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Arsenic in PDB 4eg4: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1289

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1289

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1289:
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1289, PDB code: 4eg4 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 / 3.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.478, 105.892, 207.553, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24

Other elements in 4eg4:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1289 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 1289 (pdb code 4eg4). 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 1289, PDB code: 4eg4:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 4eg4

Go back to Arsenic Binding Sites List in 4eg4
Arsenic binding site 1 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1289


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 1289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As318

b:45.2
occ:0.50
 AS A:CAS318 0.0 45.2 0.5
CE2 A:CAS318 2.0 46.1 0.5
CE1 A:CAS318 2.0 48.1 0.5
SG A:CAS318 2.2 44.0 1.0
CB A:CAS318 3.0 44.3 1.0
CA A:CAS318 3.8 44.8 1.0
CG A:PRO565 4.1 71.0 1.0
O A:PRO255 4.3 42.3 1.0
CG2 A:VAL566 4.5 73.5 1.0
C A:CAS318 4.6 43.7 1.0
CG2 A:VAL260 4.6 39.9 1.0
O A:CAS318 4.7 44.3 1.0
CG A:PRO255 4.8 39.5 1.0
CB A:PRO255 4.8 38.5 1.0
C A:PRO255 4.9 40.6 1.0
OD2 A:ASP564 5.0 78.8 1.0

Arsenic binding site 2 out of 4 in 4eg4

Go back to Arsenic Binding Sites List in 4eg4
Arsenic binding site 2 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1289


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 1289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:41.3
occ:0.70
 AS A:CAS470 0.0 41.3 0.7
CE2 A:CAS470 2.0 41.2 0.7
CE1 A:CAS470 2.0 40.7 0.7
SG A:CAS470 2.2 38.7 1.0
CB A:CAS470 3.0 37.0 1.0
O A:ALA460 3.7 39.3 1.0
CA A:CAS470 3.8 36.2 1.0
O A:HIS469 3.9 36.8 1.0
CA A:PRO462 4.1 35.9 1.0
C A:ALA460 4.1 38.5 1.0
N A:PRO462 4.1 36.2 1.0
N A:CAS470 4.2 36.0 1.0
C A:ILE461 4.2 35.8 1.0
CB A:ALA460 4.3 38.8 1.0
C A:HIS469 4.3 36.2 1.0
O A:ILE461 4.3 35.6 1.0
CB A:ARG453 4.4 49.8 1.0
CG A:PRO462 4.4 37.8 1.0
CB A:PRO462 4.5 37.2 1.0
CA A:ALA460 4.6 39.2 1.0
CA A:ASN458 4.6 49.9 1.0
N A:ALA460 4.7 40.5 1.0
N A:ILE461 4.7 36.6 1.0
CD A:PRO462 4.7 37.0 1.0
C A:ASN458 4.8 47.8 1.0
O A:ASN458 4.9 47.8 1.0
CA A:ILE461 5.0 35.8 1.0

Arsenic binding site 3 out of 4 in 4eg4

Go back to Arsenic Binding Sites List in 4eg4
Arsenic binding site 3 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1289


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 1289 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As318

b:44.6
occ:0.50
 AS B:CAS318 0.0 44.6 0.5
CE2 B:CAS318 2.0 45.4 0.5
CE1 B:CAS318 2.0 45.7 0.5
SG B:CAS318 2.2 42.2 1.0
CB B:CAS318 3.1 42.0 1.0
CG2 B:VAL566 3.7 75.0 1.0
CA B:CAS318 3.9 42.5 1.0
CB B:PRO255 4.4 43.4 1.0
OE1 B:GLN321 4.5 55.5 1.0
CG2 B:VAL260 4.5 42.6 1.0
C B:CAS318 4.7 41.1 1.0
O B:CAS318 4.7 41.2 1.0
CG B:PRO565 4.7 69.2 1.0
O B:PRO255 4.8 46.8 1.0

Arsenic binding site 4 out of 4 in 4eg4

Go back to Arsenic Binding Sites List in 4eg4
Arsenic binding site 4 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor Chem 1289


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 1289 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:39.5
occ:0.70
 AS B:CAS470 0.0 39.5 0.7
CE2 B:CAS470 2.0 40.4 0.7
CE1 B:CAS470 2.0 40.0 0.7
SG B:CAS470 2.2 39.7 1.0
CB B:CAS470 3.0 38.2 1.0
CA B:CAS470 3.8 38.0 1.0
O B:ALA460 3.8 42.1 1.0
O B:ILE461 4.1 38.2 1.0
CB B:ARG453 4.1 51.6 1.0
C B:ALA460 4.1 40.0 1.0
CA B:PRO462 4.2 39.1 1.0
C B:ILE461 4.2 38.1 1.0
N B:CAS470 4.2 39.2 1.0
N B:PRO462 4.2 38.9 1.0
O B:HIS469 4.2 40.0 1.0
CB B:ALA460 4.2 39.7 1.0
C B:HIS469 4.4 40.4 1.0
CA B:ALA460 4.6 40.3 1.0
CG B:PRO462 4.6 41.2 1.0
N B:ALA460 4.6 42.0 1.0
N B:ILE461 4.7 38.3 1.0
CB B:PRO462 4.7 40.6 1.0
CA B:ARG453 4.8 50.8 1.0
CD B:PRO462 4.8 39.9 1.0
CA B:ASN458 4.9 50.5 1.0
O B:PRO467 5.0 47.2 1.0
CA B:ILE461 5.0 37.9 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 12:06:50 2024

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