Magnesium in PDB 4ben: R39-Imipenem Acyl-Enzyme Crystal Structure

All present enzymatic activity of R39-Imipenem Acyl-Enzyme Crystal Structure:
3.4.16.4;

The structure of R39-Imipenem Acyl-Enzyme Crystal Structure, PDB code: 4ben was solved by D.Van Elder, E.Sauvage, R.Herman, F.Kerff, M.Rocaboy, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.72 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.623, 91.911, 106.924, 90.00, 94.50, 90.00
R / Rfree (%)	18.719 / 23.441

The binding sites of Magnesium atom in the R39-Imipenem Acyl-Enzyme Crystal Structure (pdb code 4ben). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the R39-Imipenem Acyl-Enzyme Crystal Structure, PDB code: 4ben:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the R39-Imipenem Acyl-Enzyme Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of R39-Imipenem Acyl-Enzyme Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg610 b:12.0 occ:1.00 O A:GLU188 2.0 32.9 1.0 NE2 A:HIS247 2.0 36.4 1.0 OE2 A:GLU251 2.1 45.2 1.0 CE1 A:HIS247 2.9 40.4 1.0 CD A:GLU251 3.0 47.6 1.0 CD2 A:HIS247 3.1 37.8 1.0 C A:GLU188 3.2 34.5 1.0 OE1 A:GLU251 3.5 47.4 1.0 CA A:GLY189 4.0 36.6 1.0 N A:GLY189 4.0 35.4 1.0 ND1 A:HIS247 4.1 39.8 1.0 CG A:HIS247 4.2 36.1 1.0 CA A:GLU188 4.2 33.8 1.0 O A:ALA186 4.3 31.3 1.0 CG A:GLU251 4.3 45.5 1.0 CB A:GLU188 4.3 34.1 1.0 C A:GLY189 4.5 36.7 1.0 N A:GLU188 4.6 31.9 1.0 N A:TYR190 4.8 35.8 1.0

Magnesium binding site 2 out of 4 in the R39-Imipenem Acyl-Enzyme Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of R39-Imipenem Acyl-Enzyme Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg611 b:36.2 occ:1.00 O A:HOH2228 2.6 42.9 1.0 O A:ALA402 2.8 41.0 1.0 O A:GLN463 3.1 55.1 1.0 ND1 A:HIS462 3.2 60.9 1.0 CB A:HIS462 3.5 55.4 1.0 CG A:HIS462 3.5 57.8 1.0 CG2 A:VAL406 3.6 44.1 1.0 C A:ALA402 3.7 41.4 1.0 N A:GLN463 3.9 56.7 1.0 CA A:ALA402 4.0 42.8 1.0 C A:GLN463 4.0 55.1 1.0 O A:GLU404 4.0 41.9 1.0 CE1 A:HIS462 4.1 62.5 1.0 CA A:HIS462 4.4 57.4 1.0 CB A:VAL406 4.5 42.0 1.0 C A:HIS462 4.5 56.6 1.0 CA A:GLN463 4.6 57.3 1.0 CD2 A:HIS462 4.6 59.3 1.0 CB A:ALA402 4.6 43.1 1.0 CD A:PRO465 4.6 52.8 1.0 O A:THR401 4.8 42.6 1.0 NE2 A:HIS462 4.9 62.0 1.0 N A:ALA403 4.9 41.0 1.0 N A:ALA464 4.9 54.4 1.0

Magnesium binding site 3 out of 4 in the R39-Imipenem Acyl-Enzyme Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of R39-Imipenem Acyl-Enzyme Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg610 b:13.8 occ:1.00 OE2 D:GLU251 1.9 43.4 1.0 O D:GLU188 2.1 32.7 1.0 NE2 D:HIS247 2.1 37.0 1.0 CD D:GLU251 2.9 45.0 1.0 CE1 D:HIS247 3.0 41.4 1.0 OE1 D:GLU251 3.1 48.1 1.0 CD2 D:HIS247 3.2 36.7 1.0 C D:GLU188 3.3 34.7 1.0 N D:GLY189 4.2 35.0 1.0 CA D:GLY189 4.2 36.1 1.0 ND1 D:HIS247 4.2 39.2 1.0 CG D:GLU251 4.2 43.9 1.0 O D:ALA186 4.2 33.9 1.0 CG D:HIS247 4.3 36.6 1.0 CA D:GLU188 4.4 34.0 1.0 CB D:GLU188 4.5 35.8 1.0 N D:GLU188 4.6 32.6 1.0 C D:GLY189 4.6 36.6 1.0 N D:TYR190 4.9 35.4 1.0

Magnesium binding site 4 out of 4 in the R39-Imipenem Acyl-Enzyme Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of R39-Imipenem Acyl-Enzyme Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg611 b:33.2 occ:1.00 ND1 D:HIS462 2.8 60.1 1.0 CG2 D:VAL406 3.6 40.3 1.0 CE1 D:HIS462 3.8 61.3 1.0 O D:HOH2252 3.8 51.8 1.0 CG D:HIS462 3.8 59.2 1.0 CB D:HIS462 3.9 58.7 1.0 O D:ALA402 4.4 44.8 1.0 CA D:HIS462 4.6 60.8 1.0 O D:GLN463 4.7 64.8 1.0 N D:GLN463 4.8 63.3 1.0 NE2 D:HIS462 4.9 60.2 1.0 CB D:VAL406 4.9 40.9 1.0 CD2 D:HIS462 5.0 57.6 1.0

E.Sauvage, D.Van Elder, R.Herman, F.Kerff, R.F.Pratt, P.Charlier. Crystal Structures of R39-Imipenem Acyl-Enzyme. To Be Published.