Atomistry » Magnesium » PDB 3efq-3eql » 3efq
Atomistry »
  Magnesium »
    PDB 3efq-3eql »
      3efq »

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

Go back to Magnesium Binding Sites List in 3efq
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

Go back to Magnesium Binding Sites List in 3efq
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

Go back to Magnesium Binding Sites List in 3efq
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

Go back to Magnesium Binding Sites List in 3efq
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

Go back to Magnesium Binding Sites List in 3efq
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy