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Magnesium in PDB 3egt: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722, PDB code: 3egt was solved by R.Cao, Y.Gao, H.Robinson, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.77 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.227, 119.153, 62.957, 90.00, 111.51, 90.00
R / Rfree (%) 20.3 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722 (pdb code 3egt). 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-722, PDB code: 3egt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3egt

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Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722


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-722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:35.5
occ:1.00
 O3 A:7223001 1.9 35.1 1.0
OD2 A:ASP107 2.0 33.5 1.0
OD2 A:ASP103 2.0 31.5 1.0
O A:HOH3121 2.0 30.2 1.0
O6 A:7223001 2.1 34.1 1.0
O A:HOH3023 2.2 35.4 1.0
CG A:ASP103 2.9 34.5 1.0
MG A:MG3004 3.1 32.6 1.0
CG A:ASP107 3.1 36.5 1.0
OD1 A:ASP103 3.2 35.5 1.0
P2 A:7223001 3.4 35.0 1.0
P1 A:7223001 3.5 34.7 1.0
CB A:ASP107 3.6 37.7 1.0
O A:HOH3019 3.8 29.8 1.0
C1 A:7223001 3.8 35.7 1.0
C2 A:7223001 3.9 35.5 1.0
O4 A:7223001 4.0 37.4 1.0
OD1 A:ASP107 4.2 36.0 1.0
NH2 A:ARG112 4.3 34.6 1.0
O A:ASP103 4.3 31.9 1.0
CB A:ASP103 4.3 33.1 1.0
O1 A:7223001 4.3 35.9 1.0
O A:HOH3011 4.3 31.8 1.0
OG A:SER109 4.3 42.1 1.0
O A:HOH3049 4.5 41.1 1.0
OD1 A:ASP104 4.5 35.2 1.0
C A:ASP103 4.5 33.6 1.0
O A:HOH3005 4.6 26.7 1.0
O A:HOH3037 4.8 34.8 1.0
O A:HOH3014 4.8 28.8 1.0
O5 A:7223001 4.8 36.8 1.0
N1 A:7223001 4.8 33.7 1.0
O2 A:7223001 4.9 38.1 1.0
O A:HOH3059 5.0 37.3 1.0
N A:ASP104 5.0 34.4 1.0
C7 A:7223001 5.0 33.9 1.0

Magnesium binding site 2 out of 6 in 3egt

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Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722


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-722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:33.1
occ:1.00
 O1 A:7223001 1.7 35.9 1.0
O4 A:7223001 1.9 37.4 1.0
O A:HOH3127 2.0 37.2 1.0
O A:HOH3031 2.1 44.8 1.0
OD2 A:ASP255 2.1 39.9 1.0
O A:HOH3005 2.2 26.7 1.0
CG A:ASP255 3.1 40.3 1.0
P1 A:7223001 3.2 34.7 1.0
P2 A:7223001 3.3 35.0 1.0
C1 A:7223001 3.6 35.7 1.0
OD1 A:ASP255 3.6 38.6 1.0
O A:HOH3035 4.0 33.0 1.0
OD1 A:ASP259 4.1 47.9 1.0
O3 A:7223001 4.2 35.1 1.0
O A:ASP255 4.2 39.4 1.0
NE2 A:GLN252 4.2 31.8 1.0
O A:HOH3023 4.3 35.4 1.0
OD2 A:ASP273 4.3 39.4 1.0
CB A:ASP255 4.3 39.0 1.0
OD1 A:ASP273 4.4 46.7 1.0
NZ A:LYS269 4.4 57.3 1.0
O6 A:7223001 4.5 34.1 1.0
C A:ASP255 4.5 39.8 1.0
OD1 A:ASP256 4.5 38.5 1.0
O2 A:7223001 4.5 38.1 1.0
O5 A:7223001 4.5 36.8 1.0
CE A:LYS269 4.6 54.0 1.0
CG A:ASP259 4.7 46.6 1.0
O A:HOH3019 4.7 29.8 1.0
CG A:ASP273 4.7 42.5 1.0
CB A:ASP259 4.8 46.8 1.0
N A:ASP256 4.9 39.6 1.0
O A:HOH3128 4.9 69.7 1.0

Magnesium binding site 3 out of 6 in 3egt

Go back to Magnesium Binding Sites List in 3egt
Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722


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-722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:32.6
occ:1.00
 O6 A:7223001 1.9 34.1 1.0
OD1 A:ASP103 2.0 35.5 1.0
OD2 A:ASP107 2.1 33.5 1.0
O A:HOH3059 2.1 37.3 1.0
O A:HOH3014 2.2 28.8 1.0
O A:HOH3011 2.2 31.8 1.0
CG A:ASP107 2.9 36.5 1.0
CG A:ASP103 3.0 34.5 1.0
OD1 A:ASP107 3.0 36.0 1.0
MG A:MG3002 3.1 35.5 1.0
OD2 A:ASP103 3.4 31.5 1.0
P2 A:7223001 3.4 35.0 1.0
O5 A:7223001 3.6 36.8 1.0
NE2 A:GLN172 4.0 32.0 1.0
OD1 A:ASP175 4.0 36.8 1.0
NZ A:LYS278 4.0 39.8 1.0
OD2 A:ASP175 4.2 33.6 1.0
O A:HOH3023 4.2 35.4 1.0
OE1 A:GLN172 4.2 32.1 1.0
CG A:ASP175 4.3 34.2 1.0
O A:HOH3035 4.3 33.0 1.0
CB A:ASP103 4.4 33.1 1.0
CB A:ASP107 4.4 37.7 1.0
O4 A:7223001 4.4 37.4 1.0
C7 A:7223001 4.5 33.9 1.0
CD A:GLN172 4.5 33.3 1.0
O3 A:7223001 4.6 35.1 1.0
NZ A:LYS212 4.6 32.3 1.0
N1 A:7223001 4.6 33.7 1.0
C2 A:7223001 4.6 35.5 1.0
C1 A:7223001 4.7 35.7 1.0
O A:ASP103 4.8 31.9 1.0
O A:HOH3121 4.8 30.2 1.0
O A:HOH3049 4.9 41.1 1.0

Magnesium binding site 4 out of 6 in 3egt

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Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722


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-722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4002

b:35.7
occ:1.00
 O3 B:7224001 2.0 37.0 1.0
O B:HOH4115 2.0 33.2 1.0
O B:HOH4056 2.0 30.9 1.0
OD2 B:ASP107 2.1 36.1 1.0
O6 B:7224001 2.1 35.0 1.0
OD2 B:ASP103 2.2 32.6 1.0
CG B:ASP103 3.1 34.4 1.0
CG B:ASP107 3.1 37.0 1.0
OD1 B:ASP103 3.3 34.7 1.0
MG B:MG4004 3.3 31.1 1.0
P2 B:7224001 3.4 34.5 1.0
CB B:ASP107 3.5 38.5 1.0
P1 B:7224001 3.5 35.5 1.0
O B:HOH4016 3.8 35.7 1.0
C1 B:7224001 3.9 35.5 1.0
C2 B:7224001 4.1 33.7 1.0
O4 B:7224001 4.2 35.6 1.0
OD1 B:ASP107 4.2 35.7 1.0
O B:HOH4038 4.2 41.3 1.0
O B:HOH4116 4.3 39.1 1.0
O B:ASP103 4.3 35.0 1.0
OG B:SER109 4.3 44.6 1.0
O1 B:7224001 4.4 39.5 1.0
CB B:ASP103 4.4 33.8 1.0
O B:HOH4040 4.4 45.3 1.0
OD1 B:ASP104 4.4 33.4 1.0
NH1 B:ARG112 4.5 31.0 1.0
C B:ASP103 4.6 35.1 1.0
O B:HOH4026 4.7 39.9 1.0
O B:HOH4124 4.9 33.6 1.0
O5 B:7224001 4.9 36.2 1.0
O2 B:7224001 4.9 38.6 1.0
O B:HOH4012 5.0 36.4 1.0
N B:ASP104 5.0 35.4 1.0

Magnesium binding site 5 out of 6 in 3egt

Go back to Magnesium Binding Sites List in 3egt
Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722


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-722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4003

b:42.8
occ:1.00
 O4 B:7224001 1.9 35.6 1.0
O B:HOH4116 2.0 39.1 1.0
O B:HOH4128 2.0 38.5 1.0
O1 B:7224001 2.0 39.5 1.0
OD2 B:ASP255 2.0 42.4 1.0
O B:HOH4010 2.2 39.5 1.0
CG B:ASP255 3.1 41.4 1.0
P2 B:7224001 3.4 34.5 1.0
P1 B:7224001 3.4 35.5 1.0
OD1 B:ASP255 3.6 43.9 1.0
C1 B:7224001 3.7 35.5 1.0
O B:HOH4080 3.7 39.7 1.0
OD1 B:ASP259 3.9 48.5 1.0
OD2 B:ASP273 4.1 41.2 1.0
NE2 B:GLN252 4.2 33.3 1.0
O B:HOH4115 4.2 33.2 1.0
O B:ASP255 4.2 38.0 1.0
OD1 B:ASP273 4.2 43.1 1.0
O3 B:7224001 4.3 37.0 1.0
CB B:ASP255 4.3 38.8 1.0
NZ B:LYS269 4.4 55.1 1.0
OD1 B:ASP256 4.4 36.6 1.0
O6 B:7224001 4.5 35.0 1.0
C B:ASP255 4.5 38.9 1.0
CG B:ASP259 4.6 48.6 1.0
CG B:ASP273 4.6 44.5 1.0
O5 B:7224001 4.6 36.2 1.0
CE B:LYS269 4.6 55.2 1.0
CB B:ASP259 4.7 47.5 1.0
O2 B:7224001 4.8 38.6 1.0
N B:ASP256 5.0 38.2 1.0
O B:HOH4016 5.0 35.7 1.0

Magnesium binding site 6 out of 6 in 3egt

Go back to Magnesium Binding Sites List in 3egt
Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-722


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-722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4004

b:31.1
occ:1.00
 O B:HOH4124 1.9 33.6 1.0
O6 B:7224001 2.0 35.0 1.0
O B:HOH4012 2.0 36.4 1.0
OD1 B:ASP103 2.1 34.7 1.0
OD2 B:ASP107 2.2 36.1 1.0
O B:HOH4038 2.3 41.3 1.0
CG B:ASP107 2.9 37.0 1.0
OD1 B:ASP107 3.0 35.7 1.0
CG B:ASP103 3.1 34.4 1.0
MG B:MG4002 3.3 35.7 1.0
P2 B:7224001 3.4 34.5 1.0
OD2 B:ASP103 3.5 32.6 1.0
O5 B:7224001 3.6 36.2 1.0
OD1 B:ASP175 3.9 36.4 1.0
NE2 B:GLN172 4.0 32.7 1.0
OE1 B:GLN172 4.1 35.5 1.0
O B:HOH4115 4.2 33.2 1.0
OD2 B:ASP175 4.2 34.2 1.0
CG B:ASP175 4.3 35.6 1.0
O B:HOH4080 4.4 39.7 1.0
CB B:ASP107 4.4 38.5 1.0
CB B:ASP103 4.4 33.8 1.0
CD B:GLN172 4.5 34.2 1.0
O4 B:7224001 4.5 35.6 1.0
NZ B:LYS278 4.5 48.7 1.0
NZ B:LYS212 4.5 33.7 1.0
C7 B:7224001 4.5 31.4 1.0
CE B:LYS278 4.6 46.2 1.0
N1 B:7224001 4.7 32.3 1.0
O3 B:7224001 4.7 37.0 1.0
C1 B:7224001 4.7 35.5 1.0
C2 B:7224001 4.8 33.7 1.0
O B:ASP103 4.8 35.0 1.0
O B:HOH4040 4.9 45.3 1.0
O B:HOH4056 5.0 30.9 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 13:03:39 2024

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