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Arsenic in PDB 4mvy: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387):
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-(3-Hydroxyphenyl)Urea (Chem 1387), PDB code: 4mvy 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 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.236, 105.995, 206.166, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 21.9

Other elements in 4mvy:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387) 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-(3-Hydroxyphenyl)Urea (Chem 1387) (pdb code 4mvy). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 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-(3-Hydroxyphenyl)Urea (Chem 1387), PDB code: 4mvy:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4mvy

Go back to Arsenic Binding Sites List in 4mvy
Arsenic binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387)


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-(3-Hydroxyphenyl)Urea (Chem 1387) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:37.6
occ:0.70
 AS A:CAS470 0.0 37.6 0.7
CE2 A:CAS470 2.0 38.8 0.7
CE1 A:CAS470 2.0 38.0 0.7
SG A:CAS470 2.2 35.3 1.0
CB A:CAS470 3.1 31.4 1.0
CA A:CAS470 3.5 28.8 1.0
CA A:PRO462 3.7 28.1 1.0
N A:PRO462 3.7 27.6 1.0
O A:ALA460 3.8 29.9 1.0
C A:ILE461 3.9 26.4 1.0
O A:ILE461 4.0 26.1 1.0
O A:HIS469 4.0 29.9 1.0
C A:ALA460 4.0 28.4 1.0
N A:CAS470 4.1 29.1 1.0
CG A:PRO462 4.2 29.8 1.0
CB A:ALA460 4.2 28.0 1.0
CB A:PRO462 4.3 29.3 1.0
CD A:PRO462 4.3 28.7 1.0
C A:HIS469 4.3 29.3 1.0
N A:ILE461 4.4 26.2 1.0
CB A:ARG453 4.5 33.4 1.0
CA A:ALA460 4.6 28.9 1.0
CA A:ILE461 4.7 26.3 1.0
N A:ALA460 4.8 31.0 1.0
C A:CAS470 4.8 26.6 1.0
CA A:ASN458 5.0 42.4 1.0

Arsenic binding site 2 out of 2 in 4mvy

Go back to Arsenic Binding Sites List in 4mvy
Arsenic binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387)


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-(3-Hydroxyphenyl)Urea (Chem 1387) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:32.3
occ:0.50
 AS B:CAS470 0.0 32.3 0.5
CE2 B:CAS470 1.9 30.9 0.5
CE1 B:CAS470 2.0 33.5 0.5
SG B:CAS470 2.2 30.9 1.0
CB B:CAS470 3.2 28.4 1.0
CA B:CAS470 3.7 26.8 1.0
O B:ALA460 3.7 26.8 1.0
CA B:PRO462 4.0 25.7 1.0
N B:PRO462 4.0 25.0 1.0
O B:HIS469 4.0 27.4 1.0
C B:ALA460 4.1 25.9 1.0
C B:ILE461 4.1 24.1 1.0
O B:ILE461 4.1 22.9 1.0
N B:CAS470 4.2 27.3 1.0
CB B:ARG453 4.3 30.5 1.0
CB B:ALA460 4.3 26.0 1.0
C B:HIS469 4.3 28.2 1.0
CG B:PRO462 4.5 27.7 1.0
CD B:PRO462 4.5 26.5 1.0
N B:ILE461 4.6 24.6 1.0
CA B:ALA460 4.6 26.3 1.0
CB B:PRO462 4.7 26.9 1.0
N B:ALA460 4.8 27.9 1.0
CA B:ARG453 4.8 29.5 1.0
CA B:ILE461 4.8 24.5 1.0
CA B:ASN458 4.9 36.4 1.0
O B:PRO467 5.0 35.1 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 23:51:21 2025

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