Magnesium in PDB 6b89: E. Coli Lptb in Complex with Adp and Novobiocin

The structure of E. Coli Lptb in Complex with Adp and Novobiocin, PDB code: 6b89 was solved by J.M.May, M.D.Lazarus, D.J.Sherman, T.W.Owens, M.D.Mandler, D.K.Kahne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.03 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	190.319, 35.100, 63.050, 90.00, 91.52, 90.00
R / Rfree (%)	17.9 / 22

The binding sites of Magnesium atom in the E. Coli Lptb in Complex with Adp and Novobiocin (pdb code 6b89). 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 Lptb in Complex with Adp and Novobiocin, PDB code: 6b89:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Lptb in Complex with Adp and Novobiocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Lptb in Complex with Adp and Novobiocin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:8.7 occ:1.00 O A:HOH530 2.0 6.8 1.0 O A:HOH523 2.0 9.6 1.0 O2B A:ADP401 2.1 7.4 1.0 OG1 A:THR43 2.1 13.6 1.0 O A:HOH521 2.1 8.1 1.0 OE1 A:GLN85 2.1 20.1 1.0 CD A:GLN85 3.2 25.7 1.0 CB A:THR43 3.2 14.2 1.0 PB A:ADP401 3.2 10.2 1.0 O3B A:ADP401 3.5 7.7 1.0 NE2 A:GLN85 3.6 23.9 1.0 OE2 A:GLU163 3.6 22.4 1.0 O2A A:ADP401 3.9 11.7 1.0 N A:THR43 3.9 9.5 1.0 OD1 A:ASP162 4.0 14.1 1.0 CA A:THR43 4.1 13.3 1.0 O3A A:ADP401 4.1 7.7 1.0 CG2 A:THR43 4.3 15.3 1.0 OD2 A:ASP162 4.3 14.9 1.0 O1B A:ADP401 4.4 9.8 1.0 O B:HOH543 4.4 20.7 1.0 CG A:GLN85 4.5 20.4 1.0 CG A:ASP162 4.6 16.6 1.0 PA A:ADP401 4.6 11.8 1.0 CD A:GLU163 4.6 20.9 1.0 O A:HOH542 4.7 24.1 1.0 O A:HOH532 4.8 14.9 1.0 CB A:GLN85 4.8 18.0 1.0 CE A:LYS42 4.9 10.4 1.0 CB A:LYS42 4.9 9.2 1.0 O1A A:ADP401 5.0 8.9 1.0

Magnesium binding site 2 out of 2 in the E. Coli Lptb in Complex with Adp and Novobiocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Lptb in Complex with Adp and Novobiocin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:10.3 occ:1.00 O B:HOH518 2.0 7.9 1.0 OG1 B:THR43 2.0 11.0 1.0 OE1 B:GLN85 2.1 14.8 1.0 O1B B:ADP401 2.1 10.5 1.0 O B:HOH520 2.1 10.9 1.0 O B:HOH509 2.2 8.6 1.0 CD B:GLN85 3.1 14.5 1.0 CB B:THR43 3.2 10.3 1.0 PB B:ADP401 3.4 11.8 1.0 NE2 B:GLN85 3.6 14.1 1.0 O3B B:ADP401 3.6 11.8 1.0 OE2 B:GLU163 3.6 15.6 1.0 N B:THR43 3.9 11.0 1.0 O1A B:ADP401 4.0 13.8 1.0 OD1 B:ASP162 4.0 11.4 1.0 CA B:THR43 4.1 9.0 1.0 OD2 B:ASP162 4.1 16.0 1.0 O B:HOH535 4.2 21.4 1.0 O3A B:ADP401 4.3 13.9 1.0 CG2 B:THR43 4.3 11.0 1.0 O2B B:ADP401 4.4 13.2 1.0 CG B:GLN85 4.4 11.7 1.0 CG B:ASP162 4.5 15.2 1.0 CD B:GLU163 4.6 17.9 1.0 PA B:ADP401 4.7 13.8 1.0 CB B:GLN85 4.7 10.5 1.0 CG B:GLU163 4.8 18.8 1.0 CB B:LYS42 4.9 8.9 1.0 O B:HOH501 4.9 16.9 1.0 C B:LYS42 5.0 8.0 1.0

J.M.May, T.W.Owens, M.D.Mandler, B.W.Simpson, M.B.Lazarus, D.J.Sherman, R.M.Davis, S.Okuda, W.Massefski, N.Ruiz, D.Kahne. The Antibiotic Novobiocin Binds and Activates the Atpase That Powers Lipopolysaccharide Transport. J. Am. Chem. Soc. V. 139 17221 2017.
ISSN: ESSN 1520-5126
PubMed: 29135241
DOI: 10.1021/JACS.7B07736