Zinc in PDB 5b1u: Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem:
3.5.2.6;

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem, PDB code: 5b1u was solved by J.Wachino, Y.Arakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.58 / 1.57
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.030, 41.460, 45.440, 108.32, 102.78, 106.28
R / Rfree (%)	12.2 / 15.5

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem also contains other interesting chemical elements:

Sodium

(Na)

15 atoms

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem (pdb code 5b1u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem, PDB code: 5b1u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:3.9 occ:1.00 O A:HOH475 1.9 2.8 1.0 NE2 A:HIS72 2.1 3.1 1.0 NE2 A:HIS150 2.1 3.1 1.0 ND1 A:HIS74 2.1 3.1 1.0 CD2 A:HIS150 2.9 3.3 1.0 CE1 A:HIS74 3.0 3.1 1.0 CD2 A:HIS72 3.0 3.1 1.0 CE1 A:HIS72 3.0 3.2 1.0 CG A:HIS74 3.1 3.2 1.0 CE1 A:HIS150 3.2 3.1 1.0 O62 A:HIW321 3.2 7.8 1.0 O32 A:HIW321 3.5 5.3 1.0 CB A:HIS74 3.5 3.2 1.0 ZN A:ZN302 3.6 3.5 1.0 CD2 A:HIS77 4.0 2.7 1.0 ND1 A:HIS72 4.1 3.4 1.0 OD1 A:ASP76 4.1 4.4 1.0 C31 A:HIW321 4.1 7.8 1.0 CG A:HIS72 4.1 3.0 1.0 NE2 A:HIS74 4.1 3.3 1.0 CG A:HIS150 4.1 3.4 1.0 N4 A:HIW321 4.2 8.3 1.0 NE2 A:HIS77 4.2 2.7 1.0 ND1 A:HIS150 4.2 3.3 1.0 CD2 A:HIS74 4.2 3.5 1.0 C61 A:HIW321 4.4 10.5 1.0 C3 A:HIW321 4.4 8.7 1.0 C62 A:HIW321 4.4 12.5 1.0 NE2 A:GLN113 4.5 4.6 1.0 OD2 A:ASP76 4.8 4.6 1.0 CA A:HIS74 4.8 3.1 1.0 CG A:ASP76 4.9 4.3 1.0 OG A:SER175 5.0 2.1 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem


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 Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:3.5 occ:1.00 O A:HOH475 2.1 2.8 1.0 NE2 A:HIS215 2.1 3.0 1.0 OD2 A:ASP76 2.2 4.6 1.0 NE2 A:HIS77 2.2 2.7 1.0 O32 A:HIW321 2.2 5.3 1.0 N4 A:HIW321 2.4 8.3 1.0 C31 A:HIW321 2.9 7.8 1.0 C3 A:HIW321 3.0 8.7 1.0 CG A:ASP76 3.1 4.3 1.0 CE1 A:HIS215 3.1 2.9 1.0 CD2 A:HIS77 3.1 2.7 1.0 CD2 A:HIS215 3.1 3.0 1.0 CE1 A:HIS77 3.2 2.7 1.0 OD1 A:ASP76 3.3 4.4 1.0 ZN A:ZN301 3.6 3.9 1.0 C5 A:HIW321 3.6 10.0 1.0 O62 A:HIW321 4.0 7.8 1.0 C6 A:HIW321 4.0 10.2 1.0 O31 A:HIW321 4.1 8.3 1.0 ND1 A:HIS215 4.2 2.9 1.0 CG A:HIS77 4.2 2.7 1.0 CG A:HIS215 4.2 3.1 1.0 ND1 A:HIS77 4.3 2.7 1.0 OG A:SER175 4.3 2.1 0.5 NE2 A:HIS72 4.4 3.1 1.0 CB A:ASP76 4.4 3.6 1.0 C2 A:HIW321 4.4 10.4 1.0 CE1 A:HIS72 4.5 3.2 1.0 C61 A:HIW321 4.5 10.5 1.0 C1 A:HIW321 4.7 10.8 1.0 NE2 A:HIS150 4.7 3.1 1.0

J.Wachino, Y.Arakawa. Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Imipenem To Be Published.