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Magnesium in PDB 2p1c: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210, PDB code: 2p1c was solved by R.Cao, Y.Gao, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.69 / 2.45
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.124, 92.124, 177.747, 90.00, 90.00, 120.00
R / Rfree (%) 26.6 / 29.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210 (pdb code 2p1c). 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-210, PDB code: 2p1c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


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-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:52.4
occ:1.00
 OD2 A:ASP107 2.5 50.7 1.0
O17 A:GG33001 2.5 41.6 1.0
O A:HOH8124 2.5 47.4 1.0
O A:HOH8135 2.5 57.3 1.0
OD2 A:ASP103 2.6 45.5 1.0
O10 A:GG33001 2.6 39.3 1.0
CG A:ASP107 3.3 44.5 1.0
CG A:ASP103 3.5 52.7 1.0
CB A:ASP107 3.5 45.4 1.0
O A:HOH8110 3.5 37.2 1.0
OD1 A:ASP103 3.7 55.0 1.0
P14 A:GG33001 3.8 48.7 1.0
OG A:SER109 3.8 50.0 1.0
P9 A:GG33001 3.9 49.8 1.0
O13 A:GG33001 4.1 47.9 1.0
MG A:MG3004 4.1 38.5 1.0
C8 A:GG33001 4.2 46.6 1.0
NH2 A:ARG112 4.3 45.6 1.0
O A:ASP103 4.4 48.8 1.0
OD1 A:ASP107 4.4 46.6 1.0
O A:HOH8134 4.5 44.0 1.0
OG1 A:THR272 4.5 49.0 1.0
O16 A:GG33001 4.6 58.3 1.0
O11 A:GG33001 4.6 50.9 1.0
C A:ASP103 4.7 48.1 1.0
CB A:ASP103 4.8 49.4 1.0
OD1 A:ASP104 4.8 49.9 1.0
O15 A:GG33001 4.9 61.7 1.0
MG A:MG3003 4.9 45.9 1.0
O A:HOH8108 4.9 42.0 1.0

Magnesium binding site 2 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


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-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:45.9
occ:1.00
 O11 A:GG33001 2.4 50.9 1.0
OD2 A:ASP255 2.7 46.2 1.0
O16 A:GG33001 2.7 58.3 1.0
O A:HOH8112 2.7 74.9 1.0
OD1 A:ASP259 3.2 52.1 1.0
OD1 A:ASP273 3.6 44.9 1.0
P9 A:GG33001 3.6 49.8 1.0
CG A:ASP259 3.7 42.7 1.0
CG A:ASP255 3.7 45.6 1.0
OD2 A:ASP273 3.7 42.4 1.0
P14 A:GG33001 3.8 48.7 1.0
O10 A:GG33001 3.8 39.3 1.0
O A:HOH8124 3.8 47.4 1.0
CB A:ASP259 4.0 41.6 1.0
CG A:ASP273 4.1 45.0 1.0
O17 A:GG33001 4.1 41.6 1.0
OD1 A:ASP255 4.2 42.3 1.0
C8 A:GG33001 4.3 46.6 1.0
O A:ASP255 4.4 45.2 1.0
OD2 A:ASP259 4.4 40.4 1.0
OD1 A:ASP256 4.6 50.2 1.0
O A:HOH8110 4.7 37.2 1.0
C A:ASP255 4.8 43.0 1.0
NZ A:LYS269 4.8 44.7 1.0
CB A:ASP255 4.9 45.1 1.0
NE2 A:GLN252 4.9 43.8 1.0
O12 A:GG33001 4.9 45.8 1.0
MG A:MG3002 4.9 52.4 1.0
C7 A:GG33001 4.9 43.2 1.0

Magnesium binding site 3 out of 6 in 2p1c

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Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


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-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:38.5
occ:1.00
 O A:HOH8115 2.5 35.9 1.0
OD2 A:ASP107 2.5 50.7 1.0
OD1 A:ASP103 2.7 55.0 1.0
OD1 A:ASP107 2.9 46.6 1.0
O10 A:GG33001 3.1 39.3 1.0
CG A:ASP107 3.1 44.5 1.0
OD1 A:ASP175 3.4 42.1 1.0
NE2 A:GLN172 3.5 55.5 1.0
NZ A:LYS278 3.5 50.6 1.0
O12 A:GG33001 3.7 45.8 1.0
CG A:ASP103 3.8 52.7 1.0
OD2 A:ASP175 3.9 36.5 1.0
CG A:ASP175 3.9 34.7 1.0
P9 A:GG33001 3.9 49.8 1.0
MG A:MG3002 4.1 52.4 1.0
OD2 A:ASP103 4.3 45.5 1.0
CD A:GLN172 4.3 53.9 1.0
CE A:LYS278 4.4 51.9 1.0
CB A:ASP107 4.6 45.4 1.0
OE1 A:GLN172 4.6 50.9 1.0
NZ A:LYS212 4.9 29.3 1.0
O13 A:GG33001 4.9 47.9 1.0
O A:HOH8124 5.0 47.4 1.0

Magnesium binding site 4 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


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-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4001

b:49.6
occ:1.00
 O B:HOH9150 2.6 41.0 1.0
O17 B:GG38004 2.6 41.7 1.0
OD2 B:ASP103 2.6 53.5 1.0
OD2 B:ASP107 2.8 56.4 1.0
O10 B:GG38004 3.1 44.8 1.0
OG B:SER109 3.3 45.1 1.0
CB B:ASP107 3.3 52.0 1.0
CG B:ASP103 3.5 44.1 1.0
O B:HOH9123 3.5 34.9 1.0
CG B:ASP107 3.5 54.9 1.0
O B:ASP103 3.7 44.2 1.0
OD1 B:ASP104 3.7 31.3 1.0
OD1 B:ASP103 3.9 39.0 1.0
NH2 B:ARG112 4.0 52.7 1.0
P14 B:GG38004 4.0 43.8 1.0
C B:ASP103 4.1 43.1 1.0
O13 B:GG38004 4.3 53.9 1.0
P9 B:GG38004 4.4 46.4 1.0
CA B:ASP104 4.4 44.0 1.0
CB B:SER109 4.5 53.5 1.0
N B:ASP104 4.5 40.5 1.0
CB B:ASP103 4.5 44.5 1.0
C8 B:GG38004 4.5 47.2 1.0
O B:HOH9065 4.6 41.7 1.0
OG1 B:THR272 4.6 53.1 1.0
CA B:ASP107 4.7 51.4 1.0
OD1 B:ASP107 4.7 60.4 1.0
MG B:MG4003 4.8 49.0 1.0
CG B:ASP104 4.8 45.1 1.0
O16 B:GG38004 4.8 53.4 1.0
CA B:ASP103 5.0 34.0 1.0
O15 B:GG38004 5.0 53.0 1.0

Magnesium binding site 5 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


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-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4002

b:45.4
occ:1.00
 O16 B:GG38004 2.5 53.4 1.0
O11 B:GG38004 2.6 46.0 1.0
O B:HOH9103 2.7 43.5 1.0
O B:HOH9131 2.8 38.4 1.0
O B:HOH9150 3.2 41.0 1.0
OD1 B:ASP259 3.2 56.2 1.0
OD2 B:ASP255 3.4 38.0 1.0
OD2 B:ASP273 3.4 39.6 1.0
OD1 B:ASP273 3.5 44.4 1.0
P14 B:GG38004 3.6 43.8 1.0
P9 B:GG38004 3.7 46.4 1.0
CG B:ASP259 3.7 52.7 1.0
CG B:ASP273 3.8 44.0 1.0
O17 B:GG38004 3.8 41.7 1.0
O10 B:GG38004 3.8 44.8 1.0
O B:HOH9123 4.2 34.9 1.0
CB B:ASP259 4.2 48.0 1.0
C8 B:GG38004 4.3 47.2 1.0
CG B:ASP255 4.4 39.9 1.0
OD2 B:ASP259 4.4 52.6 1.0
O B:ASP255 4.7 49.8 1.0
OD1 B:ASP255 4.8 41.8 1.0
NZ B:LYS269 4.9 43.5 1.0
O15 B:GG38004 4.9 53.0 1.0
C7 B:GG38004 4.9 50.5 1.0

Magnesium binding site 6 out of 6 in 2p1c

Go back to Magnesium Binding Sites List in 2p1c
Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-210


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-210 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4003

b:49.0
occ:1.00
 OD2 B:ASP107 2.6 56.4 1.0
OD1 B:ASP103 2.8 39.0 1.0
O10 B:GG38004 2.8 44.8 1.0
OD2 B:ASP175 3.3 41.0 1.0
O12 B:GG38004 3.3 44.2 1.0
CG B:ASP107 3.4 54.9 1.0
OD1 B:ASP175 3.4 44.2 1.0
OD1 B:ASP107 3.5 60.4 1.0
CG B:ASP175 3.5 41.2 1.0
P9 B:GG38004 3.5 46.4 1.0
CG B:ASP103 3.7 44.1 1.0
NE2 B:GLN172 3.8 41.5 1.0
OE1 B:GLN172 3.9 47.6 1.0
OD2 B:ASP103 3.9 53.5 1.0
NZ B:LYS212 4.0 27.1 1.0
NZ B:LYS278 4.3 58.8 1.0
CD B:GLN172 4.3 38.2 1.0
O11 B:GG38004 4.5 46.0 1.0
CB B:ASP175 4.6 39.5 1.0
C22 B:GG38004 4.7 53.2 1.0
O B:HOH9150 4.7 41.0 1.0
CE B:LYS278 4.7 48.0 1.0
C26 B:GG38004 4.8 46.8 1.0
MG B:MG4001 4.8 49.6 1.0
CB B:ASP107 4.8 52.0 1.0
O13 B:GG38004 4.9 53.9 1.0
C8 B:GG38004 5.0 47.2 1.0

Reference:

R.Cao, C.K.Chen, R.T.Guo, A.H.Wang, E.Oldfield. Structures of A Potent Phenylalkyl Bisphosphonate Inhibitor Bound to Farnesyl and Geranylgeranyl Diphosphate Synthases. Proteins V. 73 431 2008.
ISSN: ISSN 0887-3585
PubMed: 18442135
DOI: 10.1002/PROT.22066
Page generated: Wed Aug 14 02:02:18 2024

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