Zinc in PDB 7a63: Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form)

All present enzymatic activity of Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form):
3.5.2.6;

The structure of Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form), PDB code: 7a63 was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.65 / 1.57
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.3, 105.3, 98.099, 90, 90, 120
R / Rfree (%)	16.9 / 19.3

The binding sites of Zinc atom in the Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form) (pdb code 7a63). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form), PDB code: 7a63:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.7 occ:1.00 O A:HOH423 1.9 24.3 1.0 NE2 A:HIS160 2.0 22.7 1.0 NE2 A:HIS84 2.1 24.0 1.0 ND1 A:HIS86 2.1 21.6 1.0 CD2 A:HIS160 2.9 23.9 1.0 HB2 A:HIS86 2.9 26.2 1.0 CE1 A:HIS84 3.0 26.0 1.0 HD2 A:HIS160 3.0 28.7 1.0 CD2 A:HIS84 3.0 24.2 1.0 CE1 A:HIS86 3.0 24.4 1.0 CG A:HIS86 3.1 19.2 1.0 CE1 A:HIS160 3.1 26.4 1.0 HE1 A:HIS84 3.2 31.2 1.0 HE1 A:HIS86 3.2 29.3 1.0 HD2 A:HIS84 3.2 29.1 1.0 HD2 A:HIS89 3.3 28.1 1.0 O62 A:R3N307 3.4 30.6 1.0 HE1 A:HIS160 3.4 31.7 1.0 CB A:HIS86 3.4 21.8 1.0 O32 A:R3N307 3.5 29.7 1.0 ZN A:ZN302 3.6 27.0 1.0 HB3 A:HIS86 3.6 26.2 1.0 H9 A:R3N307 3.6 36.7 1.0 CD2 A:HIS89 4.0 23.4 1.0 OD1 A:ASP88 4.1 23.0 1.0 ND1 A:HIS84 4.1 23.0 1.0 CG A:HIS160 4.1 21.9 1.0 CG A:HIS84 4.1 21.9 1.0 NE2 A:HIS86 4.2 24.0 1.0 NE2 A:HIS89 4.2 23.6 1.0 ND1 A:HIS160 4.2 24.9 1.0 N4 A:R3N307 4.2 31.5 1.0 CD2 A:HIS86 4.2 21.5 1.0 H11 A:R3N307 4.3 40.3 1.0 HG A:SER185 4.4 34.8 1.0 HG23 A:THR161 4.4 29.2 1.0 HE2 A:PHE124 4.4 58.5 1.0 C31 A:R3N307 4.4 30.5 1.0 C61 A:R3N307 4.7 31.4 1.0 C3 A:R3N307 4.7 30.2 1.0 OD2 A:ASP88 4.8 25.3 1.0 HB2 A:SER185 4.8 34.4 1.0 HD1 A:HIS84 4.8 27.6 1.0 CG A:ASP88 4.9 26.2 1.0 CA A:HIS86 4.9 21.8 1.0 H A:HIS86 4.9 25.9 1.0 HZ A:PHE124 4.9 43.8 1.0 HE2 A:HIS86 4.9 28.8 1.0 C62 A:R3N307 5.0 33.6 1.0 HG21 A:THR161 5.0 29.2 1.0 HD1 A:HIS160 5.0 29.9 1.0 H2 A:R3N307 5.0 35.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:27.0 occ:1.00 O A:HOH423 2.1 24.3 1.0 NE2 A:HIS225 2.1 29.6 1.0 OD2 A:ASP88 2.1 25.3 1.0 NE2 A:HIS89 2.1 23.6 1.0 O32 A:R3N307 2.2 29.7 1.0 N4 A:R3N307 2.3 31.5 1.0 C3 A:R3N307 3.0 30.2 1.0 C31 A:R3N307 3.0 30.5 1.0 CG A:ASP88 3.0 26.2 1.0 CE1 A:HIS225 3.1 27.2 1.0 CE1 A:HIS89 3.1 24.5 1.0 CD2 A:HIS225 3.1 33.0 1.0 CD2 A:HIS89 3.2 23.4 1.0 HE1 A:HIS225 3.2 32.6 1.0 HE1 A:HIS89 3.2 29.4 1.0 OD1 A:ASP88 3.3 23.0 1.0 HD2 A:HIS225 3.3 39.7 1.0 C5 A:R3N307 3.3 30.6 1.0 HD2 A:HIS89 3.3 28.1 1.0 H5 A:R3N307 3.4 36.8 1.0 H2 A:R3N307 3.5 35.3 1.0 ZN A:ZN301 3.6 25.7 1.0 HG A:SER185 3.8 34.8 1.0 HE1 A:HIS84 3.8 31.2 1.0 C6 A:R3N307 3.9 29.4 1.0 O62 A:R3N307 3.9 30.6 1.0 ND1 A:HIS225 4.2 31.0 1.0 ND1 A:HIS89 4.2 24.6 1.0 O31 A:R3N307 4.2 29.8 1.0 CG A:HIS225 4.2 31.6 1.0 CG A:HIS89 4.3 25.6 1.0 HB2 A:ASP88 4.3 26.5 1.0 CB A:ASP88 4.3 22.1 1.0 NE2 A:HIS84 4.4 24.0 1.0 H15 A:R3N307 4.4 55.4 1.0 CE1 A:HIS84 4.4 26.0 1.0 C2 A:R3N307 4.4 34.3 1.0 C61 A:R3N307 4.5 31.4 1.0 OG A:SER185 4.6 29.0 1.0 NE2 A:HIS160 4.6 22.7 1.0 H9 A:R3N307 4.6 36.7 1.0 H14 A:R3N307 4.6 55.4 1.0 HZ3 A:TRP17 4.7 36.3 1.0 HE1 A:HIS160 4.7 31.7 1.0 HH2 A:TRP17 4.8 35.9 1.0 HB3 A:ASP88 4.9 26.5 1.0 S1 A:R3N307 4.9 33.8 1.0 HB2 A:HIS86 4.9 26.2 1.0 C15 A:R3N307 4.9 46.2 1.0 H11 A:R3N307 4.9 40.3 1.0 HD1 A:HIS89 5.0 29.5 1.0 HB2 A:PRO224 5.0 31.5 1.0 HD1 A:HIS225 5.0 37.2 1.0 H111 A:R3N307 5.0 41.2 1.0 CE1 A:HIS160 5.0 26.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of L1 with Hydrolyzed Faropenem (Imine, Ring-Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:42.2 occ:0.23 NE2 A:HIS29 1.8 66.1 0.5 NE2 A:HIS29 1.9 66.9 0.5 CE1 A:HIS29 2.6 67.8 0.5 CE1 A:HIS29 2.7 68.0 0.5 HE1 A:HIS29 2.8 81.3 0.5 HE1 A:HIS29 2.9 81.6 0.5 CD2 A:HIS29 2.9 60.3 0.5 CD2 A:HIS29 2.9 60.2 0.5 HB3 A:ASP28 3.0 52.7 1.0 O A:HOH409 3.1 27.9 0.5 HD2 A:HIS29 3.2 72.3 0.5 HD2 A:HIS29 3.2 72.2 0.5 ND1 A:HIS29 3.8 61.3 0.5 ND1 A:HIS29 3.8 60.7 0.5 CB A:ASP28 3.9 43.9 1.0 CG A:HIS29 3.9 52.1 0.5 CG A:HIS29 4.0 51.0 0.5 OD2 A:ASP28 4.0 48.5 1.0 HB2 A:ASP28 4.2 52.7 1.0 CG A:ASP28 4.4 56.3 1.0 HD1 A:HIS29 4.5 73.5 0.5 HD1 A:HIS29 4.6 72.8 0.5 HG1 A:THR172 4.6 66.7 1.0 OG1 A:THR172 4.8 55.6 1.0 O A:ASP28 4.8 51.0 1.0 C A:ASP28 4.9 44.0 1.0 CA A:ASP28 5.0 48.2 1.0

A.Lucic, P.Hinchliffe, T.R.Malla, C.L.Tooke, J.Brem, K.Calvopina, C.T.Lohans, P.Rabe, M.A.Mcdonough, T.Armistead, A.M.Orville, J.Spencer, C.J.Schofield. Faropenem Reacts with Serine and Metallo-Beta-Lactamases to Give Multiple Products Eur.J.Med.Chem. 2021.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2021.113257