Atomistry » Magnesium » PDB 3dtu-3e35 » 3dyg
Atomistry »
  Magnesium »
    PDB 3dtu-3e35 »
      3dyg »

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

Go back to Magnesium Binding Sites List in 3dyg
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy