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Chlorine in PDB 4py2: Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea

Enzymatic activity of Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea

All present enzymatic activity of Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea:
6.1.1.10;

Protein crystallography data

The structure of Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea, PDB code: 4py2 was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.43 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.010, 99.480, 104.000, 110.47, 87.24, 99.99
R / Rfree (%) 17.8 / 21.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea (pdb code 4py2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea, PDB code: 4py2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4py2

Go back to Chlorine Binding Sites List in 4py2
Chlorine binding site 1 out of 6 in the Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:39.0
occ:1.00
 CLB A:43E601 0.0 39.0 1.0
CAS A:43E601 1.7 38.8 1.0
CAG A:43E601 2.7 38.9 1.0
CAH A:43E601 2.7 36.1 1.0
CE3 A:TRP230 3.5 33.7 1.0
CZ3 A:TRP230 3.7 34.1 1.0
CD2 A:PHE268 3.9 36.3 1.0
CB A:PHE268 3.9 32.9 1.0
CAU A:43E601 4.0 36.3 1.0
CAT A:43E601 4.0 40.5 1.0
CG A:PHE268 4.1 35.2 1.0
CG2 A:VAL229 4.1 32.5 1.0
CG A:LEU234 4.2 29.2 1.0
O A:VAL229 4.3 30.3 1.0
CD2 A:LEU234 4.4 30.9 1.0
CA A:TRP230 4.4 30.6 1.0
CAI A:43E601 4.5 37.1 1.0
CB A:ALA233 4.5 27.1 1.0
CD1 A:LEU234 4.6 29.7 1.0
C A:VAL229 4.6 31.1 1.0
CG1 A:VAL229 4.7 30.9 1.0
CE2 A:PHE268 4.7 38.6 1.0
CD2 A:TRP230 4.7 33.0 1.0
O A:TRP230 4.8 30.7 1.0
N A:TRP230 4.9 30.9 1.0
CB A:VAL229 5.0 32.4 1.0

Chlorine binding site 2 out of 6 in 4py2

Go back to Chlorine Binding Sites List in 4py2
Chlorine binding site 2 out of 6 in the Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:52.5
occ:1.00
 CLC A:43E601 0.0 52.5 1.0
CAT A:43E601 1.8 40.5 1.0
CAG A:43E601 2.7 38.9 1.0
CAI A:43E601 2.9 37.1 1.0
OH A:TYR237 3.5 24.4 1.0
N A:ILE12 3.5 32.1 1.0
CG1 A:ILE12 3.6 33.9 1.0
NE2 A:HIS269 3.8 33.5 1.0
CB A:ALA11 3.8 32.5 1.0
CA A:ALA11 3.9 31.6 1.0
CE1 A:HIS269 3.9 33.9 1.0
CAS A:43E601 4.1 38.8 1.0
CAU A:43E601 4.2 36.3 1.0
CZ A:TYR237 4.2 24.7 1.0
C A:ALA11 4.2 33.0 1.0
ND2 A:ASN236 4.3 26.4 1.0
O A:ALA233 4.4 28.4 1.0
O A:ILE12 4.5 33.0 1.0
CA A:ILE12 4.5 34.4 1.0
CD1 A:ILE12 4.5 37.2 1.0
CB A:ALA233 4.6 27.1 1.0
CB A:ILE12 4.6 33.6 1.0
CAH A:43E601 4.7 36.1 1.0
CE2 A:TYR237 4.7 24.6 1.0
C A:ALA233 4.7 28.0 1.0
CD2 A:LEU234 4.8 30.9 1.0
CD1 A:ILE265 4.9 36.9 1.0
C A:ILE12 5.0 32.9 1.0
CE1 A:TYR237 5.0 25.8 1.0

Chlorine binding site 3 out of 6 in 4py2

Go back to Chlorine Binding Sites List in 4py2
Chlorine binding site 3 out of 6 in the Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:34.1
occ:1.00
 CLB B:43E601 0.0 34.1 1.0
CAS B:43E601 1.7 31.0 1.0
CAG B:43E601 2.7 30.6 1.0
CAH B:43E601 2.7 28.8 1.0
CE3 B:TRP230 3.6 23.9 1.0
CZ3 B:TRP230 3.9 24.6 1.0
CB B:PHE268 4.0 23.8 1.0
CD2 B:PHE268 4.0 25.9 1.0
CAU B:43E601 4.0 29.8 1.0
CAT B:43E601 4.0 33.0 1.0
CG2 B:VAL229 4.1 24.3 1.0
CG B:LEU234 4.1 22.0 1.0
CG B:PHE268 4.2 24.3 1.0
O B:VAL229 4.2 22.1 1.0
CD2 B:LEU234 4.3 22.5 1.0
CB B:ALA233 4.3 20.9 1.0
CA B:TRP230 4.4 22.6 1.0
CD1 B:LEU234 4.5 22.2 1.0
CAI B:43E601 4.5 31.9 1.0
C B:VAL229 4.6 22.4 1.0
O B:TRP230 4.7 21.3 1.0
CG1 B:VAL229 4.7 23.6 1.0
CD2 B:TRP230 4.8 23.6 1.0
N B:TRP230 4.8 23.0 1.0
CE2 B:PHE268 4.8 25.2 1.0
CB B:VAL229 5.0 23.4 1.0

Chlorine binding site 4 out of 6 in 4py2

Go back to Chlorine Binding Sites List in 4py2
Chlorine binding site 4 out of 6 in the Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:41.3
occ:1.00
 CLC B:43E601 0.0 41.3 1.0
CAT B:43E601 1.8 33.0 1.0
CAG B:43E601 2.7 30.6 1.0
CAI B:43E601 3.0 31.9 1.0
OH B:TYR237 3.3 22.5 1.0
N B:ILE12 3.5 24.3 1.0
NE2 B:HIS269 3.6 21.4 1.0
CG1 B:ILE12 3.7 24.2 1.0
CA B:ALA11 3.7 23.9 1.0
CE1 B:HIS269 3.8 22.1 1.0
CB B:ALA11 3.8 24.4 1.0
CZ B:TYR237 4.0 22.9 1.0
CAS B:43E601 4.1 31.0 1.0
C B:ALA11 4.2 25.1 1.0
ND2 B:ASN236 4.2 21.4 1.0
CAU B:43E601 4.3 29.8 1.0
O B:ALA233 4.5 23.3 1.0
CE2 B:TYR237 4.5 22.1 1.0
CA B:ILE12 4.6 24.6 1.0
O B:ILE12 4.6 23.5 1.0
CD1 B:ILE12 4.6 25.2 1.0
CB B:ILE12 4.6 24.8 1.0
CB B:ALA233 4.7 20.9 1.0
CAH B:43E601 4.7 28.8 1.0
CE1 B:TYR237 4.7 23.3 1.0
CD2 B:LEU234 4.7 22.5 1.0
C B:ALA233 4.8 21.9 1.0
CD1 B:ILE265 4.9 25.3 1.0
CD2 B:HIS269 5.0 21.9 1.0

Chlorine binding site 5 out of 6 in 4py2

Go back to Chlorine Binding Sites List in 4py2
Chlorine binding site 5 out of 6 in the Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:40.1
occ:1.00
 CLB C:43E601 0.0 40.1 1.0
CAS C:43E601 1.7 40.5 1.0
CAG C:43E601 2.7 40.5 1.0
CAH C:43E601 2.7 39.1 1.0
CE3 C:TRP230 3.5 33.0 1.0
CZ3 C:TRP230 3.8 34.1 1.0
CB C:PHE268 3.8 31.4 1.0
CD2 C:PHE268 3.8 33.0 1.0
CG C:PHE268 4.0 32.5 1.0
CAT C:43E601 4.0 39.4 1.0
CAU C:43E601 4.0 40.8 1.0
CG C:LEU234 4.2 30.3 1.0
CG2 C:VAL229 4.2 36.7 1.0
CD2 C:LEU234 4.4 31.7 1.0
O C:VAL229 4.4 31.5 1.0
CD1 C:LEU234 4.5 29.4 1.0
CA C:TRP230 4.5 31.1 1.0
CAI C:43E601 4.5 41.2 1.0
CB C:ALA233 4.5 31.2 1.0
CE2 C:PHE268 4.7 33.7 1.0
CD2 C:TRP230 4.7 32.3 1.0
C C:VAL229 4.7 33.0 1.0
CG1 C:VAL229 4.8 36.3 1.0
O C:TRP230 4.8 28.2 1.0
N C:TRP230 4.9 31.9 1.0

Chlorine binding site 6 out of 6 in 4py2

Go back to Chlorine Binding Sites List in 4py2
Chlorine binding site 6 out of 6 in the Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl) Amino]Propyl}-3-Thiophen-3-Ylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:46.7
occ:1.00
 CLC C:43E601 0.0 46.7 1.0
CAT C:43E601 1.8 39.4 1.0
CAG C:43E601 2.7 40.5 1.0
CAI C:43E601 2.9 41.2 1.0
OH C:TYR237 3.3 26.6 1.0
N C:ILE12 3.6 32.3 1.0
NE2 C:HIS269 3.6 31.4 1.0
CG1 C:ILE12 3.7 30.6 1.0
CE1 C:HIS269 3.7 30.5 1.0
CA C:ALA11 3.8 33.4 1.0
CB C:ALA11 3.8 34.6 1.0
CZ C:TYR237 4.0 27.7 1.0
CAS C:43E601 4.0 40.5 1.0
CAU C:43E601 4.2 40.8 1.0
C C:ALA11 4.3 34.4 1.0
ND2 C:ASN236 4.3 28.9 1.0
O C:ALA233 4.4 28.9 1.0
CE2 C:TYR237 4.5 29.0 1.0
CA C:ILE12 4.6 32.5 1.0
O C:ILE12 4.6 33.6 1.0
CB C:ALA233 4.6 31.2 1.0
CD1 C:ILE12 4.6 31.8 1.0
CAH C:43E601 4.7 39.1 1.0
CD2 C:LEU234 4.7 31.7 1.0
CB C:ILE12 4.7 32.6 1.0
C C:ALA233 4.8 29.4 1.0
CE1 C:TYR237 4.8 27.9 1.0
CD1 C:ILE265 4.9 33.6 1.0
CD2 C:HIS269 4.9 30.4 1.0

Reference:

D.M.Dranow, T.E.Edwards, D.Lorimer, Seattle Structural Genomics Center For Infectious Disease. Crystal Structure of Methionyl-Trna Synthetase Metrs From Brucella Melitensis in Complex with Inhibitor Chem 1433 To Be Published.
Page generated: Fri Jul 26 00:13:02 2024

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