Atomistry » Magnesium » PDB 4dv6-4e7s » 4dwb
Atomistry »
  Magnesium »
    PDB 4dv6-4e7s »
      4dwb »

Magnesium in PDB 4dwb: Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+

Enzymatic activity of Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+

All present enzymatic activity of Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+:
2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4dwb was solved by S.Aripirala, L.M.Amzel, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.871, 57.871, 392.442, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 27.9

Other elements in 4dwb:

The structure of Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ (pdb code 4dwb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4dwb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4dwb

Go back to Magnesium Binding Sites List in 4dwb
Magnesium binding site 1 out of 3 in the Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:40.9
occ:1.00
 O A:HOH601 2.2 30.2 1.0
OD2 A:ASP102 2.2 37.1 1.0
OD1 A:ASP98 2.3 32.6 1.0
O A:HOH623 2.3 46.0 1.0
O14 A:0M7509 2.5 35.9 1.0
O A:HOH602 2.6 39.3 1.0
MG A:MG507 3.1 43.3 1.0
CG A:ASP102 3.1 38.1 1.0
CG A:ASP98 3.2 31.2 1.0
OD1 A:ASP102 3.4 38.4 1.0
OD2 A:ASP98 3.4 31.7 1.0
OD2 A:ASP170 3.6 33.0 1.0
P1 A:0M7509 3.7 33.6 1.0
O16 A:0M7509 3.8 35.3 1.0
NE2 A:GLN167 3.9 27.8 1.0
CG A:ASP170 4.1 25.8 1.0
NZ A:LYS273 4.1 38.8 1.0
OE1 A:GLN167 4.3 33.0 1.0
OD1 A:ASP170 4.3 35.0 1.0
CD A:GLN167 4.4 31.5 1.0
C4 A:0M7509 4.5 35.8 1.0
O A:HOH604 4.6 29.3 1.0
CB A:ASP102 4.6 38.0 1.0
CB A:ASP98 4.6 27.1 1.0
C7 A:0M7509 4.7 39.0 1.0
C2 A:0M7509 4.8 34.1 1.0
O15 A:0M7509 4.8 31.4 1.0
O13 A:0M7509 4.8 30.6 1.0
NZ A:LYS207 4.8 28.8 1.0
O A:HOH603 4.9 24.7 1.0

Magnesium binding site 2 out of 3 in 4dwb

Go back to Magnesium Binding Sites List in 4dwb
Magnesium binding site 2 out of 3 in the Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:43.3
occ:1.00
 O14 A:0M7509 2.0 35.9 1.0
O A:HOH604 2.0 29.3 1.0
O13 A:0M7509 2.1 30.6 1.0
OD2 A:ASP102 2.3 37.1 1.0
O A:HOH603 2.5 24.7 1.0
OD2 A:ASP98 2.5 31.7 1.0
MG A:MG506 3.1 40.9 1.0
P1 A:0M7509 3.3 33.6 1.0
P3 A:0M7509 3.3 29.9 1.0
CG A:ASP102 3.4 38.1 1.0
CG A:ASP98 3.4 31.2 1.0
OD1 A:ASP98 3.5 32.6 1.0
C2 A:0M7509 3.6 34.1 1.0
C4 A:0M7509 3.7 35.8 1.0
O15 A:0M7509 3.9 31.4 1.0
CB A:ASP102 3.9 38.0 1.0
O11 A:0M7509 4.1 33.3 1.0
NH2 A:ARG107 4.1 20.2 1.0
O A:HOH602 4.2 39.3 1.0
O A:HOH605 4.3 18.7 1.0
O16 A:0M7509 4.4 35.3 1.0
OD1 A:ASP102 4.5 38.4 1.0
O12 A:0M7509 4.5 34.7 1.0
OG A:SER104 4.7 40.5 1.0
O A:HOH623 4.7 46.0 1.0
MG A:MG508 4.9 30.6 1.0
CB A:ASP98 4.9 27.1 1.0
O A:HOH601 4.9 30.2 1.0
OD1 A:ASP99 4.9 22.5 1.0
O A:ASP98 5.0 28.5 1.0

Magnesium binding site 3 out of 3 in 4dwb

Go back to Magnesium Binding Sites List in 4dwb
Magnesium binding site 3 out of 3 in the Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:30.6
occ:1.00
 O15 A:0M7509 1.8 31.4 1.0
O11 A:0M7509 2.1 33.3 1.0
O A:HOH606 2.1 26.3 1.0
O A:HOH605 2.2 18.7 1.0
O A:HOH607 2.2 30.1 1.0
OD2 A:ASP250 2.3 37.9 1.0
P1 A:0M7509 3.2 33.6 1.0
CG A:ASP250 3.2 34.4 1.0
P3 A:0M7509 3.3 29.9 1.0
C2 A:0M7509 3.4 34.1 1.0
OD1 A:ASP250 3.6 36.8 1.0
OD1 A:ASP254 4.0 29.9 1.0
NZ A:LYS264 4.0 40.4 1.0
O14 A:0M7509 4.1 35.9 1.0
O13 A:0M7509 4.1 30.6 1.0
NE2 A:GLN247 4.1 24.5 1.0
O16 A:0M7509 4.2 35.3 1.0
O A:HOH604 4.2 29.3 1.0
OD2 A:ASP268 4.3 36.7 1.0
O12 A:0M7509 4.4 34.7 1.0
CB A:ASP250 4.4 31.7 1.0
OD1 A:ASP251 4.5 28.4 1.0
OD1 A:ASP268 4.5 41.3 1.0
CE A:LYS264 4.5 43.9 1.0
C A:ASP250 4.8 30.9 1.0
CG A:ASP254 4.8 35.5 1.0
CG A:ASP268 4.8 43.0 1.0
O A:ASP250 4.8 28.5 1.0
MG A:MG507 4.9 43.3 1.0
CB A:ASP254 4.9 36.7 1.0
C4 A:0M7509 4.9 35.8 1.0
N A:ASP251 5.0 32.1 1.0

Reference:

S.Aripirala, S.H.Szajnman, J.Jakoncic, J.B.Rodriguez, R.Docampo, S.B.Gabelli, L.M.Amzel. Design, Synthesis, Calorimetry, and Crystallographic Analysis of 2-Alkylaminoethyl-1,1-Bisphosphonates As Inhibitors of Trypanosoma Cruzi Farnesyl Diphosphate Synthase. J.Med.Chem. V. 55 6445 2012.
ISSN: ISSN 0022-2623
PubMed: 22715997
DOI: 10.1021/JM300425Y
Page generated: Fri Aug 16 13:27:40 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