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Magnesium in PDB 2ogd: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527, PDB code: 2ogd 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) 30.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.613, 118.370, 62.758, 90.00, 112.16, 90.00
R / Rfree (%) 19.3 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527 (pdb code 2ogd). 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-527, PDB code: 2ogd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2ogd

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Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527


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-527 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:21.9
occ:1.00
 O5 A:SUF3001 2.0 21.1 1.0
O A:HOH9171 2.0 21.4 1.0
O1 A:SUF3001 2.1 24.2 1.0
OD2 A:ASP107 2.2 17.9 1.0
O A:HOH9231 2.2 25.5 1.0
OD2 A:ASP103 2.2 21.6 1.0
CG A:ASP103 3.1 17.5 1.0
MG A:MG3004 3.1 19.1 1.0
CG A:ASP107 3.2 15.0 1.0
P2 A:SUF3001 3.3 23.6 1.0
OD1 A:ASP103 3.3 17.7 1.0
P1 A:SUF3001 3.3 23.5 1.0
O A:HOH9032 3.6 25.6 1.0
C1 A:SUF3001 3.7 26.1 1.0
CB A:ASP107 3.7 19.9 1.0
C2 A:SUF3001 4.0 20.1 1.0
O7 A:SUF3001 4.0 30.9 1.0
O4 A:SUF3001 4.1 25.6 1.0
O A:HOH9232 4.2 15.6 1.0
NH2 A:ARG112 4.3 15.3 1.0
O A:HOH9170 4.3 19.5 1.0
OD1 A:ASP107 4.3 21.5 1.0
O A:ASP103 4.4 20.3 1.0
OG A:SER109 4.4 20.3 1.0
O A:HOH9015 4.4 23.5 1.0
CB A:ASP103 4.4 14.0 1.0
O6 A:SUF3001 4.5 20.9 1.0
OD1 A:ASP104 4.5 19.0 1.0
O3 A:SUF3001 4.6 15.1 1.0
C A:ASP103 4.6 13.6 1.0
O A:HOH9007 4.7 24.7 1.0
O A:HOH9002 4.9 16.1 1.0
MG A:MG3003 4.9 21.6 1.0
O A:HOH9172 5.0 21.4 1.0

Magnesium binding site 2 out of 6 in 2ogd

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Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527


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-527 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:21.6
occ:1.00
 O7 A:SUF3001 2.1 30.9 1.0
O A:HOH9233 2.1 23.1 1.0
OD2 A:ASP255 2.1 21.5 1.0
O4 A:SUF3001 2.1 25.6 1.0
O A:HOH9006 2.2 17.9 1.0
O A:HOH9170 2.2 19.5 1.0
CG A:ASP255 3.0 20.8 1.0
P1 A:SUF3001 3.3 23.5 1.0
P2 A:SUF3001 3.3 23.6 1.0
O2 A:SUF3001 3.4 23.4 1.0
OD1 A:ASP255 3.4 21.3 1.0
C1 A:SUF3001 3.5 26.1 1.0
O A:HOH9020 4.0 17.2 1.0
OD1 A:ASP259 4.0 25.5 1.0
O A:HOH9171 4.1 21.4 1.0
O5 A:SUF3001 4.1 21.1 1.0
O A:ASP255 4.2 22.6 1.0
O1 A:SUF3001 4.2 24.2 1.0
NE2 A:GLN252 4.2 19.1 1.0
NZ A:LYS269 4.3 22.8 1.0
OD2 A:ASP273 4.3 24.4 1.0
CB A:ASP255 4.3 18.0 1.0
O3 A:SUF3001 4.4 15.1 1.0
O6 A:SUF3001 4.4 20.9 1.0
OD1 A:ASP273 4.4 28.7 1.0
CE A:LYS269 4.5 27.3 1.0
CG A:ASP259 4.5 33.8 1.0
C A:ASP255 4.5 18.8 1.0
O A:HOH9032 4.6 25.6 1.0
OD1 A:ASP256 4.6 23.4 1.0
CB A:ASP259 4.7 27.1 1.0
CG A:ASP273 4.8 29.5 1.0
MG A:MG3002 4.9 21.9 1.0

Magnesium binding site 3 out of 6 in 2ogd

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Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527


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-527 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:19.1
occ:1.00
 O1 A:SUF3001 2.1 24.2 1.0
O A:HOH9232 2.1 15.6 1.0
OD2 A:ASP107 2.1 17.9 1.0
OD1 A:ASP103 2.2 17.7 1.0
O A:HOH9172 2.2 21.4 1.0
O A:HOH9002 2.2 16.1 1.0
CG A:ASP107 2.9 15.0 1.0
MG A:MG3002 3.1 21.9 1.0
OD1 A:ASP107 3.1 21.5 1.0
CG A:ASP103 3.1 17.5 1.0
P2 A:SUF3001 3.3 23.6 1.0
OD2 A:ASP103 3.4 21.6 1.0
O3 A:SUF3001 3.5 15.1 1.0
OD1 A:ASP175 3.9 27.2 1.0
NZ A:LYS278 4.0 16.3 1.0
O A:HOH9171 4.2 21.4 1.0
OD2 A:ASP175 4.2 28.1 1.0
CG A:ASP175 4.3 28.3 1.0
O7 A:SUF3001 4.3 30.9 1.0
OE1 A:GLN172 4.3 20.9 1.0
NE2 A:GLN172 4.4 18.3 1.0
CB A:ASP107 4.4 19.9 1.0
O A:HOH9020 4.4 17.2 1.0
S A:SUF3001 4.5 26.2 1.0
CB A:ASP103 4.5 14.0 1.0
C1 A:SUF3001 4.6 26.1 1.0
O5 A:SUF3001 4.7 21.1 1.0
C2 A:SUF3001 4.7 20.1 1.0
O A:ASP103 4.8 20.3 1.0
CD A:GLN172 4.8 28.2 1.0
NZ A:LYS212 4.9 17.4 1.0
O A:HOH9231 4.9 25.5 1.0
O A:HOH9015 5.0 23.5 1.0

Magnesium binding site 4 out of 6 in 2ogd

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Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527


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-527 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4002

b:21.6
occ:1.00
 OD2 B:ASP103 2.0 20.3 1.0
O5 B:SUF4001 2.0 23.4 1.0
O B:HOH9297 2.1 19.9 1.0
OD2 B:ASP107 2.2 21.9 1.0
O1 B:SUF4001 2.2 29.5 1.0
O B:HOH9217 2.3 17.2 1.0
CG B:ASP103 3.0 14.8 1.0
MG B:MG4004 3.2 20.2 1.0
CG B:ASP107 3.3 19.0 1.0
P1 B:SUF4001 3.3 23.7 1.0
P2 B:SUF4001 3.3 21.2 1.0
OD1 B:ASP103 3.4 19.4 1.0
C1 B:SUF4001 3.7 26.9 1.0
O B:HOH9021 3.8 20.2 1.0
CB B:ASP107 3.8 19.3 1.0
C2 B:SUF4001 3.9 19.2 1.0
O4 B:SUF4001 4.0 25.4 1.0
O7 B:SUF4001 4.1 33.0 1.0
O B:ASP103 4.2 21.8 1.0
CB B:ASP103 4.3 14.3 1.0
O B:HOH9218 4.3 18.3 1.0
O B:HOH9220 4.4 18.5 1.0
OD1 B:ASP107 4.4 21.1 1.0
OG B:SER109 4.4 24.6 1.0
O6 B:SUF4001 4.5 18.8 1.0
OD1 B:ASP104 4.5 23.0 1.0
C B:ASP103 4.5 13.1 1.0
NH1 B:ARG112 4.5 20.9 1.0
O B:HOH9062 4.6 26.6 1.0
O3 B:SUF4001 4.6 13.9 1.0
O B:HOH9219 4.8 20.6 1.0
O B:HOH9300 4.9 18.9 1.0
O B:HOH9013 5.0 27.9 1.0
N B:ASP104 5.0 16.7 1.0
S B:SUF4001 5.0 23.2 1.0

Magnesium binding site 5 out of 6 in 2ogd

Go back to Magnesium Binding Sites List in 2ogd
Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527


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-527 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4003

b:23.8
occ:1.00
 O B:HOH9221 2.0 22.7 1.0
O4 B:SUF4001 2.1 25.4 1.0
OD2 B:ASP255 2.1 22.0 1.0
O B:HOH9218 2.2 18.3 1.0
O B:HOH9301 2.2 20.4 1.0
O7 B:SUF4001 2.2 33.0 1.0
CG B:ASP255 3.0 20.3 1.0
P1 B:SUF4001 3.3 23.7 1.0
OD1 B:ASP255 3.4 21.5 1.0
P2 B:SUF4001 3.5 21.2 1.0
O2 B:SUF4001 3.5 24.0 1.0
C1 B:SUF4001 3.6 26.9 1.0
NZ B:LYS269 3.9 25.9 1.0
OD1 B:ASP259 3.9 27.8 1.0
O B:HOH9043 4.0 19.7 1.0
O B:ASP255 4.0 26.0 1.0
O5 B:SUF4001 4.2 23.4 1.0
NE2 B:GLN252 4.3 15.4 1.0
CB B:ASP255 4.3 23.5 1.0
O B:HOH9217 4.3 17.2 1.0
OD2 B:ASP273 4.3 27.2 1.0
O6 B:SUF4001 4.3 18.8 1.0
O1 B:SUF4001 4.3 29.5 1.0
C B:ASP255 4.4 19.0 1.0
OD1 B:ASP273 4.5 29.9 1.0
OD1 B:ASP256 4.5 26.8 1.0
CG B:ASP259 4.5 33.7 1.0
CE B:LYS269 4.5 28.3 1.0
O3 B:SUF4001 4.6 13.9 1.0
CB B:ASP259 4.6 23.4 1.0
O B:HOH9021 4.7 20.2 1.0
CG B:ASP273 4.8 34.0 1.0
CA B:ASP255 4.9 23.1 1.0
N B:ASP256 4.9 21.4 1.0

Magnesium binding site 6 out of 6 in 2ogd

Go back to Magnesium Binding Sites List in 2ogd
Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-527


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-527 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4004

b:20.2
occ:1.00
 O B:HOH9300 2.0 18.9 1.0
O B:HOH9219 2.0 20.6 1.0
O B:HOH9220 2.1 18.5 1.0
O1 B:SUF4001 2.1 29.5 1.0
OD2 B:ASP107 2.1 21.9 1.0
OD1 B:ASP103 2.2 19.4 1.0
CG B:ASP107 2.9 19.0 1.0
OD1 B:ASP107 3.1 21.1 1.0
CG B:ASP103 3.1 14.8 1.0
MG B:MG4002 3.2 21.6 1.0
P2 B:SUF4001 3.3 21.2 1.0
OD2 B:ASP103 3.3 20.3 1.0
O3 B:SUF4001 3.5 13.9 1.0
OD1 B:ASP175 3.8 24.2 1.0
NZ B:LYS278 4.0 37.4 1.0
O B:HOH9217 4.3 17.2 1.0
CG B:ASP175 4.3 26.9 1.0
OD2 B:ASP175 4.3 26.3 1.0
O7 B:SUF4001 4.3 33.0 1.0
O B:HOH9043 4.4 19.7 1.0
CB B:ASP107 4.4 19.3 1.0
OE1 B:GLN172 4.4 22.2 1.0
NE2 B:GLN172 4.5 16.1 1.0
CB B:ASP103 4.5 14.3 1.0
S B:SUF4001 4.5 23.2 1.0
C1 B:SUF4001 4.7 26.9 1.0
CE B:LYS278 4.7 32.8 1.0
C2 B:SUF4001 4.7 19.2 1.0
O5 B:SUF4001 4.7 23.4 1.0
O B:ASP103 4.8 21.8 1.0
O B:HOH9062 4.9 26.6 1.0
CD B:GLN172 4.9 28.4 1.0
O B:HOH9297 4.9 19.9 1.0
NZ B:LYS212 5.0 16.4 1.0

Reference:

Y.Zhang, R.Cao, A.Leon, R.T.Guo, K.Krysiak, F.Yin, M.P.Hudock, S.Mukherjee, Y.Gao, H.Robinson, Y.Song, J.H.No, W.Hong, C.Morita, A.H.-J.Wang, E.Oldfield. Bisphosphonates: Teaching Old Drugs with New Tricks To Be Published.
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