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

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) and Atp Analog Amppcp

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) and Atp Analog Amppcp:
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) and Atp Analog Amppcp, PDB code: 4mwd 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 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.267, 105.880, 206.676, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.1

Other elements in 4mwd:

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) and Atp Analog Amppcp 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) and Atp Analog Amppcp (pdb code 4mwd). 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) and Atp Analog Amppcp, PDB code: 4mwd:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 4mwd

Go back to Arsenic Binding Sites List in 4mwd
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) and Atp Analog Amppcp


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) and Atp Analog Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As318

b:50.2
occ:0.70
 AS A:CAS318 0.0 50.2 0.7
CE1 A:CAS318 2.0 49.2 0.7
CE2 A:CAS318 2.0 51.1 0.7
SG A:CAS318 2.2 43.7 1.0
CB A:CAS318 3.1 41.9 1.0
CA A:CAS318 3.8 40.4 1.0
CG2 A:VAL566 4.0 57.0 1.0
CG A:PRO255 4.5 37.6 1.0
C A:CAS318 4.5 38.4 1.0
CG2 A:VAL260 4.6 36.5 1.0
O A:CAS318 4.6 36.8 1.0
O A:HOH1234 4.6 49.3 1.0
O A:PRO255 4.8 38.0 1.0
CB A:PRO255 4.9 36.5 1.0
N A:CAS318 5.0 41.3 1.0

Arsenic binding site 2 out of 4 in 4mwd

Go back to Arsenic Binding Sites List in 4mwd
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) and Atp Analog Amppcp


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) and Atp Analog Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:33.8
occ:0.70
 AS A:CAS470 0.0 33.8 0.7
CE1 A:CAS470 2.0 35.6 0.7
CE2 A:CAS470 2.0 35.4 0.7
SG A:CAS470 2.2 35.0 1.0
CB A:CAS470 3.0 32.4 1.0
CA A:CAS470 3.5 30.7 1.0
O A:ALA460 3.6 31.2 1.0
N A:PRO462 3.8 29.9 1.0
CA A:PRO462 3.8 30.4 1.0
C A:ALA460 3.9 30.3 1.0
C A:ILE461 3.9 29.4 1.0
O A:ILE461 3.9 28.9 1.0
O A:HIS469 4.0 31.4 1.0
N A:CAS470 4.1 30.9 1.0
CG A:PRO462 4.1 31.1 1.0
CB A:ALA460 4.2 30.7 1.0
CD A:PRO462 4.2 30.6 1.0
C A:HIS469 4.3 30.9 1.0
N A:ILE461 4.4 29.4 1.0
CB A:PRO462 4.4 30.7 1.0
CA A:ALA460 4.5 30.9 1.0
CB A:ARG453 4.6 33.1 1.0
CA A:ILE461 4.7 29.4 1.0
N A:ALA460 4.7 32.1 1.0
C A:CAS470 4.8 30.0 1.0

Arsenic binding site 3 out of 4 in 4mwd

Go back to Arsenic Binding Sites List in 4mwd
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) and Atp Analog Amppcp


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) and Atp Analog Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As318

b:42.1
occ:0.70
 AS B:CAS318 0.0 42.1 0.7
CE2 B:CAS318 2.0 44.6 0.7
CE1 B:CAS318 2.0 42.1 0.7
SG B:CAS318 2.2 37.6 1.0
CB B:CAS318 3.1 37.5 1.0
CA B:CAS318 3.7 37.1 1.0
CB B:PRO255 4.3 36.0 1.0
O B:HOH1122 4.3 54.0 1.0
CG2 B:VAL566 4.4 48.5 1.0
O B:HOH1017 4.4 39.9 1.0
C B:CAS318 4.5 35.7 1.0
O B:CAS318 4.5 35.6 1.0
CG2 B:VAL260 4.5 30.1 1.0
O B:HOH1136 4.7 34.6 1.0
CG B:PRO565 4.8 43.8 1.0
O B:PRO255 4.9 37.6 1.0
N B:CAS318 4.9 37.1 1.0
CE B:MET322 5.0 41.2 1.0
CG B:PRO255 5.0 36.2 1.0

Arsenic binding site 4 out of 4 in 4mwd

Go back to Arsenic Binding Sites List in 4mwd
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) and Atp Analog Amppcp


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) and Atp Analog Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:30.5
occ:0.70
 AS B:CAS470 0.0 30.5 0.7
CE1 B:CAS470 1.9 30.6 0.7
CE2 B:CAS470 2.0 31.5 0.7
SG B:CAS470 2.2 30.9 1.0
CB B:CAS470 3.1 29.4 1.0
CA B:CAS470 3.7 28.5 1.0
O B:ALA460 3.8 27.5 1.0
CA B:PRO462 3.9 27.6 1.0
N B:PRO462 4.0 27.2 1.0
O B:ILE461 4.0 26.7 1.0
O B:HIS469 4.0 28.4 1.0
C B:ILE461 4.0 26.9 1.0
C B:ALA460 4.1 27.1 1.0
N B:CAS470 4.2 28.5 1.0
CB B:ALA460 4.3 27.2 1.0
C B:HIS469 4.3 29.4 1.0
CB B:ARG453 4.4 28.8 1.0
N B:ILE461 4.5 26.4 1.0
CB B:PRO462 4.6 28.3 1.0
CG B:PRO462 4.6 28.3 1.0
CA B:ALA460 4.6 27.0 1.0
CD B:PRO462 4.7 27.6 1.0
N B:ALA460 4.8 27.3 1.0
O B:HOH1034 4.8 40.2 1.0
CA B:ILE461 4.8 26.6 1.0
CA B:ARG453 4.9 28.6 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: Sun Jul 6 23:53:35 2025

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