Magnesium in PDB 6p85: E.Coli Lpxd in Complex with Compound 3

All present enzymatic activity of E.Coli Lpxd in Complex with Compound 3:
2.3.1.191;

The structure of E.Coli Lpxd in Complex with Compound 3, PDB code: 6p85 was solved by X.Ma, S.Shia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.83 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.911, 98.911, 215.312, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 19.9

The binding sites of Magnesium atom in the E.Coli Lpxd in Complex with Compound 3 (pdb code 6p85). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the E.Coli Lpxd in Complex with Compound 3, PDB code: 6p85:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E.Coli Lpxd in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E.Coli Lpxd in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:23.4 occ:1.00 O B:HOH718 2.1 22.5 1.0 O C:HOH692 2.1 22.7 1.0 O C:HOH880 2.1 21.4 1.0 O A:HOH733 2.1 20.9 1.0 O A:HOH543 2.1 21.2 1.0 O B:HOH875 2.2 23.5 1.0 O A:HOH566 4.0 21.4 1.0 O C:HOH653 4.0 21.7 1.0 O B:HOH698 4.0 25.0 1.0 O A:HOH593 4.2 36.3 1.0 O B:HOH651 4.2 24.3 1.0 CD1 B:ILE254 4.3 29.7 1.0 O C:HOH667 4.3 31.8 1.0 O C:HOH664 4.3 20.9 1.0 O B:HOH621 4.3 51.9 1.0 O A:HOH559 4.3 22.7 1.0 O A:GLY252 4.4 26.6 1.0 O B:GLY252 4.4 25.1 1.0 O C:GLY252 4.4 25.2 1.0 CG1 A:ILE254 4.9 27.7 1.0 CG1 C:ILE254 4.9 23.5 1.0

Magnesium binding site 2 out of 2 in the E.Coli Lpxd in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E.Coli Lpxd in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:28.4 occ:1.00 O B:HOH713 2.0 29.8 1.0 O C:HOH652 2.0 25.6 1.0 OD1 A:ASN121 2.1 26.5 1.0 O A:HOH516 2.1 29.7 1.0 OD1 B:ASN121 2.2 26.7 1.0 OD1 C:ASN121 2.2 31.5 1.0 CG A:ASN121 3.2 28.7 1.0 CG B:ASN121 3.2 26.8 1.0 CG C:ASN121 3.3 32.9 1.0 ND2 A:ASN121 3.7 26.0 1.0 ND2 B:ASN121 3.7 26.7 1.0 ND2 C:ASN121 3.8 32.4 1.0 O A:SER103 4.2 25.9 1.0 O C:SER103 4.2 27.9 1.0 O B:SER103 4.2 30.7 1.0 O A:HOH747 4.3 44.7 1.0 O B:HOH888 4.3 41.7 1.0 CB A:ASN121 4.4 28.1 1.0 CB C:SER103 4.5 29.6 1.0 CB B:ASN121 4.5 26.0 1.0 CB C:ASN121 4.5 29.6 1.0 CB A:SER103 4.5 28.7 1.0 CB B:SER103 4.5 30.3 1.0 CA C:ASN121 4.9 28.8 1.0 CA A:ASN121 4.9 27.8 1.0 CA B:ASN121 4.9 28.8 1.0

X.Ma, R.Prathapam, C.Wartchow, B.Chie Leon, C.M.Ho, J.De Vicente, W.Han, M.Li, Y.Lu, S.Ramurthy, S.Shia, M.Steffek, T.Uehara. Structural and Biological Basis of Small Molecule Inhibition of Escherichia Coli Lpxd Acyltransferase Essential For Lipopolysaccharide Biosynthesis. Acs Infect Dis. 2019.
ISSN: ESSN 2373-8227
PubMed: 31402665
DOI: 10.1021/ACSINFECDIS.9B00127