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Magnesium in PDB 3efq: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714, PDB code: 3efq 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) 28.75 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.961, 119.157, 63.040, 90.00, 111.38, 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-714 (pdb code 3efq). 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-714, PDB code: 3efq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3efq

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Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714


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-714 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:29.9
occ:1.00
 OD2 A:ASP103 1.9 30.3 1.0
OD2 A:ASP107 2.0 32.0 1.0
O A:HOH3131 2.0 30.1 1.0
O6 A:7143001 2.0 29.0 1.0
O3 A:7143001 2.1 30.2 1.0
O A:HOH3007 2.1 27.7 1.0
MG A:MG3004 2.8 28.8 1.0
CG A:ASP103 2.9 33.3 1.0
CG A:ASP107 3.2 34.3 1.0
OD1 A:ASP103 3.2 33.8 1.0
P2 A:7143001 3.3 32.9 1.0
P1 A:7143001 3.4 32.5 1.0
C1 A:7143001 3.7 31.3 1.0
O A:HOH3011 3.8 27.5 1.0
C2 A:7143001 3.8 30.1 1.0
CB A:ASP107 3.8 35.7 1.0
O4 A:7143001 4.0 33.0 1.0
O1 A:7143001 4.1 34.4 1.0
OD1 A:ASP107 4.1 31.9 1.0
CB A:ASP103 4.3 30.7 1.0
NH2 A:ARG112 4.3 29.5 1.0
O A:ASP103 4.3 30.8 1.0
O A:HOH3019 4.3 24.9 1.0
O A:HOH3112 4.4 31.0 1.0
O5 A:7143001 4.4 27.6 1.0
OD1 A:ASP104 4.5 31.4 1.0
OG A:SER109 4.5 39.8 1.0
C A:ASP103 4.5 31.5 1.0
O2 A:7143001 4.5 33.0 1.0
O A:HOH3059 4.5 35.9 1.0
O A:HOH3088 4.6 40.4 1.0
N1 A:7143001 4.8 25.4 1.0
O A:HOH3033 4.8 45.6 1.0
O A:HOH3109 4.9 42.4 1.0
MG A:MG3003 4.9 38.2 1.0
C7 A:7143001 4.9 27.1 1.0
N A:ASP104 5.0 32.3 1.0
CA A:ASP103 5.0 31.1 1.0

Magnesium binding site 2 out of 6 in 3efq

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Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714


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-714 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:38.2
occ:1.00
 O1 A:7143001 2.0 34.4 1.0
O A:HOH3135 2.0 30.0 1.0
O A:HOH3065 2.0 41.5 1.0
O4 A:7143001 2.2 33.0 1.0
OD2 A:ASP255 2.3 34.7 1.0
O A:HOH3059 2.3 35.9 1.0
P1 A:7143001 3.3 32.5 1.0
CG A:ASP255 3.3 35.7 1.0
P2 A:7143001 3.5 32.9 1.0
OD1 A:ASP259 3.6 51.5 1.0
C1 A:7143001 3.7 31.3 1.0
OD1 A:ASP255 3.8 35.5 1.0
O3 A:7143001 4.0 30.2 1.0
O A:HOH3131 4.0 30.1 1.0
O A:HOH3083 4.1 31.2 1.0
NZ A:LYS269 4.1 52.0 1.0
OD1 A:ASP273 4.2 42.6 1.0
OD2 A:ASP273 4.2 38.8 1.0
O6 A:7143001 4.2 29.0 1.0
O A:ASP255 4.3 36.3 1.0
CG A:ASP259 4.3 47.7 1.0
NE2 A:GLN252 4.4 26.6 1.0
O2 A:7143001 4.4 33.0 1.0
CE A:LYS269 4.5 50.0 1.0
O A:HOH3011 4.5 27.5 1.0
CB A:ASP255 4.6 37.1 1.0
CB A:ASP259 4.6 46.2 1.0
CG A:ASP273 4.6 41.8 1.0
O5 A:7143001 4.6 27.6 1.0
C A:ASP255 4.6 37.3 1.0
OD1 A:ASP256 4.7 35.4 1.0
MG A:MG3002 4.9 29.9 1.0

Magnesium binding site 3 out of 6 in 3efq

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Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714


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-714 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:28.8
occ:1.00
 O A:HOH3112 2.0 31.0 1.0
O6 A:7143001 2.0 29.0 1.0
OD2 A:ASP107 2.1 32.0 1.0
OD1 A:ASP103 2.2 33.8 1.0
O A:HOH3019 2.2 24.9 1.0
O A:HOH3109 2.3 42.4 1.0
MG A:MG3002 2.8 29.9 1.0
CG A:ASP107 2.8 34.3 1.0
OD1 A:ASP107 2.9 31.9 1.0
CG A:ASP103 3.0 33.3 1.0
OD2 A:ASP103 3.3 30.3 1.0
P2 A:7143001 3.3 32.9 1.0
O5 A:7143001 3.6 27.6 1.0
O A:HOH3131 3.6 30.1 1.0
NZ A:LYS278 4.0 38.6 1.0
OD1 A:ASP175 4.2 33.4 1.0
NE2 A:GLN172 4.2 30.6 1.0
OD2 A:ASP175 4.2 31.2 1.0
CB A:ASP107 4.3 35.7 1.0
O4 A:7143001 4.3 33.0 1.0
O A:HOH3083 4.3 31.2 1.0
CB A:ASP103 4.4 30.7 1.0
CG A:ASP175 4.5 31.6 1.0
O3 A:7143001 4.5 30.2 1.0
OE1 A:GLN172 4.5 30.7 1.0
O A:HOH3007 4.6 27.7 1.0
C1 A:7143001 4.6 31.3 1.0
C7 A:7143001 4.6 27.1 1.0
O A:ASP103 4.7 30.8 1.0
C2 A:7143001 4.7 30.1 1.0
CD A:GLN172 4.8 31.2 1.0
N1 A:7143001 4.8 25.4 1.0
O A:HOH3088 4.8 40.4 1.0
NZ A:LYS212 5.0 33.5 1.0

Magnesium binding site 4 out of 6 in 3efq

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Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714


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-714 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4002

b:35.1
occ:1.00
 OD2 B:ASP103 2.0 32.4 1.0
O B:HOH4007 2.0 31.8 1.0
O3 B:7144001 2.1 37.8 1.0
OD2 B:ASP107 2.1 30.8 1.0
O6 B:7144001 2.2 34.2 1.0
O B:HOH4006 2.3 29.2 1.0
CG B:ASP103 3.1 31.9 1.0
MG B:MG4004 3.2 31.8 1.0
CG B:ASP107 3.2 36.4 1.0
P2 B:7144001 3.4 32.6 1.0
P1 B:7144001 3.4 33.8 1.0
OD1 B:ASP103 3.5 32.1 1.0
CB B:ASP107 3.6 36.3 1.0
O B:HOH4011 3.7 34.1 1.0
C1 B:7144001 3.7 33.4 1.0
C2 B:7144001 4.0 31.1 1.0
O4 B:7144001 4.0 33.0 1.0
O1 B:7144001 4.2 36.8 1.0
OG B:SER109 4.3 38.6 1.0
OD1 B:ASP107 4.3 31.9 1.0
O B:ASP103 4.4 31.4 1.0
CB B:ASP103 4.4 32.2 1.0
OD1 B:ASP104 4.4 36.8 1.0
NH1 B:ARG112 4.5 35.8 1.0
O B:HOH4107 4.5 51.6 1.0
O B:HOH4009 4.5 31.6 1.0
O B:HOH4037 4.5 39.8 1.0
O2 B:7144001 4.6 36.5 1.0
O B:HOH4017 4.6 40.5 1.0
C B:ASP103 4.6 32.5 1.0
O5 B:7144001 4.7 32.1 1.0
O B:HOH4124 4.8 33.3 1.0
MG B:MG4003 4.8 37.5 1.0
N1 B:7144001 4.9 30.8 1.0
O B:HOH4045 5.0 34.6 1.0
O B:HOH4029 5.0 27.5 1.0

Magnesium binding site 5 out of 6 in 3efq

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Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714


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-714 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4003

b:37.5
occ:1.00
 O4 B:7144001 2.1 33.0 1.0
O1 B:7144001 2.1 36.8 1.0
O B:HOH4009 2.1 31.6 1.0
O B:HOH4023 2.2 37.7 1.0
OD2 B:ASP255 2.2 38.5 1.0
P2 B:7144001 3.3 32.6 1.0
P1 B:7144001 3.3 33.8 1.0
CG B:ASP255 3.3 39.2 1.0
O B:HOH4045 3.6 34.6 1.0
C1 B:7144001 3.6 33.4 1.0
OD1 B:ASP259 3.7 48.8 1.0
OD1 B:ASP255 3.9 40.4 1.0
O3 B:7144001 3.9 37.8 1.0
O B:HOH4006 4.1 29.2 1.0
O6 B:7144001 4.2 34.2 1.0
NE2 B:GLN252 4.3 28.6 1.0
OD1 B:ASP273 4.3 43.9 1.0
OD2 B:ASP273 4.3 45.1 1.0
O B:ASP255 4.4 36.5 1.0
NZ B:LYS269 4.4 52.2 1.0
O5 B:7144001 4.4 32.1 1.0
CG B:ASP259 4.4 48.1 1.0
CB B:ASP255 4.5 36.8 1.0
CE B:LYS269 4.6 51.7 1.0
O2 B:7144001 4.6 36.5 1.0
OD1 B:ASP256 4.6 28.2 1.0
O B:HOH4011 4.6 34.1 1.0
C B:ASP255 4.7 36.6 1.0
CG B:ASP273 4.7 43.4 1.0
CB B:ASP259 4.7 46.8 1.0
MG B:MG4002 4.8 35.1 1.0

Magnesium binding site 6 out of 6 in 3efq

Go back to Magnesium Binding Sites List in 3efq
Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-714


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-714 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4004

b:31.8
occ:1.00
 OD2 B:ASP107 2.0 30.8 1.0
O B:HOH4124 2.0 33.3 1.0
O B:HOH4029 2.1 27.5 1.0
OD1 B:ASP103 2.1 32.1 1.0
O6 B:7144001 2.1 34.2 1.0
O B:HOH4107 2.2 51.6 1.0
CG B:ASP107 2.8 36.4 1.0
CG B:ASP103 3.0 31.9 1.0
OD1 B:ASP107 3.0 31.9 1.0
MG B:MG4002 3.2 35.1 1.0
OD2 B:ASP103 3.2 32.4 1.0
P2 B:7144001 3.4 32.6 1.0
O5 B:7144001 3.6 32.1 1.0
OD1 B:ASP175 3.9 35.5 1.0
NE2 B:GLN172 4.0 33.3 1.0
O4 B:7144001 4.2 33.0 1.0
CB B:ASP107 4.3 36.3 1.0
O B:HOH4006 4.3 29.2 1.0
O B:HOH4045 4.3 34.6 1.0
OE1 B:GLN172 4.3 34.9 1.0
CB B:ASP103 4.4 32.2 1.0
CG B:ASP175 4.4 34.7 1.0
OD2 B:ASP175 4.4 33.8 1.0
CD B:GLN172 4.6 35.1 1.0
NZ B:LYS278 4.6 42.1 1.0
C7 B:7144001 4.6 29.4 1.0
C1 B:7144001 4.7 33.4 1.0
N1 B:7144001 4.7 30.8 1.0
CE B:LYS278 4.7 39.8 1.0
C2 B:7144001 4.7 31.1 1.0
O B:ASP103 4.8 31.4 1.0
O B:HOH4007 4.8 31.8 1.0
O B:HOH4037 4.8 39.8 1.0
O3 B:7144001 4.8 37.8 1.0
NZ B:LYS212 4.8 33.4 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 13:03:39 2024

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