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Chlorine in PDB 4qrd: Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine

Enzymatic activity of Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine

All present enzymatic activity of Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine:
6.1.1.10;

Protein crystallography data

The structure of Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine, PDB code: 4qrd was solved by X.Li, M.T.Hilgers, M.Stidham, V.Brown-Driver, K.J.Shaw, J.Finn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.25 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.438, 76.726, 118.222, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 28.3

Other elements in 4qrd:

The structure of Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine (pdb code 4qrd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine, PDB code: 4qrd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4qrd

Go back to Chlorine Binding Sites List in 4qrd
Chlorine binding site 1 out of 2 in the Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:26.3
occ:1.00
 CL2 A:3BJ602 0.0 26.3 1.0
C30 A:3BJ602 1.8 24.1 1.0
C29 A:3BJ602 2.8 23.4 1.0
C25 A:3BJ602 2.8 23.9 1.0
N24 A:3BJ602 3.0 24.4 1.0
CE3 A:TRP237 3.6 13.4 1.0
CB A:PHE276 3.6 15.4 1.0
CZ3 A:TRP237 3.6 15.3 1.0
CD2 A:PHE276 3.8 11.2 1.0
CG A:PHE276 3.9 16.4 1.0
C28 A:3BJ602 4.0 23.9 1.0
C16 A:3BJ602 4.1 26.0 1.0
C26 A:3BJ602 4.1 25.0 1.0
CG A:LEU241 4.2 12.1 1.0
CD2 A:LEU241 4.3 12.6 1.0
CD1 A:LEU241 4.3 10.8 1.0
N15 A:3BJ602 4.6 24.9 1.0
C27 A:3BJ602 4.6 25.0 1.0
CE2 A:PHE276 4.8 11.9 1.0
CA A:TRP237 4.8 13.8 1.0
O A:TRP237 4.8 13.8 1.0
CD2 A:TRP237 4.9 12.9 1.0
CB A:ALA240 4.9 12.7 1.0
CD1 A:PHE276 4.9 15.4 1.0
CG2 A:VAL236 4.9 13.6 1.0
CE1 A:HIS277 5.0 10.7 1.0
CH2 A:TRP237 5.0 14.4 1.0

Chlorine binding site 2 out of 2 in 4qrd

Go back to Chlorine Binding Sites List in 4qrd
Chlorine binding site 2 out of 2 in the Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Methionyl-Trna Synthetase in Complex with N-(1H- Benzimidazol-2-Ylmethyl)-N'-(2,4-Dichlorophenyl)-6-(Morpholin-4-Yl)- 1,3,5-Triazine-2,4-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:22.8
occ:1.00
 CL1 A:3BJ602 0.0 22.8 1.0
C28 A:3BJ602 1.8 23.9 1.0
C29 A:3BJ602 2.7 23.4 1.0
C27 A:3BJ602 2.8 25.0 1.0
ND2 A:ASN243 3.3 18.9 1.0
OH A:TYR244 3.4 12.5 1.0
N A:ILE12 3.6 18.1 1.0
CG1 A:ILE12 3.7 15.2 1.0
NE2 A:HIS277 3.8 9.8 1.0
CZ A:TYR244 3.9 11.5 1.0
CA A:PRO11 3.9 16.3 1.0
CB A:PRO11 4.0 15.8 1.0
O A:ALA240 4.0 12.2 1.0
CE1 A:HIS277 4.0 10.7 1.0
C30 A:3BJ602 4.0 24.1 1.0
C26 A:3BJ602 4.1 25.0 1.0
CE2 A:TYR244 4.2 10.3 1.0
C A:PRO11 4.3 18.1 1.0
CB A:ALA240 4.4 12.7 1.0
CD1 A:ILE12 4.5 15.6 1.0
C A:ALA240 4.5 12.5 1.0
C25 A:3BJ602 4.6 23.9 1.0
CB A:ILE12 4.6 17.9 1.0
CG A:ASN243 4.6 14.8 1.0
CA A:ILE12 4.6 17.7 1.0
CD2 A:LEU241 4.7 12.6 1.0
CE1 A:TYR244 4.7 9.9 1.0
O A:ILE12 4.7 17.1 1.0
CD1 A:ILE273 4.9 16.4 1.0
CA A:ALA240 5.0 13.9 1.0

Reference:

X.Li, M.T.Hilgers, M.Stidham, V.Brown-Driver, K.J.Shaw, J.Finn. Discovery and Sar of A Novel Series of Pyrimidine Antibacterials Targeting Methionyl-Trna Synthetase To Be Published.
Page generated: Fri Jul 26 00:45:28 2024

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