Magnesium in PDB 7uy4: Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp

All present enzymatic activity of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp:
2.7.7.47;

The structure of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp, PDB code: 7uy4 was solved by S.M.Reeve, R.E.Lee, N.Das, S.Jayaraman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.043, 106.958, 114.148, 90, 90, 90
R / Rfree (%)	17.8 / 22.1

The binding sites of Magnesium atom in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp (pdb code 7uy4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp, PDB code: 7uy4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:36.3 occ:1.00 OD1 A:ASP45 2.0 28.1 1.0 OD2 A:ASP43 2.1 31.7 1.0 OE1 A:GLU83 2.1 34.3 1.0 O A:HOH449 2.2 34.7 1.0 O2A A:ANP301 2.2 41.6 1.0 O11 A:SMI302 2.2 38.7 1.0 CD A:GLU83 2.9 40.8 1.0 CG A:ASP45 3.0 37.3 1.0 CG A:ASP43 3.1 34.2 1.0 PA A:ANP301 3.2 56.9 1.0 OE2 A:GLU83 3.3 38.0 1.0 OD2 A:ASP45 3.4 34.4 1.0 OD1 A:ASP43 3.4 35.4 1.0 O5' A:ANP301 3.5 50.7 1.0 C11 A:SMI302 3.6 43.9 1.0 MG A:MG304 3.7 34.1 1.0 O A:HOH431 3.7 39.5 1.0 N10 A:SMI302 3.8 40.6 1.0 O A:HOH433 3.9 36.5 1.0 O1A A:ANP301 3.9 53.1 1.0 C10 A:SMI302 4.0 38.4 1.0 CG A:GLU83 4.1 37.4 1.0 CB A:GLU83 4.1 34.0 1.0 CB A:ASP45 4.2 26.6 1.0 C12 A:SMI302 4.4 35.9 1.0 CB A:ASP43 4.4 32.0 1.0 O A:HOH480 4.5 40.2 1.0 C1M A:SMI302 4.6 36.8 1.0 O3A A:ANP301 4.6 44.8 1.0 O2B A:SMI302 4.6 42.6 1.0 CA A:ASP45 4.8 28.0 1.0 C5' A:ANP301 4.9 44.0 1.0 O2B A:ANP301 4.9 38.6 1.0 O1G A:ANP301 4.9 37.9 1.0

Magnesium binding site 2 out of 4 in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:34.1 occ:1.00 O2B A:ANP301 2.0 38.6 1.0 OD2 A:ASP45 2.0 34.4 1.0 OD1 A:ASP43 2.1 35.4 1.0 O A:HOH429 2.1 35.5 1.0 O1G A:ANP301 2.2 37.9 1.0 O2A A:ANP301 2.2 41.6 1.0 CG A:ASP45 3.0 37.3 1.0 CG A:ASP43 3.1 34.2 1.0 PB A:ANP301 3.1 40.6 1.0 PG A:ANP301 3.3 37.5 1.0 PA A:ANP301 3.3 56.9 1.0 OD1 A:ASP45 3.4 28.1 1.0 O3A A:ANP301 3.5 44.8 1.0 N3B A:ANP301 3.5 41.9 1.0 OD2 A:ASP43 3.6 31.7 1.0 MG A:MG303 3.7 36.3 1.0 OG A:SER32 3.9 32.1 1.0 O A:ASP43 3.9 30.4 1.0 O A:HOH480 4.0 40.2 1.0 O3G A:ANP301 4.0 31.0 1.0 N A:SER32 4.1 35.1 1.0 O A:HOH431 4.1 39.5 1.0 O1A A:ANP301 4.1 53.1 1.0 N A:ASP43 4.2 31.4 1.0 O A:HOH411 4.2 32.7 1.0 CB A:ASP45 4.4 26.6 1.0 C A:ASP43 4.4 35.8 1.0 CB A:ASP43 4.4 32.0 1.0 O1B A:ANP301 4.5 47.3 1.0 O2G A:ANP301 4.5 36.5 1.0 CA A:ASP43 4.5 34.8 1.0 O5' A:ANP301 4.6 50.7 1.0 CB A:SER32 4.6 37.5 1.0 CA A:GLY31 4.7 32.1 1.0 O A:HOH449 4.8 34.7 1.0 C A:GLY31 4.9 33.4 1.0 N A:ASP45 4.9 33.2 1.0 O11 A:SMI302 4.9 38.7 1.0 CA A:SER32 5.0 35.2 1.0

Magnesium binding site 3 out of 4 in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:45.7 occ:1.00 OD1 B:ASP43 1.9 41.6 1.0 O2B B:ANP301 2.0 45.6 1.0 O B:HOH413 2.1 35.2 1.0 OD2 B:ASP45 2.1 37.0 1.0 O1G B:ANP301 2.1 41.8 1.0 O2A B:ANP301 2.3 44.8 1.0 CG B:ASP43 3.0 39.1 1.0 CG B:ASP45 3.0 43.1 1.0 PB B:ANP301 3.2 47.4 1.0 OD1 B:ASP45 3.3 36.0 1.0 PA B:ANP301 3.4 51.8 1.0 PG B:ANP301 3.4 45.3 1.0 O3A B:ANP301 3.5 42.8 1.0 OD2 B:ASP43 3.5 40.7 1.0 MG B:MG304 3.6 44.7 1.0 N3B B:ANP301 3.7 45.7 1.0 O B:ASP43 3.8 37.2 1.0 OG B:SER32 3.9 39.1 1.0 O B:HOH417 4.0 41.1 1.0 O1A B:ANP301 4.0 46.7 1.0 O B:HOH419 4.0 38.5 1.0 N B:ASP43 4.1 40.5 1.0 O B:HOH504 4.1 51.0 1.0 N B:SER32 4.1 37.6 1.0 O3G B:ANP301 4.1 45.3 1.0 CB B:ASP43 4.2 43.7 1.0 C B:ASP43 4.3 41.2 1.0 CB B:ASP45 4.3 37.8 1.0 CA B:ASP43 4.4 38.9 1.0 O2G B:ANP301 4.5 46.6 1.0 O1B B:ANP301 4.5 48.2 1.0 CB B:SER32 4.6 37.6 1.0 CA B:GLY31 4.6 40.5 1.0 O5' B:ANP301 4.7 49.5 1.0 O B:HOH479 4.8 41.8 1.0 N B:ASP45 4.8 37.2 1.0 O11 B:SMI302 4.9 47.3 1.0 C B:GLY31 4.9 38.5 1.0

Magnesium binding site 4 out of 4 in the Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Aminoglycoside-Modifying Enzyme Ant-3,9 in Complex with Spectinomycin and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:44.7 occ:1.00 O B:HOH479 2.0 41.8 1.0 OD2 B:ASP43 2.1 40.7 1.0 OD1 B:ASP45 2.1 36.0 1.0 O11 B:SMI302 2.2 47.3 1.0 OE1 B:GLU83 2.2 41.8 1.0 O2A B:ANP301 2.2 44.8 1.0 CD B:GLU83 3.0 39.9 1.0 CG B:ASP45 3.1 43.1 1.0 CG B:ASP43 3.1 39.1 1.0 PA B:ANP301 3.1 51.8 1.0 OE2 B:GLU83 3.3 43.0 1.0 OD1 B:ASP43 3.4 41.6 1.0 C11 B:SMI302 3.4 48.2 1.0 OD2 B:ASP45 3.5 37.0 1.0 O1A B:ANP301 3.6 46.7 1.0 O5' B:ANP301 3.6 49.5 1.0 O B:HOH417 3.6 41.1 1.0 N10 B:SMI302 3.6 43.5 1.0 MG B:MG303 3.6 45.7 1.0 C10 B:SMI302 3.8 43.1 1.0 CG B:GLU83 4.2 41.9 1.0 O B:HOH496 4.2 38.1 1.0 CB B:GLU83 4.2 35.7 1.0 CB B:ASP45 4.3 37.8 1.0 C12 B:SMI302 4.4 44.2 1.0 CB B:ASP43 4.4 43.7 1.0 C1M B:SMI302 4.5 40.7 1.0 O3A B:ANP301 4.6 42.8 1.0 O2B B:SMI302 4.6 40.7 1.0 O B:HOH504 4.7 51.0 1.0 O2B B:ANP301 4.8 45.6 1.0 O1G B:ANP301 4.9 41.8 1.0 C5' B:ANP301 4.9 53.7 1.0 CA B:ASP45 4.9 37.6 1.0

N.Das, S.M.Reeve, R.E.Lee. Characterization of the Spectinomycin Deactivating Enzyme Ant-3,9 To Be Published.