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Magnesium in PDB 2ewg: T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate, PDB code: 2ewg was solved by R.Cao, J.Mao, Y.Gao, H.Robinson, S.Odeh, 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 / 2.48
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.981, 118.098, 63.246, 90.00, 112.48, 90.00
R / Rfree (%) 24.2 / 26

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 2ewg

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Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate


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

b:17.6
occ:1.00
 O3 A:M0N3001 2.0 31.0 1.0
OD2 A:ASP107 2.1 50.0 1.0
O A:HOH6001 2.1 30.1 1.0
O A:HOH6326 2.1 20.8 0.5
O4 A:M0N3001 2.2 31.4 1.0
OD1 A:ASP103 2.5 40.0 1.0
CG A:ASP107 2.7 31.8 1.0
CB A:ASP107 3.1 29.4 1.0
MG A:MG3003 3.3 19.6 1.0
P1 A:M0N3001 3.4 33.9 1.0
CG A:ASP103 3.4 41.8 1.0
P2 A:M0N3001 3.4 34.6 1.0
OD1 A:ASP107 3.4 30.4 1.0
C9 A:M0N3001 3.7 33.3 1.0
OD2 A:ASP103 4.0 51.2 1.0
C8 A:M0N3001 4.0 36.1 1.0
NH2 A:ARG112 4.0 24.8 1.0
OG A:SER109 4.0 34.1 1.0
O1 A:M0N3001 4.1 33.5 1.0
O A:HOH6217 4.1 42.4 1.0
O5 A:M0N3001 4.1 37.2 1.0
O A:ASP103 4.3 40.5 1.0
O2 A:M0N3001 4.3 29.0 1.0
CB A:ASP103 4.6 33.2 1.0
OD1 A:ASP104 4.6 29.9 1.0
CA A:ASP107 4.6 30.5 1.0
O6 A:M0N3001 4.6 35.4 1.0
C A:ASP103 4.7 21.9 1.0
O A:HOH6130 4.9 25.5 1.0

Magnesium binding site 2 out of 6 in 2ewg

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Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate


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

b:19.6
occ:1.00
 OD2 A:ASP103 2.0 51.2 1.0
OD1 A:ASP107 2.0 30.4 1.0
O3 A:M0N3001 2.3 31.0 1.0
O A:HOH6009 2.5 20.9 1.0
OD2 A:ASP107 2.6 50.0 1.0
CG A:ASP107 2.7 31.8 1.0
CG A:ASP103 2.7 41.8 1.0
OD1 A:ASP103 2.8 40.0 1.0
O2 A:M0N3001 2.8 29.0 1.0
P1 A:M0N3001 3.3 33.9 1.0
MG A:MG3002 3.3 17.6 1.0
OE1 A:GLN172 3.7 50.9 1.0
CB A:ASP107 4.0 29.4 1.0
CB A:ASP103 4.2 33.2 1.0
OD2 A:ASP175 4.2 40.5 1.0
C8 A:M0N3001 4.2 36.1 1.0
O A:HOH6326 4.3 20.8 0.5
C9 A:M0N3001 4.4 33.3 1.0
C3 A:M0N3001 4.4 36.3 1.0
O1 A:M0N3001 4.5 33.5 1.0
CD A:GLN172 4.6 20.0 1.0
CG A:ASP175 4.6 37.1 1.0
O A:HOH6001 4.6 30.1 1.0
CE A:LYS278 4.6 40.6 1.0
NE2 A:GLN172 4.7 31.4 1.0
C2 A:M0N3001 4.7 37.9 1.0
N2 A:M0N3001 4.7 37.3 1.0
O A:ASP103 4.7 40.5 1.0
OD1 A:ASP175 4.7 41.6 1.0
NZ A:LYS278 4.7 41.9 1.0
O4 A:M0N3001 4.8 31.4 1.0
CA A:ASP103 4.9 24.5 1.0
CA A:ASP107 5.0 30.5 1.0

Magnesium binding site 3 out of 6 in 2ewg

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Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate


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

b:21.5
occ:1.00
 O A:HOH6003 1.9 55.6 1.0
OD2 A:ASP255 1.9 16.6 1.0
O A:HOH6002 2.1 18.4 1.0
O A:HOH6132 2.4 22.4 1.0
O1 A:M0N3001 2.5 33.5 1.0
O5 A:M0N3001 2.6 37.2 1.0
CG A:ASP255 3.0 22.0 1.0
O A:M0N3001 3.3 35.9 1.0
OD1 A:ASP255 3.6 23.2 1.0
OD2 A:ASP273 3.7 44.5 1.0
P2 A:M0N3001 3.7 34.6 1.0
P1 A:M0N3001 3.9 33.9 1.0
C9 A:M0N3001 3.9 33.3 1.0
OD1 A:ASP259 4.0 34.9 1.0
O A:HOH6249 4.0 42.8 1.0
O A:HOH6229 4.1 46.7 1.0
NE2 A:GLN252 4.2 15.9 1.0
O A:HOH6326 4.2 20.8 0.5
CB A:ASP255 4.2 25.5 1.0
OD1 A:ASP256 4.5 32.6 1.0
C A:ASP255 4.5 26.6 1.0
CG A:ASP259 4.5 33.7 1.0
CB A:ASP259 4.6 33.5 1.0
CG A:ASP273 4.6 44.0 1.0
O A:ASP255 4.6 30.0 1.0
OD1 A:ASP273 4.6 35.5 1.0
N A:ASP256 4.6 26.7 1.0
NZ A:LYS269 4.6 35.1 1.0
O6 A:M0N3001 4.7 35.4 1.0
O3 A:M0N3001 4.8 31.0 1.0
O4 A:M0N3001 4.8 31.4 1.0
CA A:ASP255 5.0 26.5 1.0

Magnesium binding site 4 out of 6 in 2ewg

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Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate


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

b:35.7
occ:1.00
 O B:HOH6004 2.0 51.6 1.0
O3 B:M0N4001 2.0 34.4 1.0
O B:HOH6006 2.1 43.6 1.0
OD2 B:ASP107 2.2 29.1 1.0
O4 B:M0N4001 2.4 36.2 1.0
OD1 B:ASP103 2.5 29.1 1.0
CG B:ASP107 3.1 30.5 1.0
CB B:ASP107 3.2 28.6 1.0
CG B:ASP103 3.4 29.3 1.0
P2 B:M0N4001 3.5 36.9 1.0
OG B:SER109 3.6 28.9 1.0
P1 B:M0N4001 3.6 34.6 1.0
O B:HOH6116 3.6 14.2 1.0
O5 B:M0N4001 3.8 40.2 1.0
MG B:MG4004 3.9 11.7 1.0
OD2 B:ASP103 3.9 33.0 1.0
O B:HOH6010 3.9 29.9 0.5
C9 B:M0N4001 4.1 34.8 1.0
O1 B:M0N4001 4.2 34.5 1.0
O B:HOH6008 4.2 28.3 1.0
OD1 B:ASP107 4.3 32.0 1.0
OD2 B:ASP104 4.3 20.4 1.0
O B:HOH6319 4.5 31.9 1.0
C8 B:M0N4001 4.5 32.7 1.0
O B:HOH6129 4.5 38.7 1.0
O B:ASP103 4.5 25.2 1.0
CB B:ASP103 4.6 25.6 1.0
O2 B:M0N4001 4.6 30.6 1.0
CA B:ASP107 4.7 29.3 1.0
C B:ASP103 4.7 23.7 1.0
NH1 B:ARG112 4.8 31.1 1.0
O6 B:M0N4001 4.9 33.7 1.0
CB B:SER109 4.9 29.8 1.0
NH2 B:ARG112 5.0 35.3 1.0

Magnesium binding site 5 out of 6 in 2ewg

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Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate


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

b:19.0
occ:1.00
 O B:HOH6325 2.0 51.6 1.0
O B:HOH6008 2.2 28.3 1.0
O5 B:M0N4001 2.3 40.2 1.0
OD1 B:ASP255 2.4 37.1 1.0
O1 B:M0N4001 2.6 34.5 1.0
O B:M0N4001 2.9 37.3 1.0
OD2 B:ASP259 3.1 78.1 1.0
OD2 B:ASP255 3.1 32.9 1.0
CG B:ASP255 3.2 36.0 1.0
P2 B:M0N4001 3.3 36.9 1.0
C9 B:M0N4001 3.3 34.8 1.0
P1 B:M0N4001 3.5 34.6 1.0
OD2 B:ASP273 3.7 45.1 1.0
O3 B:M0N4001 4.0 34.4 1.0
O B:HOH6040 4.1 22.1 1.0
O6 B:M0N4001 4.2 33.7 1.0
CG B:ASP259 4.2 44.5 1.0
NE2 B:GLN252 4.3 25.7 1.0
O4 B:M0N4001 4.4 36.2 1.0
CE B:LYS269 4.4 36.9 1.0
OD1 B:ASP256 4.5 32.4 1.0
O B:ASP255 4.5 26.2 1.0
CG B:ASP273 4.6 48.8 1.0
CB B:ASP255 4.6 34.1 1.0
O B:HOH6006 4.7 43.6 1.0
C8 B:M0N4001 4.7 32.7 1.0
C B:ASP255 4.8 28.1 1.0
O2 B:M0N4001 4.8 30.6 1.0
CD B:LYS269 4.9 38.0 1.0
CB B:ASP259 4.9 33.2 1.0
OD1 B:ASP273 4.9 61.9 1.0

Magnesium binding site 6 out of 6 in 2ewg

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Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Minodronate


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

b:11.7
occ:1.00
 O B:HOH6005 2.0 52.5 1.0
OD2 B:ASP107 2.1 29.1 1.0
O B:HOH6010 2.4 29.9 0.5
O B:HOH6007 2.4 17.9 1.0
OD2 B:ASP103 2.5 33.0 1.0
O2 B:M0N4001 2.7 30.6 1.0
O3 B:M0N4001 2.8 34.4 1.0
CG B:ASP107 2.9 30.5 1.0
OD1 B:ASP107 2.9 32.0 1.0
P1 B:M0N4001 3.2 34.6 1.0
CG B:ASP103 3.4 29.3 1.0
OD1 B:ASP103 3.5 29.1 1.0
OD1 B:ASP175 3.8 24.7 1.0
MG B:MG4002 3.9 35.7 1.0
O1 B:M0N4001 3.9 34.5 1.0
CG B:ASP175 4.2 27.0 1.0
OD2 B:ASP175 4.2 28.4 1.0
O B:HOH6006 4.2 43.6 1.0
CB B:ASP107 4.3 28.6 1.0
NE2 B:GLN172 4.4 21.4 1.0
OE1 B:GLN172 4.4 24.8 1.0
O B:HOH6040 4.5 22.1 1.0
NZ B:LYS212 4.6 16.4 1.0
C9 B:M0N4001 4.7 34.8 1.0
C8 B:M0N4001 4.8 32.7 1.0
CB B:ASP103 4.8 25.6 1.0
CD B:GLN172 4.8 20.2 1.0
C3 B:M0N4001 4.9 25.4 1.0
C2 B:M0N4001 4.9 29.2 1.0
N2 B:M0N4001 4.9 29.1 1.0

Reference:

J.Mao, S.Mukherjee, Y.Zhang, R.Cao, J.M.Sanders, Y.Song, Y.Zhang, G.A.Meints, Y.G.Gao, D.Mukkamala, M.P.Hudock, E.Oldfield. Solid-State uc(Nmr), Crystallographic, and Computational Investigation of Bisphosphonates and Farnesyl Diphosphate Synthase-Bisphosphonate Complexes. J.Am.Chem.Soc. V. 128 14485 2006.
ISSN: ISSN 0002-7863
PubMed: 17090032
DOI: 10.1021/JA061737C
Page generated: Tue Aug 13 22:49:29 2024

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