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Arsenic in PDB 4ega: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320:
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320, PDB code: 4ega was solved by C.Y.Koh, J.E.Kim, S.Shibata, 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 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.536, 105.921, 207.591, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.8

Other elements in 4ega:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320 also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320 (pdb code 4ega). 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 Chem 1320, PDB code: 4ega:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 4ega

Go back to Arsenic Binding Sites List in 4ega
Arsenic binding site 1 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320


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 Chem 1320 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As318

b:57.4
occ:0.50
 AS A:CAS318 0.0 57.4 0.5
CE1 A:CAS318 2.0 58.2 0.5
CE2 A:CAS318 2.0 59.4 0.5
SG A:CAS318 2.2 53.5 1.0
CB A:CAS318 3.0 51.4 1.0
CA A:CAS318 3.7 51.4 1.0
CG A:PRO565 4.0 71.8 1.0
CG2 A:VAL566 4.5 68.5 1.0
C A:CAS318 4.5 50.8 1.0
O A:CAS318 4.5 50.3 1.0
CG A:PRO255 4.7 46.6 1.0
CE A:MET322 4.8 61.4 1.0
CG2 A:VAL260 4.8 40.0 1.0
CB A:VAL566 4.8 71.9 1.0
CB A:PRO255 4.9 45.7 1.0
CD A:PRO565 4.9 73.8 1.0
O A:PRO255 4.9 47.5 1.0
N A:CAS318 4.9 51.2 1.0

Arsenic binding site 2 out of 4 in 4ega

Go back to Arsenic Binding Sites List in 4ega
Arsenic binding site 2 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320


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 Chem 1320 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:49.9
occ:0.70
 AS A:CAS470 0.0 49.9 0.7
CE2 A:CAS470 2.0 47.3 0.7
CE1 A:CAS470 2.0 50.4 0.7
SG A:CAS470 2.2 45.9 1.0
CB A:CAS470 3.1 43.8 1.0
O A:HIS469 3.6 45.5 1.0
CA A:CAS470 3.8 42.3 1.0
O A:ALA460 4.1 39.8 1.0
CA A:PRO462 4.1 39.9 1.0
CB A:ALA460 4.1 40.2 1.0
N A:PRO462 4.2 39.5 1.0
C A:HIS469 4.2 43.6 1.0
O A:ILE461 4.2 39.0 1.0
C A:ILE461 4.3 38.6 1.0
N A:CAS470 4.3 42.5 1.0
C A:ALA460 4.3 40.0 1.0
CG A:PRO462 4.4 41.0 1.0
CB A:ARG453 4.4 50.4 1.0
CB A:PRO462 4.5 40.6 1.0
CA A:ALA460 4.7 40.9 1.0
CD A:PRO462 4.7 40.6 1.0
N A:ILE461 4.8 38.9 1.0
N A:ALA460 4.8 43.6 1.0
CA A:ASN458 4.8 56.2 1.0
O A:PRO467 4.9 49.5 1.0
CA A:ARG453 5.0 49.6 1.0

Arsenic binding site 3 out of 4 in 4ega

Go back to Arsenic Binding Sites List in 4ega
Arsenic binding site 3 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320


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 Chem 1320 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As318

b:47.4
occ:0.40
 AS B:CAS318 0.0 47.4 0.4
CE2 B:CAS318 2.0 46.6 0.4
CE1 B:CAS318 2.0 48.5 0.4
SG B:CAS318 2.2 47.4 1.0
CB B:CAS318 3.0 47.9 1.0
CA B:CAS318 3.8 48.5 1.0
CG2 B:VAL566 3.8 78.7 1.0
CB B:PRO255 4.1 51.1 1.0
OE1 B:GLN321 4.4 53.2 0.5
CG2 B:VAL260 4.6 50.2 1.0
C B:CAS318 4.6 47.2 1.0
O B:CAS318 4.6 46.8 1.0
O B:HOH1014 4.8 48.7 1.0
O B:PRO255 4.8 56.5 1.0
N B:CAS318 4.9 49.5 1.0
CG B:PRO255 4.9 50.5 1.0
C B:PRO255 5.0 53.2 1.0

Arsenic binding site 4 out of 4 in 4ega

Go back to Arsenic Binding Sites List in 4ega
Arsenic binding site 4 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1320


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 Chem 1320 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:55.0
occ:0.70
 AS B:CAS470 0.0 55.0 0.7
CE2 B:CAS470 2.0 55.0 0.7
CE1 B:CAS470 2.0 54.1 0.7
SG B:CAS470 2.2 53.3 1.0
CB B:CAS470 3.0 49.0 1.0
CA B:CAS470 3.7 46.8 1.0
CA B:PRO462 3.8 43.7 1.0
N B:PRO462 3.9 44.1 1.0
C B:ILE461 3.9 42.7 1.0
O B:ILE461 4.0 42.4 1.0
O B:ALA460 4.0 43.3 1.0
O B:HIS469 4.1 45.8 1.0
N B:CAS470 4.1 47.0 1.0
C B:ALA460 4.2 42.4 1.0
CB B:ARG453 4.3 55.8 1.0
C B:HIS469 4.3 47.6 1.0
CB B:ALA460 4.3 41.2 1.0
CB B:PRO462 4.4 44.7 1.0
N B:ILE461 4.5 42.9 1.0
CG B:PRO462 4.5 44.7 1.0
CA B:ALA460 4.7 42.0 1.0
CD B:PRO462 4.7 44.2 1.0
CA B:ILE461 4.7 42.4 1.0
N B:ALA460 4.9 42.6 1.0
CA B:ARG453 4.9 54.5 1.0

Reference:

C.Y.Koh, J.E.Kim, S.Shibata, R.M.Ranade, M.Yu, J.Liu, J.R.Gillespie, F.S.Buckner, C.L.Verlinde, E.Fan, W.G.Hol. Distinct States of Methionyl-Trna Synthetase Indicate Inhibitor Binding By Conformational Selection. Structure V. 20 1681 2012.
ISSN: ISSN 0969-2126
PubMed: 22902861
DOI: 10.1016/J.STR.2012.07.011
Page generated: Wed Jul 10 12:08:09 2024

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