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Magnesium in PDB 4qre: Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone

Enzymatic activity of Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone

All present enzymatic activity of Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone:
6.1.1.10;

Protein crystallography data

The structure of Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone, PDB code: 4qre was solved by M.T.Hilgers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.45 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.932, 75.672, 119.160, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone (pdb code 4qre). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone, PDB code: 4qre:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4qre

Go back to Magnesium Binding Sites List in 4qre
Magnesium binding site 1 out of 2 in the Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:19.0
occ:1.00
 O A:HOH1213 2.3 20.0 1.0
O A:HOH1211 2.4 16.3 1.0
O A:HOH726 2.5 22.3 1.0
O A:HOH1212 2.5 16.7 1.0
OG1 A:THR5 2.5 12.8 1.0
O A:HOH852 2.6 13.8 1.0
CB A:THR5 3.7 13.2 1.0
O A:LYS260 4.0 15.2 1.0
CG2 A:THR5 4.0 14.5 1.0
N A:THR5 4.1 13.9 1.0
O A:HOH904 4.3 23.9 1.0
CA A:THR5 4.4 12.8 1.0
O A:HOH830 4.4 17.1 1.0
O A:HOH721 4.4 14.9 1.0
O A:THR5 4.5 12.4 1.0
O A:HOH784 4.5 16.2 1.0
OE1 A:GLU4 4.6 24.9 1.0
O A:HOH846 4.7 29.6 1.0
O A:HOH1037 4.8 38.4 1.0
C A:THR5 4.8 12.6 1.0
O A:HOH1214 4.8 31.8 1.0
O A:HOH873 4.9 22.4 1.0

Magnesium binding site 2 out of 2 in 4qre

Go back to Magnesium Binding Sites List in 4qre
Magnesium binding site 2 out of 2 in the Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Methionyl-Trna Synthetase in Complex with 1-(4-{4-[(1H- Benzimidazol-2-Ylmethyl)Amino]-6-(4,5-Dimethoxy-2-Methylphenoxy) Pyrimidin-2-Yl}Piperazin-1-Yl)Ethanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:18.9
occ:1.00
 O A:HOH1270 1.9 21.6 1.0
O2B A:ATP602 2.0 20.0 1.0
O2A A:ATP602 2.0 22.0 1.0
O A:HOH1269 2.1 24.9 1.0
OG A:SER310 2.1 21.4 1.0
O2G A:ATP602 2.2 25.4 1.0
PB A:ATP602 3.1 21.9 1.0
PA A:ATP602 3.3 20.3 1.0
CB A:SER310 3.3 22.1 1.0
PG A:ATP602 3.5 26.8 1.0
O3A A:ATP602 3.5 20.5 1.0
O3B A:ATP602 3.7 24.1 1.0
NZ A:LYS308 3.9 24.0 1.0
O A:HOH1228 3.9 21.3 1.0
CE A:LYS308 4.0 22.5 1.0
O A:HOH1278 4.1 30.2 1.0
CA A:SER310 4.1 20.8 1.0
O A:MET309 4.3 18.6 1.0
O3G A:ATP602 4.3 25.9 1.0
O5' A:ATP602 4.3 19.5 1.0
O1A A:ATP602 4.4 19.0 1.0
O A:HOH1275 4.4 26.5 1.0
N7 A:ATP602 4.4 16.9 1.0
O1B A:ATP602 4.5 22.1 1.0
O1G A:ATP602 4.6 27.2 1.0
CD A:LYS308 4.7 23.4 1.0
O A:HOH1274 4.7 27.1 1.0
C8 A:ATP602 4.8 17.3 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: Mon Aug 11 22:34:23 2025

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