Magnesium in PDB 8xbk: Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor

The structure of Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor, PDB code: 8xbk was solved by H.Cao, X.Zhang, Y.Ren, J.Wan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.80 / 2.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.115, 82.95, 275.921, 90, 90, 90
R / Rfree (%)	18.3 / 23.4

The structure of Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor (pdb code 8xbk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor, PDB code: 8xbk:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor


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 Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg409 b:57.1 occ:1.00 OD2 B:ASP118 2.1 38.5 1.0 O B:HOH602 2.7 55.1 1.0 OE2 B:GLU280 2.8 41.6 1.0 OD1 B:ASP121 3.0 45.7 1.0 CG B:ASP118 3.1 35.3 1.0 OD1 B:ASP118 3.6 35.3 1.0 CD B:GLU97 3.8 40.9 1.0 OE2 B:GLU97 3.8 54.0 1.0 CG B:GLU97 3.9 37.6 1.0 CG B:ASP121 3.9 52.2 1.0 CD B:GLU280 4.0 36.8 1.0 CA B:ASP121 4.0 43.7 1.0 CB B:ASP121 4.2 44.0 1.0 O B:HOH521 4.2 43.8 1.0 CB B:ASP118 4.4 33.6 1.0 OE1 B:GLU97 4.4 44.7 1.0 N B:GLY122 4.5 52.0 1.0 CG B:GLU280 4.7 33.2 1.0 C B:ASP121 4.8 46.3 1.0 OE1 B:GLU280 4.8 34.6 1.0 O1 B:EDO406 4.8 58.4 1.0 CB B:GLU97 4.9 32.9 1.0 N B:ASP121 4.9 40.4 1.0 O B:LEU120 5.0 30.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor


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 Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:58.4 occ:1.00 OE1 C:GLU97 1.8 55.0 1.0 OE2 C:GLU280 2.2 50.4 1.0 OD2 C:ASP118 2.3 51.9 1.0 CD C:GLU97 2.5 58.8 1.0 OD1 C:ASP121 2.6 50.8 1.0 OE2 C:GLU97 2.7 74.9 1.0 O C:HOH554 3.1 55.1 1.0 CG C:ASP118 3.3 48.5 1.0 CD C:GLU280 3.5 46.2 1.0 OD1 C:ASP118 3.6 46.4 1.0 CG C:ASP121 3.8 51.0 1.0 CG C:GLU97 4.0 51.6 1.0 OE1 C:GLU280 4.3 42.4 1.0 CB C:ASP121 4.4 51.3 1.0 CA C:ASP121 4.4 45.7 1.0 CG C:GLU280 4.4 40.4 1.0 CB C:GLU97 4.5 48.5 1.0 CB C:ASP118 4.6 41.4 1.0 OD2 C:ASP121 4.8 47.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Liver Fructose-1,6-Bisphosphatase Complexed with A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg405 b:61.5 occ:1.00 OD2 D:ASP118 2.2 54.3 1.0 OE2 D:GLU280 2.2 52.2 1.0 OE1 D:GLU97 3.0 71.2 1.0 OD2 D:ASP121 3.2 46.3 1.0 CG D:ASP118 3.3 44.7 1.0 CD D:GLU280 3.5 42.2 1.0 CB D:ASP121 3.6 50.0 1.0 CA D:ASP121 3.7 48.7 1.0 OD1 D:ASP118 3.7 47.7 1.0 O D:HOH540 3.8 50.0 1.0 CG D:ASP121 3.9 51.3 1.0 CD D:GLU97 4.1 69.1 1.0 OE1 D:GLU280 4.2 46.4 1.0 CG D:GLU280 4.4 43.4 1.0 CB D:ASP118 4.5 37.7 1.0 N D:GLY122 4.6 53.8 1.0 N D:ASP121 4.7 43.9 1.0 C D:ASP121 4.7 46.7 1.0 O D:HOH512 4.8 45.5 1.0 OE2 D:GLU97 4.9 68.7 1.0 CG D:GLU97 5.0 51.9 1.0 O D:LEU120 5.0 44.3 1.0

H.Cao, Z.Huang, Z.Liu, X.Zhang, Y.Ren, M.S.Hameed, L.Rao, N.P.Makunga, G.M.Dobrikov, J.Wan. Structure-Guided Design of Affinity/Covalent-Bond Dual-Driven Inhibitors Targeting the Amp Site of Fbpase J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.4C01886