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

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

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

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461, PDB code: 3dyg 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) 29.22 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.565, 118.520, 63.186, 90.00, 112.36, 90.00
R / Rfree (%) 20.7 / 25

Other elements in 3dyg:

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 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 (pdb code 3dyg). 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, PDB code: 3dyg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3dyg

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


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

b:23.9
occ:1.00
 O7 A:NI93001 2.1 22.8 1.0
O A:HOH5003 2.1 18.7 1.0
OD2 A:ASP103 2.1 22.3 1.0
O3 A:NI93001 2.1 42.4 1.0
O A:HOH5516 2.2 28.8 1.0
OD2 A:ASP107 2.3 21.9 1.0
P2 A:NI93001 2.9 29.3 1.0
O1 A:NI93001 3.1 43.0 1.0
P1 A:NI93001 3.1 22.7 1.0
CG A:ASP103 3.2 16.7 1.0
O A:HOH5252 3.4 34.4 1.0
CG A:ASP107 3.4 17.2 1.0
C1 A:NI93001 3.4 29.0 1.0
MG A:MG3004 3.5 20.2 1.0
OD1 A:ASP103 3.5 16.8 1.0
O6 A:NI93001 3.8 27.9 1.0
C2 A:NI93001 3.8 19.4 1.0
CB A:ASP107 3.9 19.7 1.0
NH2 A:ARG112 4.1 11.7 1.0
O A:HOH5006 4.2 25.1 1.0
O A:HOH5001 4.2 21.3 1.0
O5 A:NI93001 4.3 41.8 1.0
OD1 A:ASP104 4.4 19.0 1.0
O4 A:NI93001 4.4 19.0 1.0
OD1 A:ASP107 4.5 24.8 1.0
CB A:ASP103 4.5 17.7 1.0
OG A:SER109 4.5 25.7 1.0
O A:HOH5041 4.5 25.7 1.0
MG A:MG3003 4.5 22.6 1.0
O A:ASP103 4.7 20.7 1.0
O2 A:NI93001 4.8 23.1 1.0
O A:HOH5026 4.8 24.0 1.0
N A:NI93001 4.8 22.8 1.0
C A:ASP103 4.8 15.3 1.0

Magnesium binding site 2 out of 6 in 3dyg

Go back to Magnesium Binding Sites List in 3dyg
Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461


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

b:22.6
occ:1.00
 O6 A:NI93001 2.1 27.9 1.0
OD2 A:ASP255 2.2 18.9 1.0
O A:HOH5002 2.2 18.6 1.0
O A:HOH5001 2.3 21.3 1.0
O A:HOH5012 2.4 22.5 1.0
O3 A:NI93001 2.8 42.4 1.0
O5 A:NI93001 2.9 41.8 1.0
P2 A:NI93001 3.1 29.3 1.0
CG A:ASP255 3.1 20.0 1.0
P1 A:NI93001 3.2 22.7 1.0
O2 A:NI93001 3.3 23.1 1.0
C1 A:NI93001 3.3 29.0 1.0
OD1 A:ASP255 3.4 22.0 1.0
NZ A:LYS269 3.7 35.9 1.0
O A:HOH5081 3.9 24.0 1.0
O7 A:NI93001 4.1 22.8 1.0
O A:HOH5516 4.2 28.8 1.0
OD1 A:ASP259 4.2 28.1 1.0
OE1 A:GLN252 4.2 19.6 1.0
O A:ASP255 4.3 21.1 1.0
O4 A:NI93001 4.3 19.0 1.0
OD2 A:ASP273 4.4 26.9 1.0
CB A:ASP255 4.4 17.9 1.0
MG A:MG3002 4.5 23.9 1.0
O1 A:NI93001 4.6 43.0 1.0
OD1 A:ASP273 4.6 30.6 1.0
CE A:LYS269 4.7 34.0 1.0
C A:ASP255 4.7 19.0 1.0
O A:HOH5252 4.7 34.4 1.0
OD1 A:ASP256 4.8 26.8 1.0
CG A:ASP259 4.8 29.9 1.0
C2 A:NI93001 4.9 19.4 1.0
CG A:ASP273 4.9 28.8 1.0
CB A:ASP259 5.0 29.1 1.0

Magnesium binding site 3 out of 6 in 3dyg

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


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

b:20.2
occ:1.00
 O A:HOH5006 1.8 25.1 1.0
O A:HOH5005 2.0 20.3 1.0
OD1 A:ASP103 2.1 16.8 1.0
O A:HOH5014 2.1 16.0 1.0
O7 A:NI93001 2.2 22.8 1.0
OD2 A:ASP107 2.4 21.9 1.0
OD1 A:ASP107 3.0 24.8 1.0
CG A:ASP107 3.0 17.2 1.0
CG A:ASP103 3.1 16.7 1.0
P1 A:NI93001 3.4 22.7 1.0
OD2 A:ASP103 3.4 22.3 1.0
O4 A:NI93001 3.4 19.0 1.0
MG A:MG3002 3.5 23.9 1.0
OD2 A:ASP175 3.8 23.3 1.0
OD1 A:ASP175 4.0 26.4 1.0
CG A:ASP175 4.1 27.2 1.0
NE2 A:GLN172 4.1 15.9 1.0
OE1 A:GLN172 4.2 20.5 1.0
NZ A:LYS278 4.2 23.0 1.0
O6 A:NI93001 4.3 27.9 1.0
O A:HOH5516 4.4 28.8 1.0
CB A:ASP103 4.4 17.7 1.0
CB A:ASP107 4.5 19.7 1.0
O A:HOH5081 4.6 24.0 1.0
C3 A:NI93001 4.6 17.5 1.0
CD A:GLN172 4.6 20.8 1.0
C1 A:NI93001 4.7 29.0 1.0
O A:HOH5003 4.8 18.7 1.0
N A:NI93001 4.8 22.8 1.0
NZ A:LYS212 4.8 13.6 1.0
C2 A:NI93001 4.8 19.4 1.0
O A:ASP103 4.9 20.7 1.0

Magnesium binding site 4 out of 6 in 3dyg

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


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

b:23.1
occ:1.00
 O B:HOH5004 1.9 18.3 1.0
OD2 B:ASP103 2.0 22.5 1.0
OD2 B:ASP107 2.1 20.6 1.0
O B:HOH5082 2.2 19.2 1.0
O7 B:NI94001 2.2 28.9 1.0
O3 B:NI94001 2.5 40.5 1.0
CG B:ASP103 3.0 16.1 1.0
CG B:ASP107 3.2 21.3 1.0
O1 B:NI94001 3.2 43.7 1.0
P2 B:NI94001 3.3 28.5 1.0
MG B:MG4004 3.3 18.1 1.0
OD1 B:ASP103 3.4 19.3 1.0
P1 B:NI94001 3.4 21.9 1.0
O B:HOH5184 3.5 31.0 1.0
CB B:ASP107 3.6 23.0 1.0
C1 B:NI94001 3.7 29.7 1.0
C2 B:NI94001 4.0 20.3 1.0
O6 B:NI94001 4.1 30.1 1.0
NH2 B:ARG112 4.1 20.0 1.0
OG B:SER109 4.2 23.9 1.0
O B:HOH5008 4.2 22.3 1.0
OD1 B:ASP104 4.3 19.4 1.0
OD1 B:ASP107 4.3 23.2 1.0
O B:ASP103 4.3 19.1 1.0
CB B:ASP103 4.3 16.7 1.0
C B:ASP103 4.5 17.0 1.0
O B:HOH5298 4.6 19.8 1.0
O4 B:NI94001 4.6 19.0 1.0
O5 B:NI94001 4.7 38.2 1.0
N B:ASP104 4.8 17.8 1.0
O B:HOH5198 4.9 33.0 1.0
O B:HOH5028 4.9 26.8 1.0
O B:HOH5007 5.0 17.5 1.0
O B:HOH5009 5.0 19.5 1.0
N B:NI94001 5.0 22.9 1.0

Magnesium binding site 5 out of 6 in 3dyg

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


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

b:29.8
occ:1.00
 OD2 B:ASP255 1.9 24.4 1.0
O B:HOH5010 2.1 21.7 1.0
O B:HOH5015 2.2 25.9 1.0
O6 B:NI94001 2.2 30.1 1.0
O B:HOH5298 2.5 19.8 1.0
CG B:ASP255 2.7 24.5 1.0
OD1 B:ASP255 2.9 25.9 1.0
O3 B:NI94001 3.1 40.5 1.0
O5 B:NI94001 3.1 38.2 1.0
P2 B:NI94001 3.4 28.5 1.0
O2 B:NI94001 3.4 26.0 1.0
P1 B:NI94001 3.4 21.9 1.0
C1 B:NI94001 3.6 29.7 1.0
NE2 B:GLN252 4.0 19.9 1.0
O B:ASP255 4.0 19.7 1.0
CB B:ASP255 4.0 21.4 1.0
O B:HOH5185 4.1 24.1 1.0
NZ B:LYS269 4.2 24.0 1.0
OD1 B:ASP259 4.3 31.8 1.0
C B:ASP255 4.3 20.8 1.0
O B:HOH5335 4.4 36.2 1.0
O7 B:NI94001 4.4 28.9 1.0
OD2 B:ASP273 4.4 30.4 1.0
O4 B:NI94001 4.4 19.0 1.0
OD1 B:ASP256 4.4 29.5 1.0
O B:HOH5082 4.6 19.2 1.0
CE B:LYS269 4.6 30.8 1.0
OD1 B:ASP273 4.7 34.0 1.0
CB B:ASP259 4.7 29.7 1.0
CA B:ASP255 4.7 22.4 1.0
CG B:ASP259 4.8 31.6 1.0
N B:ASP256 4.9 22.3 1.0
O1 B:NI94001 4.9 43.7 1.0
CG B:ASP273 5.0 34.6 1.0

Magnesium binding site 6 out of 6 in 3dyg

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


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

b:18.1
occ:1.00
 O B:HOH5008 1.9 22.3 1.0
O B:HOH5007 1.9 17.5 1.0
OD1 B:ASP103 2.1 19.3 1.0
O B:HOH5009 2.1 19.5 1.0
OD2 B:ASP107 2.1 20.6 1.0
O7 B:NI94001 2.2 28.9 1.0
CG B:ASP107 2.9 21.3 1.0
OD1 B:ASP107 3.0 23.2 1.0
CG B:ASP103 3.1 16.1 1.0
MG B:MG4002 3.3 23.1 1.0
P1 B:NI94001 3.3 21.9 1.0
OD2 B:ASP103 3.4 22.5 1.0
O4 B:NI94001 3.4 19.0 1.0
OD1 B:ASP175 3.8 22.2 1.0
OD2 B:ASP175 4.1 25.4 1.0
O B:HOH5082 4.1 19.2 1.0
CG B:ASP175 4.1 25.4 1.0
O B:HOH5185 4.2 24.1 1.0
NE2 B:GLN172 4.2 19.9 1.0
O6 B:NI94001 4.3 30.1 1.0
CB B:ASP107 4.3 23.0 1.0
OE1 B:GLN172 4.4 23.1 1.0
NZ B:LYS278 4.4 32.6 1.0
CB B:ASP103 4.4 16.7 1.0
C3 B:NI94001 4.6 20.0 1.0
C1 B:NI94001 4.7 29.7 1.0
C2 B:NI94001 4.7 20.3 1.0
CD B:GLN172 4.8 23.5 1.0
N B:NI94001 4.8 22.9 1.0
O B:ASP103 4.8 19.1 1.0
O B:HOH5004 4.9 18.3 1.0
NZ B:LYS212 4.9 16.1 1.0
O B:HOH5198 4.9 33.0 1.0
CE B:LYS278 4.9 29.2 1.0
O3 B:NI94001 5.0 40.5 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 12:46:02 2024

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