Atomistry » Arsenic » PDB 4j9t-4mwc » 4mvw
Atomistry »
  Arsenic »
    PDB 4j9t-4mwc »
      4mvw »

Arsenic in PDB 4mvw: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433), PDB code: 4mvw was solved by C.Y.Koh, J.E.Kim, A.B.Wetzel, W.J.De Van Der Schueren, S.Shibata, J.Liu, Z.Zhang, E.Fan, C.L.M.J.Verlinde, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.066, 105.858, 206.974, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.9

Other elements in 4mvw:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) (pdb code 4mvw). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433), PDB code: 4mvw:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 4mvw

Go back to Arsenic Binding Sites List in 4mvw
Arsenic binding site 1 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As318

b:54.4
occ:0.50
 AS A:CAS318 0.0 54.4 0.5
CE1 A:CAS318 2.0 53.5 0.5
CE2 A:CAS318 2.0 56.1 0.5
SG A:CAS318 2.2 46.7 1.0
CB A:CAS318 3.1 46.2 1.0
CA A:CAS318 3.9 46.1 1.0
CG2 A:VAL566 3.9 70.9 1.0
CG A:PRO565 4.1 68.8 1.0
C A:CAS318 4.6 44.0 1.0
CG2 A:VAL260 4.6 38.0 1.0
CG A:PRO255 4.7 42.3 1.0
O A:CAS318 4.7 44.2 1.0
OD1 A:ASP564 4.7 78.8 1.0
O A:PRO255 4.8 45.4 1.0
OE1 A:GLN321 4.8 64.0 1.0
CD A:PRO565 4.8 71.6 1.0
CB A:VAL566 4.9 72.7 1.0
CB A:PRO255 4.9 40.6 1.0

Arsenic binding site 2 out of 4 in 4mvw

Go back to Arsenic Binding Sites List in 4mvw
Arsenic binding site 2 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:50.7
occ:0.70
 AS A:CAS470 0.0 50.7 0.7
CE1 A:CAS470 2.0 51.1 0.7
CE2 A:CAS470 2.0 51.2 0.7
SG A:CAS470 2.2 44.2 1.0
CB A:CAS470 3.1 40.5 1.0
CA A:CAS470 3.7 38.1 1.0
O A:ALA460 3.8 36.5 1.0
CA A:PRO462 3.8 34.2 1.0
N A:PRO462 3.8 34.2 1.0
O A:HIS469 3.9 37.6 1.0
C A:ILE461 4.0 33.0 1.0
CG A:PRO462 4.1 36.5 1.0
C A:ALA460 4.1 35.2 1.0
O A:ILE461 4.1 32.4 1.0
N A:CAS470 4.1 37.1 1.0
CD A:PRO462 4.2 35.4 1.0
C A:HIS469 4.3 37.1 1.0
CB A:PRO462 4.3 35.7 1.0
CB A:ALA460 4.4 35.1 1.0
N A:ILE461 4.6 33.2 1.0
CA A:ALA460 4.7 35.9 1.0
N A:ALA460 4.8 38.1 1.0
CA A:ILE461 4.8 32.8 1.0
CG A:ARG453 4.9 45.9 1.0
CA A:ASN458 5.0 47.3 1.0

Arsenic binding site 3 out of 4 in 4mvw

Go back to Arsenic Binding Sites List in 4mvw
Arsenic binding site 3 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As318

b:46.0
occ:0.50
 AS B:CAS318 0.0 46.0 0.5
CE2 B:CAS318 2.0 45.2 0.5
CE1 B:CAS318 2.0 46.3 0.5
SG B:CAS318 2.2 39.9 1.0
CB B:CAS318 3.0 40.5 1.0
CA B:CAS318 3.6 40.6 1.0
CG2 B:VAL566 3.6 55.2 1.0
O B:CAS318 3.9 38.7 1.0
C B:CAS318 4.0 38.8 1.0
CG2 B:VAL260 4.4 37.5 1.0
OE1 B:GLN321 4.5 51.5 1.0
CG B:MET322 4.7 36.9 1.0
CB B:PRO255 4.7 40.4 1.0
N B:CAS318 4.9 41.3 1.0

Arsenic binding site 4 out of 4 in 4mvw

Go back to Arsenic Binding Sites List in 4mvw
Arsenic binding site 4 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:45.0
occ:0.70
 AS B:CAS470 0.0 45.0 0.7
CE1 B:CAS470 2.0 45.1 0.7
CE2 B:CAS470 2.0 45.6 0.7
SG B:CAS470 2.2 40.4 1.0
CB B:CAS470 3.1 37.4 1.0
CA B:CAS470 3.7 35.7 1.0
O B:ALA460 3.7 34.0 1.0
CA B:PRO462 3.7 32.0 1.0
N B:PRO462 3.8 31.9 1.0
O B:ILE461 3.8 30.0 1.0
C B:ILE461 3.8 30.9 1.0
C B:ALA460 4.1 32.5 1.0
N B:CAS470 4.2 35.7 1.0
O B:HIS469 4.2 35.3 1.0
CB B:PRO462 4.3 33.8 1.0
C B:HIS469 4.4 36.2 1.0
CD B:PRO462 4.4 33.3 1.0
CB B:ARG453 4.4 40.1 1.0
CB B:ALA460 4.5 31.6 1.0
N B:ILE461 4.5 31.3 1.0
CA B:ALA460 4.7 32.4 1.0
CA B:ILE461 4.7 31.1 1.0
N B:ALA460 4.8 34.0 1.0
O B:PRO467 4.8 43.4 1.0
CA B:ARG453 5.0 39.0 1.0

Reference:

C.Y.Koh, J.E.Kim, A.B.Wetzel, W.J.De Van Der Schueren, S.Shibata, R.M.Ranade, J.Liu, Z.Zhang, J.R.Gillespie, F.S.Buckner, C.L.Verlinde, E.Fan, W.G.Hol. Structures of Trypanosoma Brucei Methionyl-Trna Synthetase with Urea-Based Inhibitors Provide Guidance For Drug Design Against Sleeping Sickness. Plos Negl Trop Dis V. 8 E2775 2014.
ISSN: ISSN 1935-2727
PubMed: 24743796
DOI: 10.1371/JOURNAL.PNTD.0002775
Page generated: Wed Jul 10 12:16:45 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