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Arsenic in PDB 4mvx: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Phenylurea (Chem 1356)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Phenylurea (Chem 1356)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Phenylurea (Chem 1356):
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-Phenylurea (Chem 1356), PDB code: 4mvx 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 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.058, 105.956, 206.672, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.4

Other elements in 4mvx:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Phenylurea (Chem 1356) 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-Phenylurea (Chem 1356) (pdb code 4mvx). 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-Phenylurea (Chem 1356), PDB code: 4mvx:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 4mvx

Go back to Arsenic Binding Sites List in 4mvx
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-Phenylurea (Chem 1356)


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-Phenylurea (Chem 1356) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As318

b:44.4
occ:0.30
 AS A:CAS318 0.0 44.4 0.3
CE2 A:CAS318 2.0 43.8 0.3
CE1 A:CAS318 2.0 44.6 0.3
SG A:CAS318 2.2 40.4 1.0
CB A:CAS318 3.2 39.6 1.0
CG2 A:VAL566 3.4 62.1 1.0
CA A:CAS318 3.9 39.0 1.0
CG A:PRO565 4.2 66.8 1.0
O A:HOH1010 4.3 51.7 1.0
CB A:VAL566 4.5 63.0 1.0
C A:CAS318 4.7 37.6 1.0
CG2 A:VAL260 4.7 29.0 1.0
O A:CAS318 4.8 36.6 1.0
CG A:PRO255 4.8 33.3 1.0
OD1 A:ASP564 4.8 74.3 1.0
CD A:PRO565 4.8 67.1 1.0
N A:VAL566 4.9 62.4 1.0
CB A:PRO255 5.0 32.6 1.0
O A:PRO255 5.0 34.6 1.0

Arsenic binding site 2 out of 4 in 4mvx

Go back to Arsenic Binding Sites List in 4mvx
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-Phenylurea (Chem 1356)


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-Phenylurea (Chem 1356) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:45.0
occ:0.60
 AS A:CAS470 0.0 45.0 0.6
CE2 A:CAS470 2.0 45.0 0.6
CE1 A:CAS470 2.0 44.1 0.6
SG A:CAS470 2.2 39.6 1.0
CB A:CAS470 3.1 35.2 1.0
CA A:CAS470 3.6 32.2 1.0
CA A:PRO462 3.7 30.0 1.0
O A:ALA460 3.7 31.1 1.0
N A:PRO462 3.7 29.9 1.0
C A:ILE461 3.9 29.2 1.0
O A:HIS469 4.0 31.6 1.0
O A:ILE461 4.0 29.2 1.0
C A:ALA460 4.0 30.4 1.0
N A:CAS470 4.1 31.5 1.0
CG A:PRO462 4.2 30.7 1.0
CB A:ALA460 4.2 30.9 1.0
CB A:PRO462 4.3 30.3 1.0
C A:HIS469 4.3 31.8 1.0
CD A:PRO462 4.4 30.4 1.0
CB A:ARG453 4.5 36.7 1.0
N A:ILE461 4.5 29.6 1.0
CA A:ALA460 4.6 31.1 1.0
N A:ALA460 4.7 32.7 1.0
CA A:ILE461 4.8 29.0 1.0
CA A:ASN458 4.9 41.9 1.0
O A:ASN458 5.0 40.4 1.0
C A:ASN458 5.0 39.9 1.0
C A:PRO462 5.0 29.6 1.0
C A:CAS470 5.0 29.8 1.0

Arsenic binding site 3 out of 4 in 4mvx

Go back to Arsenic Binding Sites List in 4mvx
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-Phenylurea (Chem 1356)


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-Phenylurea (Chem 1356) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As318

b:40.0
occ:0.30
 AS B:CAS318 0.0 40.0 0.3
CE2 B:CAS318 2.0 39.7 0.3
CE1 B:CAS318 2.0 40.4 0.3
SG B:CAS318 2.2 36.9 1.0
CB B:CAS318 3.1 35.9 1.0
CG2 B:VAL566 3.4 50.6 1.0
CA B:CAS318 3.7 35.9 1.0
O B:CAS318 4.4 34.6 1.0
C B:CAS318 4.5 35.1 1.0
CG2 B:VAL260 4.5 28.3 1.0
CB B:VAL566 4.6 50.1 1.0
CB B:PRO255 4.7 37.5 1.0
CG B:PRO565 4.9 48.2 1.0
N B:CAS318 5.0 36.2 1.0

Arsenic binding site 4 out of 4 in 4mvx

Go back to Arsenic Binding Sites List in 4mvx
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-Phenylurea (Chem 1356)


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-Phenylurea (Chem 1356) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:37.7
occ:0.60
 AS B:CAS470 0.0 37.7 0.6
CE2 B:CAS470 2.0 37.8 0.6
CE1 B:CAS470 2.0 37.0 0.6
SG B:CAS470 2.2 34.7 1.0
CB B:CAS470 3.1 32.3 1.0
O B:ALA460 3.6 26.5 1.0
CA B:CAS470 3.6 30.6 1.0
O B:ILE461 3.7 25.0 1.0
N B:PRO462 3.7 25.8 1.0
CA B:PRO462 3.8 26.1 1.0
C B:ILE461 3.8 25.3 1.0
C B:ALA460 4.0 25.6 1.0
O B:HIS469 4.1 30.2 1.0
N B:CAS470 4.2 30.7 1.0
CB B:ALA460 4.3 25.7 1.0
CB B:PRO462 4.3 26.4 1.0
CB B:ARG453 4.4 32.2 1.0
CG B:PRO462 4.4 26.6 1.0
C B:HIS469 4.4 31.6 1.0
N B:ILE461 4.5 25.2 1.0
CD B:PRO462 4.5 26.1 1.0
CA B:ALA460 4.5 25.7 1.0
CA B:ILE461 4.6 25.2 1.0
N B:ALA460 4.7 26.3 1.0
O B:PRO467 4.9 37.0 1.0
C B:CAS470 5.0 28.6 1.0
CA B:ARG453 5.0 31.4 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 12:16:51 2024

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