Atomistry » Magnesium » PDB 3i5y-3ig8 » 3icz
Atomistry »
  Magnesium »
    PDB 3i5y-3ig8 »
      3icz »

Magnesium in PDB 3icz: Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate

Enzymatic activity of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate

All present enzymatic activity of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate:
2.5.1.10;

Protein crystallography data

The structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate, PDB code: 3icz was solved by L.M.Amzel, C.H.Huang, S.B.Gabelli, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.94 / 2.15
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.398, 58.398, 391.809, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate (pdb code 3icz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate, PDB code: 3icz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3icz

Go back to Magnesium Binding Sites List in 3icz
Magnesium binding site 1 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:26.8
occ:1.00
 O12 A:PB6363 2.0 22.5 1.0
O A:HOH365 2.1 26.9 1.0
OD2 A:ASP98 2.1 25.4 1.0
O A:HOH366 2.1 29.3 1.0
O15 A:PB6363 2.2 26.7 1.0
OD2 A:ASP102 2.2 23.9 1.0
CG A:ASP98 3.0 24.3 1.0
MG A:MG403 3.2 11.7 1.0
P9 A:PB6363 3.3 29.0 1.0
CG A:ASP102 3.3 28.6 1.0
OD1 A:ASP98 3.3 22.8 1.0
P14 A:PB6363 3.4 28.1 1.0
C8 A:PB6363 3.6 27.7 1.0
CB A:ASP102 3.8 28.0 1.0
O A:HOH434 3.8 28.1 1.0
C7 A:PB6363 3.8 28.8 1.0
O11 A:PB6363 4.0 28.2 1.0
O17 A:PB6363 4.1 22.3 1.0
O A:HOH364 4.3 25.2 1.0
CB A:ASP98 4.4 22.6 1.0
O A:HOH369 4.4 27.4 1.0
OG A:SER104 4.4 32.2 1.0
OD1 A:ASP102 4.4 24.8 1.0
O10 A:PB6363 4.4 24.1 1.0
O A:ASP98 4.4 24.2 1.0
OD1 A:ASP99 4.5 29.1 1.0
O16 A:PB6363 4.6 25.4 1.0
NH1 A:ARG107 4.6 27.9 1.0
O A:HOH414 4.6 31.1 1.0
O A:HOH391 4.7 24.7 1.0
C A:ASP98 4.7 24.2 1.0
O A:HOH367 4.8 23.8 1.0
O A:HOH370 4.8 19.8 1.0
N12 A:PB6363 4.9 27.7 1.0
MG A:MG402 4.9 24.8 1.0

Magnesium binding site 2 out of 3 in 3icz

Go back to Magnesium Binding Sites List in 3icz
Magnesium binding site 2 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:24.8
occ:1.00
 O11 A:PB6363 2.0 28.2 1.0
OD2 A:ASP250 2.0 24.9 1.0
O17 A:PB6363 2.1 22.3 1.0
O A:HOH369 2.1 27.4 1.0
O A:HOH368 2.2 23.8 1.0
O A:HOH371 2.2 25.2 1.0
CG A:ASP250 2.9 26.5 1.0
P9 A:PB6363 3.2 29.0 1.0
P14 A:PB6363 3.3 28.1 1.0
OD1 A:ASP250 3.3 22.3 1.0
C8 A:PB6363 3.5 27.7 1.0
O A:HOH377 4.0 28.9 1.0
O12 A:PB6363 4.0 22.5 1.0
NZ A:LYS264 4.0 31.9 1.0
CB A:ASP250 4.2 27.4 1.0
NE2 A:GLN247 4.2 25.3 1.0
OD1 A:ASP254 4.2 41.6 1.0
OD2 A:ASP268 4.2 28.8 1.0
O A:ASP250 4.3 27.2 1.0
O15 A:PB6363 4.3 26.7 1.0
O10 A:PB6363 4.3 24.1 1.0
O A:HOH366 4.4 29.3 1.0
O16 A:PB6363 4.4 25.4 1.0
OD1 A:ASP268 4.5 32.5 1.0
OD1 A:ASP251 4.5 31.0 1.0
C A:ASP250 4.5 28.4 1.0
CE A:LYS264 4.6 34.6 1.0
CB A:ASP254 4.7 34.5 1.0
O A:HOH434 4.8 28.1 1.0
CG A:ASP268 4.8 31.7 1.0
CG A:ASP254 4.8 39.9 1.0
MG A:MG401 4.9 26.8 1.0
N A:ASP251 5.0 27.8 1.0
CA A:ASP250 5.0 28.3 1.0

Magnesium binding site 3 out of 3 in 3icz

Go back to Magnesium Binding Sites List in 3icz
Magnesium binding site 3 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:11.7
occ:1.00
 O A:HOH370 2.0 19.8 1.0
O A:HOH367 2.0 23.8 1.0
OD1 A:ASP98 2.0 22.8 1.0
O A:HOH364 2.0 25.2 1.0
O15 A:PB6363 2.1 26.7 1.0
OD2 A:ASP102 2.1 23.9 1.0
CG A:ASP102 3.0 28.6 1.0
CG A:ASP98 3.0 24.3 1.0
OD1 A:ASP102 3.1 24.8 1.0
MG A:MG401 3.2 26.8 1.0
P14 A:PB6363 3.3 28.1 1.0
OD2 A:ASP98 3.4 25.4 1.0
O16 A:PB6363 3.4 25.4 1.0
OD2 A:ASP170 3.7 37.9 1.0
NE2 A:GLN167 4.0 20.0 1.0
OE1 A:GLN167 4.0 29.0 1.0
O A:HOH366 4.1 29.3 1.0
NZ A:LYS273 4.1 32.5 1.0
OD1 A:ASP170 4.2 34.5 1.0
CG A:ASP170 4.2 32.4 1.0
O A:HOH377 4.3 28.9 1.0
O17 A:PB6363 4.4 22.3 1.0
CB A:ASP98 4.4 22.6 1.0
CB A:ASP102 4.4 28.0 1.0
CD A:GLN167 4.5 23.1 1.0
C7 A:PB6363 4.5 28.8 1.0
C17 A:PB6363 4.5 27.8 1.0
C8 A:PB6363 4.6 27.7 1.0
N12 A:PB6363 4.7 27.7 1.0
O12 A:PB6363 4.7 22.5 1.0
O A:HOH414 4.7 31.1 1.0
NZ A:LYS207 4.8 20.0 1.0
O A:HOH365 4.8 26.9 1.0
O A:ASP98 4.9 24.2 1.0

Reference:

C.H.Huang, S.B.Gabelli, E.Oldfield, L.M.Amzel. Binding of Nitrogen-Containing Bisphosphonates (N-Bps) to the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer. Proteins V. 78 888 2010.
ISSN: ISSN 0887-3585
PubMed: 19876942
DOI: 10.1002/PROT.22614
Page generated: Wed Aug 14 16:05:22 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy