:HOH3102 2.3 40.0 1.0
CG A:ASP107 3.0 32.8 1.0
CG A:ASP103 3.0 29.1 1.0
OD1 A:ASP107 3.1 34.8 1.0
MG A:MG3002 3.2 29.9 1.0
P2 A:7213001 3.3 31.5 1.0
OD2 A:ASP103 3.4 29.8 1.0
O5 A:7213001 3.5 31.6 1.0
NE2 A:GLN172 3.9 24.7 1.0
OD1 A:ASP175 3.9 35.8 1.0
OE1 A:GLN172 4.1 28.2 1.0
O A:HOH3022 4.2 29.6 1.0
O4 A:7213001 4.2 33.1 1.0
OD2 A:ASP175 4.3 36.8 1.0
CG A:ASP175 4.3 34.0 1.0
CB A:ASP103 4.4 27.5 1.0
CD A:GLN172 4.4 28.9 1.0
C7 A:7213001 4.4 28.3 1.0
O A:HOH3047 4.4 35.3 1.0
CB A:ASP107 4.4 34.5 1.0
NZ A:LYS278 4.6 48.4 1.0
C1 A:7213001 4.7 32.4 1.0
N1 A:7213001 4.7 28.0 1.0
NZ A:LYS212 4.7 28.0 1.0
C2 A:7213001 4.7 29.7 1.0
O3 A:7213001 4.8 32.1 1.0
O A:ASP103 4.9 28.5 1.0
O A:HOH3016 4.9 39.0 1.0
C6 A:7213001 4.9 25.6 1.0
CE A:LYS278 5.0 45.8 1.0
CA A:ASP103 5.0 27.6 1.0

Magnesium binding site 4 out of 6 in 3dyh

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Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721


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-721 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4002

b:32.0
occ:1.00
 O3 B:7214001 1.9 34.4 1.0
O B:HOH4008 2.1 28.7 1.0
OD2 B:ASP103 2.1 31.8 1.0
O B:HOH4006 2.2 27.8 1.0
OD2 B:ASP107 2.2 33.4 1.0
O6 B:7214001 2.3 35.3 1.0
CG B:ASP103 3.0 30.9 1.0
P1 B:7214001 3.2 32.3 1.0
OD1 B:ASP103 3.3 28.7 1.0
CG B:ASP107 3.3 35.1 1.0
MG B:MG4004 3.3 29.7 1.0
P2 B:7214001 3.4 34.4 1.0
C1 B:7214001 3.6 34.2 1.0
O B:HOH4032 3.7 45.6 1.0
CB B:ASP107 3.8 36.3 1.0
C2 B:7214001 3.9 32.4 1.0
O1 B:7214001 3.9 32.9 1.0
O4 B:7214001 4.0 36.2 1.0
O B:ASP103 4.3 31.4 1.0
NH1 B:ARG112 4.3 37.5 1.0
OG B:SER109 4.3 39.0 1.0
O2 B:7214001 4.4 32.7 1.0
O B:HOH4020 4.4 31.4 1.0
OD1 B:ASP104 4.4 33.7 1.0
OD1 B:ASP107 4.4 32.8 1.0
CB B:ASP103 4.4 30.0 1.0
O B:HOH4179 4.5 34.3 1.0
O B:HOH4023 4.5 39.2 1.0
C B:ASP103 4.6 31.1 1.0
O B:HOH4031 4.6 43.0 1.0
O5 B:7214001 4.7 34.6 1.0
N1 B:7214001 4.9 33.0 1.0
MG B:MG4003 4.9 34.9 1.0
N B:ASP104 4.9 31.6 1.0
O B:HOH4117 5.0 32.5 1.0
O B:HOH4069 5.0 32.5 1.0
O B:HOH4021 5.0 27.1 1.0

Magnesium binding site 5 out of 6 in 3dyh

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Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721


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-721 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4003

b:34.9
occ:1.00
 O4 B:7214001 1.9 36.2 1.0
O B:HOH4179 2.0 34.3 1.0
O1 B:7214001 2.0 32.9 1.0
O B:HOH4041 2.2 31.7 1.0
OD2 B:ASP255 2.2 37.6 1.0
O B:HOH4039 2.4 40.2 1.0
P2 B:7214001 3.3 34.4 1.0
CG B:ASP255 3.3 37.6 1.0
P1 B:7214001 3.3 32.3 1.0
C1 B:7214001 3.6 34.2 1.0
OD1 B:ASP255 3.8 35.0 1.0
O B:HOH4044 3.9 35.4 1.0
NE2 B:GLN252 4.1 28.1 1.0
O3 B:7214001 4.1 34.4 1.0
O6 B:7214001 4.2 35.3 1.0
OD1 B:ASP273 4.2 48.2 1.0
OD1 B:ASP259 4.2 43.8 1.0
OD2 B:ASP273 4.2 46.2 1.0
O B:HOH4006 4.2 27.8 1.0
O5 B:7214001 4.3 34.6 1.0
NZ B:LYS269 4.3 56.3 1.0
O2 B:7214001 4.4 32.7 1.0
CE B:LYS269 4.4 57.0 1.0
OD1 B:ASP256 4.5 37.6 1.0
CB B:ASP255 4.5 36.9 1.0
CG B:ASP273 4.6 49.0 1.0
O B:ASP255 4.6 37.4 1.0
C B:ASP255 4.8 36.9 1.0
CG B:ASP259 4.8 43.4 1.0
O B:HOH4032 4.8 45.6 1.0
MG B:MG4002 4.9 32.0 1.0

Magnesium binding site 6 out of 6 in 3dyh

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Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-721


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-721 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4004

b:29.7
occ:1.00
 O B:HOH4117 2.0 32.5 1.0
OD1 B:ASP103 2.0 28.7 1.0
O6 B:7214001 2.1 35.3 1.0
O B:HOH4021 2.1 27.1 1.0
OD2 B:ASP107 2.3 33.4 1.0
O B:HOH4020 2.3 31.4 1.0
CG B:ASP103 3.1 30.9 1.0
CG B:ASP107 3.1 35.1 1.0
OD1 B:ASP107 3.2 32.8 1.0
P2 B:7214001 3.3 34.4 1.0
MG B:MG4002 3.3 32.0 1.0
OD2 B:ASP103 3.4 31.8 1.0
O5 B:7214001 3.6 34.6 1.0
OD1 B:ASP175 3.9 28.6 1.0
NE2 B:GLN172 4.0 27.9 1.0
OE1 B:GLN172 4.1 27.9 1.0
OD2 B:ASP175 4.2 30.4 1.0
O B:HOH4044 4.3 35.4 1.0
CG B:ASP175 4.3 28.6 1.0
O4 B:7214001 4.3 36.2 1.0
CB B:ASP103 4.4 30.0 1.0
C7 B:7214001 4.4 32.8 1.0
CD B:GLN172 4.4 28.6 1.0
O B:HOH4006 4.5 27.8 1.0
CB B:ASP107 4.6 36.3 1.0
N1 B:7214001 4.6 33.0 1.0
C1 B:7214001 4.6 34.2 1.0
C2 B:7214001 4.6 32.4 1.0
O3 B:7214001 4.7 34.4 1.0
NZ B:LYS212 4.7 27.8 1.0
O B:ASP103 4.8 31.4 1.0
CE B:LYS278 4.9 46.1 1.0
NZ B:LYS278 4.9 47.0 1.0
O B:HOH4008 5.0 28.7 1.0
C6 B:7214001 5.0 30.1 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 12:46:09 2024

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