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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: Sat Dec 12 01:44:18 2020

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