Chlorine in PDB 7wmf: Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor

Enzymatic activity of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor

All present enzymatic activity of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor:
6.1.1.3;

Protein crystallography data

The structure of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor, PDB code: 7wmf was solved by Z.Cai, B.Chen, Y.Yu, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.792, 102.521, 103.171, 90, 90, 90
R / Rfree (%) 22.4 / 26.7

Other elements in 7wmf:

The structure of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Fluorine (F) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor (pdb code 7wmf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor, PDB code: 7wmf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7wmf

Go back to Chlorine Binding Sites List in 7wmf
Chlorine binding site 1 out of 4 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:49.9
occ:1.00
 CL1 A:9I9701 0.0 49.9 1.0
C7 A:9I9701 1.7 46.6 1.0
C8 A:9I9701 2.7 47.1 1.0
C6 A:9I9701 2.7 48.1 1.0
CL A:9I9701 3.2 51.5 1.0
CG A:PRO331 3.3 34.5 1.0
CE A:MET317 3.6 51.2 1.0
CB A:HIS309 3.7 52.8 1.0
CB A:TYR313 4.0 51.8 1.0
C9 A:9I9701 4.0 45.8 1.0
CG A:HIS309 4.0 52.3 1.0
C5 A:9I9701 4.0 47.8 1.0
CB A:PRO331 4.1 34.6 1.0
CG A:MET317 4.3 48.0 1.0
SD A:MET317 4.4 50.7 1.0
ND1 A:HIS309 4.4 52.7 1.0
CG A:TYR313 4.5 51.2 1.0
C4 A:9I9701 4.5 46.5 1.0
CD2 A:HIS309 4.6 52.4 1.0
CD2 A:TYR313 4.6 52.4 1.0
CZ3 A:TRP304 4.6 41.0 1.0
CD A:PRO331 4.6 34.8 1.0
O A:HIS309 4.9 55.9 1.0
O A:TYR313 4.9 52.5 1.0
SD A:MET332 4.9 44.3 1.0
CA A:HIS309 4.9 53.4 1.0
CE3 A:TRP304 5.0 40.5 1.0

Chlorine binding site 2 out of 4 in 7wmf

Go back to Chlorine Binding Sites List in 7wmf
Chlorine binding site 2 out of 4 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:51.5
occ:1.00
 CL A:9I9701 0.0 51.5 1.0
C6 A:9I9701 1.7 48.1 1.0
C5 A:9I9701 2.7 47.8 1.0
C7 A:9I9701 2.7 46.6 1.0
CL1 A:9I9701 3.2 49.9 1.0
CB A:ALA316 3.5 48.3 1.0
CB A:PRO331 3.5 34.6 1.0
O A:ALA316 3.6 45.7 1.0
CG A:PRO331 3.9 34.5 1.0
C A:ALA316 3.9 47.6 1.0
CG A:MET317 4.0 48.0 1.0
CB A:TYR313 4.0 51.8 1.0
C4 A:9I9701 4.0 46.5 1.0
C8 A:9I9701 4.0 47.1 1.0
CG A:ARG363 4.0 52.5 1.0
O A:TYR313 4.1 52.5 1.0
NE A:ARG363 4.3 58.8 1.0
CA A:ALA316 4.3 48.4 1.0
CD A:ARG363 4.3 56.2 1.0
N A:MET317 4.5 46.5 1.0
C9 A:9I9701 4.5 45.8 1.0
CG A:TYR313 4.6 51.2 1.0
CA A:MET317 4.7 45.3 1.0
CB A:ARG363 4.8 48.4 1.0
CD1 A:TYR313 4.9 49.8 1.0
CB A:MET317 4.9 46.1 1.0
CA A:PRO331 5.0 34.8 1.0

Chlorine binding site 3 out of 4 in 7wmf

Go back to Chlorine Binding Sites List in 7wmf
Chlorine binding site 3 out of 4 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:61.8
occ:1.00
 CL1 B:9I9701 0.0 61.8 1.0
C7 B:9I9701 1.7 58.0 1.0
C8 B:9I9701 2.7 55.5 1.0
C6 B:9I9701 2.7 57.2 1.0
CL B:9I9701 3.2 55.5 1.0
CG B:PRO331 3.3 46.2 1.0
CE B:MET317 3.5 55.6 1.0
CB B:HIS309 3.7 64.6 1.0
CG B:HIS309 3.9 65.4 1.0
C9 B:9I9701 4.0 53.2 1.0
C5 B:9I9701 4.0 55.0 1.0
CB B:PRO331 4.0 46.1 1.0
CE B:MET332 4.0 56.5 1.0
CB B:TYR313 4.1 60.4 1.0
ND1 B:HIS309 4.3 63.7 1.0
CG B:MET317 4.3 53.0 1.0
SD B:MET317 4.3 55.2 1.0
C4 B:9I9701 4.5 54.2 1.0
CD2 B:HIS309 4.6 64.5 1.0
CZ3 B:TRP304 4.6 56.9 1.0
CD B:PRO331 4.7 46.1 1.0
CG B:TYR313 4.7 61.4 1.0
CD2 B:TYR313 4.8 61.8 1.0
CE3 B:TRP304 4.8 56.9 1.0
O B:HIS309 4.8 63.2 1.0
CA B:HIS309 4.9 64.9 1.0
SD B:MET332 5.0 57.9 1.0
CE1 B:HIS309 5.0 64.8 1.0

Chlorine binding site 4 out of 4 in 7wmf

Go back to Chlorine Binding Sites List in 7wmf
Chlorine binding site 4 out of 4 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:55.5
occ:1.00
 CL B:9I9701 0.0 55.5 1.0
C6 B:9I9701 1.7 57.2 1.0
C5 B:9I9701 2.7 55.0 1.0
C7 B:9I9701 2.7 58.0 1.0
CL1 B:9I9701 3.2 61.8 1.0
CB B:ALA316 3.4 51.9 1.0
O B:ALA316 3.5 52.2 1.0
CD B:ARG363 3.6 51.3 1.0
CB B:PRO331 3.6 46.1 1.0
C B:ALA316 3.6 51.5 1.0
CG B:MET317 3.7 53.0 1.0
O B:TYR313 3.8 56.5 1.0
CB B:TYR313 3.9 60.4 1.0
C4 B:9I9701 4.0 54.2 1.0
C8 B:9I9701 4.0 55.5 1.0
CG B:PRO331 4.0 46.2 1.0
CA B:ALA316 4.1 52.6 1.0
N B:MET317 4.1 50.5 1.0
NE B:ARG363 4.1 53.7 1.0
C9 B:9I9701 4.5 53.2 1.0
CA B:MET317 4.5 48.7 1.0
CZ B:ARG363 4.7 54.2 1.0
CG B:TYR313 4.7 61.4 1.0
CB B:MET317 4.7 50.9 1.0
C B:TYR313 4.7 58.0 1.0
CE B:MET317 4.8 55.6 1.0
NH1 B:ARG363 4.8 54.0 1.0
N B:ALA316 4.9 53.8 1.0
CA B:TYR313 4.9 60.5 1.0
SD B:MET317 5.0 55.2 1.0
CG B:ARG363 5.0 49.6 1.0

Reference:

Z.Cai, B.Chen, Y.Yu, J.Guo, Z.Luo, B.Cheng, J.Xu, Q.Gu, H.Zhou. Design, Synthesis, and Proof-of-Concept of Triple-Site Inhibitors Against Aminoacyl-Trna Synthetases. J.Med.Chem. V. 65 5800 2022.
ISSN: ISSN 0022-2623
PubMed: 35363470
DOI: 10.1021/ACS.JMEDCHEM.2C00134
Page generated: Tue Jul 30 05:39:44 2024

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