Magnesium in PDB 5ze6: Crystal Structure of Octaprenyl Pyrophosphate Synthase From Escherichia Coli with Bph-981

All present enzymatic activity of Crystal Structure of Octaprenyl Pyrophosphate Synthase From Escherichia Coli with Bph-981:
2.5.1.90;

The structure of Crystal Structure of Octaprenyl Pyrophosphate Synthase From Escherichia Coli with Bph-981, PDB code: 5ze6 was solved by X.Han, W.D.Liu, Y.Y.Zheng, T.P.Ko, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.032, 111.999, 133.822, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 26.4

The binding sites of Magnesium atom in the Crystal Structure of Octaprenyl Pyrophosphate Synthase From Escherichia Coli with Bph-981 (pdb code 5ze6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Octaprenyl Pyrophosphate Synthase From Escherichia Coli with Bph-981, PDB code: 5ze6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Octaprenyl Pyrophosphate Synthase From Escherichia Coli with Bph-981


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Octaprenyl Pyrophosphate Synthase From Escherichia Coli with Bph-981 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:38.4 occ:1.00 OD1 B:ASP84 2.3 32.4 1.0 O B:HOH504 2.3 28.2 1.0 OD2 B:ASP88 2.5 35.4 1.0 O B:HOH502 2.5 22.0 1.0 OD1 B:ASP88 2.9 34.2 1.0 CG B:ASP88 3.0 29.3 1.0 CG B:ASP84 3.4 31.7 1.0 OE2 B:GLU146 3.5 47.4 1.0 OD2 B:ASP84 3.8 35.9 1.0 OE1 B:GLU146 4.0 37.9 1.0 CD B:GLU146 4.2 39.1 1.0 OAC B:HJX401 4.2 50.7 1.0 MG B:MG403 4.3 35.8 1.0 OE2 B:GLU233 4.4 38.5 1.0 CB B:ASP88 4.5 30.6 1.0 CAV B:HJX401 4.5 50.2 1.0 CB B:ASP84 4.6 30.2 1.0 O B:ASP84 4.7 28.2 1.0 NZ B:LYS235 4.7 57.4 1.0 OAB B:HJX401 4.7 54.7 1.0 CA B:ASP84 4.9 27.9 1.0 CE B:LYS235 4.9 51.4 1.0 CG1 B:VAL87 4.9 27.2 1.0 CD B:GLU233 4.9 42.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Octaprenyl Pyrophosphate Synthase From Escherichia Coli with Bph-981


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Octaprenyl Pyrophosphate Synthase From Escherichia Coli with Bph-981 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:35.8 occ:1.00 OD2 B:ASP84 2.1 35.9 1.0 O B:HOH502 2.4 22.0 1.0 OD2 B:ASP88 2.5 35.4 1.0 CG B:ASP84 3.2 31.7 1.0 CG B:ASP88 3.5 29.3 1.0 OD1 B:ASP84 3.7 32.4 1.0 CB B:ASP88 3.7 30.6 1.0 OAC B:HJX401 3.8 50.7 1.0 OG B:SER90 3.9 32.1 1.0 NH2 B:ARG93 4.1 27.1 1.0 O B:HOH529 4.2 37.3 1.0 OE1 B:GLU233 4.2 38.5 1.0 MG B:MG402 4.3 38.4 1.0 OD1 B:ASP85 4.3 26.3 1.0 CB B:ASP84 4.4 30.2 1.0 O B:ASP84 4.4 28.2 1.0 OD2 B:ASP229 4.5 50.9 1.0 OAD B:HJX401 4.5 46.3 1.0 O B:HOH530 4.6 28.9 1.0 OD1 B:ASP88 4.6 34.2 1.0 C B:ASP84 4.7 27.9 1.0 O B:HOH524 4.8 41.0 1.0 CAV B:HJX401 4.9 50.2 1.0 O B:HOH504 5.0 28.2 1.0 CB B:SER90 5.0 32.0 1.0

S.R.Malwal, L.Chen, H.Hicks, F.Qu, W.Liu, A.Shillo, W.X.Law, J.Zhang, N.Chandnani, X.Han, Y.Zheng, C.C.Chen, R.T.Guo, A.Abdelkhalek, M.N.Seleem, E.Oldfield. Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis. J.Med.Chem. V. 62 2564 2019.
ISSN: ISSN 0022-2623
PubMed: 30730737
DOI: 10.1021/ACS.JMEDCHEM.8B01878