Zinc in PDB 6s0h: Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem

All present enzymatic activity of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem:
3.5.2.6;

The structure of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem, PDB code: 6s0h was solved by K.M.Zak, C.Softley, M.Kolonko, M.Sattler, G.M.Popowicz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.51 / 2.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.430, 72.318, 62.933, 90.00, 111.72, 90.00
R / Rfree (%)	22.8 / 26.3

The binding sites of Zinc atom in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem (pdb code 6s0h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem, PDB code: 6s0h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:66.4 occ:1.00 ND1 A:HIS79 1.9 52.1 1.0 NE2 A:HIS139 2.0 94.0 1.0 NE2 A:HIS77 2.3 66.8 1.0 O4 A:KQ8310 2.4 0.7 1.0 C12 A:KQ8310 2.7 93.2 1.0 O3 A:KQ8310 2.7 90.1 1.0 CG A:HIS79 2.9 56.2 1.0 CE1 A:HIS79 2.9 55.1 1.0 CE1 A:HIS139 2.9 93.5 1.0 CD2 A:HIS139 3.0 89.8 1.0 CD2 A:HIS77 3.0 68.0 1.0 CB A:HIS79 3.2 58.3 1.0 CE1 A:HIS77 3.4 69.6 1.0 N3 A:KQ8310 3.7 85.1 1.0 C9 A:KQ8310 3.9 90.6 1.0 CD2 A:HIS79 4.0 56.0 1.0 NE2 A:HIS79 4.0 55.6 1.0 ND1 A:HIS139 4.1 86.0 1.0 CG A:HIS139 4.1 82.7 1.0 SG A:CYS158 4.1 65.6 1.0 ZN A:ZN302 4.2 69.5 1.0 OD1 A:ASP81 4.3 83.1 1.0 CG A:HIS77 4.3 66.9 1.0 CB A:CYS158 4.3 67.2 1.0 ND1 A:HIS77 4.4 64.0 1.0 C8 A:KQ8310 4.5 90.4 1.0 CG2 A:THR140 4.5 81.5 1.0 CA A:HIS79 4.6 56.8 1.0 C6 A:KQ8310 4.7 83.5 1.0 O A:HOH409 4.8 52.1 1.0 C7 A:KQ8310 4.8 77.4 1.0 OD2 A:ASP81 4.9 87.2 1.0 CG A:ASP81 4.9 75.5 1.0 O2 A:KQ8310 4.9 78.6 1.0 N A:HIS79 5.0 57.8 1.0 O1 A:KQ8310 5.0 65.9 1.0

Zinc binding site 2 out of 4 in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:69.5 occ:1.00 O3 A:KQ8310 1.9 90.1 1.0 OD2 A:ASP81 2.0 87.2 1.0 NE2 A:HIS197 2.1 66.4 1.0 SG A:CYS158 2.4 65.6 1.0 O A:KQ8310 2.4 79.0 1.0 N3 A:KQ8310 3.0 85.1 1.0 C7 A:KQ8310 3.0 77.4 1.0 C12 A:KQ8310 3.0 93.2 1.0 CE1 A:HIS197 3.0 63.5 1.0 CG A:ASP81 3.1 75.5 1.0 C6 A:KQ8310 3.1 83.5 1.0 CD2 A:HIS197 3.1 69.4 1.0 OD1 A:ASP81 3.5 83.1 1.0 CB A:CYS158 3.7 67.2 1.0 C8 A:KQ8310 3.8 90.4 1.0 C5 A:KQ8310 3.8 86.8 1.0 O4 A:KQ8310 3.9 0.7 1.0 C9 A:KQ8310 3.9 90.6 1.0 C13 A:KQ8310 4.0 86.7 1.0 O1 A:KQ8310 4.1 65.9 1.0 ND1 A:HIS197 4.2 61.9 1.0 ZN A:ZN301 4.2 66.4 1.0 CG A:HIS197 4.2 65.4 1.0 CB A:ASP81 4.3 68.5 1.0 C11 A:KQ8310 4.4 90.3 1.0 CB A:SER196 4.4 57.5 1.0 C10 A:KQ8310 4.6 87.9 1.0 NE2 A:HIS139 4.6 94.0 1.0 CA A:CYS158 4.7 66.8 1.0 OG A:SER196 4.7 50.9 1.0 CE1 A:HIS139 4.8 93.5 1.0 O2 A:KQ8310 4.8 78.6 1.0 CD A:LYS33 4.8 73.8 1.0 CE1 A:HIS77 4.9 69.6 1.0 NE2 A:HIS77 4.9 66.8 1.0 NZ A:LYS161 5.0 74.3 1.0

Zinc binding site 3 out of 4 in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:65.4 occ:1.00 NE2 B:HIS139 1.9 78.8 1.0 O3 B:KQ8404 2.1 81.3 1.0 NE2 B:HIS77 2.1 57.1 1.0 ND1 B:HIS79 2.2 53.8 1.0 C12 B:KQ8404 2.8 88.3 1.0 O4 B:KQ8404 2.8 91.5 1.0 CE1 B:HIS139 2.9 84.1 1.0 CD2 B:HIS139 3.0 73.7 1.0 CD2 B:HIS77 3.0 55.4 1.0 CG B:HIS79 3.1 57.4 1.0 CE1 B:HIS77 3.2 56.6 1.0 CE1 B:HIS79 3.2 57.3 1.0 CB B:HIS79 3.3 63.5 1.0 N3 B:KQ8404 3.7 92.3 1.0 SG B:CYS158 3.9 67.3 1.0 ZN B:ZN403 3.9 64.7 1.0 ND1 B:HIS139 4.0 80.2 1.0 CB B:CYS158 4.0 64.3 1.0 CG B:HIS139 4.1 72.1 1.0 OD1 B:ASP81 4.1 78.3 1.0 CG B:HIS77 4.2 56.3 1.0 C9 B:KQ8404 4.2 88.2 1.0 CD2 B:HIS79 4.3 57.2 1.0 ND1 B:HIS77 4.3 56.3 1.0 NE2 B:HIS79 4.3 55.6 1.0 O2 B:KQ8404 4.4 76.3 1.0 O B:KQ8404 4.5 71.5 1.0 C8 B:KQ8404 4.6 95.4 1.0 C6 B:KQ8404 4.6 89.6 1.0 C7 B:KQ8404 4.6 77.9 1.0 CG2 B:THR140 4.7 73.3 1.0 CA B:HIS79 4.7 63.3 1.0 OD2 B:ASP81 4.7 75.4 1.0 CG B:ASP81 4.8 72.8 1.0 C10 B:KQ8404 5.0 83.0 1.0

Zinc binding site 4 out of 4 in the Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Metallo-Beta-Lactamase Complexed with Hydrolysed Doripenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:64.7 occ:1.00 OD2 B:ASP81 2.0 75.4 1.0 NE2 B:HIS197 2.1 80.5 1.0 SG B:CYS158 2.4 67.3 1.0 O B:KQ8404 2.5 71.5 1.0 N3 B:KQ8404 2.9 92.3 1.0 CG B:ASP81 3.0 72.8 1.0 CE1 B:HIS197 3.1 84.9 1.0 CD2 B:HIS197 3.1 79.5 1.0 C6 B:KQ8404 3.1 89.6 1.0 O3 B:KQ8404 3.2 81.3 1.0 C7 B:KQ8404 3.2 77.9 1.0 OD1 B:ASP81 3.4 78.3 1.0 CB B:CYS158 3.6 64.3 1.0 ZN B:ZN402 3.9 65.4 1.0 C12 B:KQ8404 3.9 88.3 1.0 C8 B:KQ8404 4.0 95.4 1.0 C5 B:KQ8404 4.0 96.2 1.0 ND1 B:HIS197 4.2 78.6 1.0 O2 B:KQ8404 4.2 76.3 1.0 C13 B:KQ8404 4.2 97.4 1.0 CG B:HIS197 4.2 76.6 1.0 CB B:ASP81 4.3 68.1 1.0 CB B:SER196 4.4 63.0 1.0 C9 B:KQ8404 4.4 88.2 1.0 O1 B:KQ8404 4.5 74.2 1.0 NE2 B:HIS139 4.6 78.8 1.0 CA B:CYS158 4.6 64.7 1.0 OG B:SER196 4.6 66.5 1.0 C10 B:KQ8404 4.7 83.0 1.0 O4 B:KQ8404 4.7 91.5 1.0 CE1 B:HIS77 4.7 56.6 1.0 CE1 B:HIS139 4.8 84.1 1.0 NE2 B:HIS77 4.8 57.1 1.0 CD B:LYS33 4.8 73.1 1.0 C11 B:KQ8404 4.9 84.2 1.0 CE B:LYS33 5.0 73.3 1.0

C.Softley, K.M.Zak, R.Fino, M.Kolonko, R.Mejdi-Nitiu, H.Meyer, M.Sattler, G.M.Popowicz. Structure and Molecular Recognition Mechanism of Imp-13 B-Lactamase To Be Published.