Zinc in PDB 5b15: Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem

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

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem, PDB code: 5b15 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)	40.70 / 1.39
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.010, 40.920, 45.320, 107.57, 102.56, 107.01
R / Rfree (%)	13.6 / 15.8

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

Sodium

(Na)

7 atoms

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to Hydrolyzed Doripenem (pdb code 5b15). 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 Doripenem, PDB code: 5b15:
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 Doripenem


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 Doripenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:5.7 occ:1.00 O A:HOH425 1.8 7.2 1.0 NE2 A:HIS72 2.0 5.7 1.0 ND1 A:HIS74 2.1 5.6 1.0 NE2 A:HIS150 2.1 4.8 1.0 CE1 A:HIS74 3.0 5.6 1.0 CE1 A:HIS72 3.0 5.6 1.0 CD2 A:HIS150 3.0 5.1 1.0 CD2 A:HIS72 3.0 5.2 1.0 CG A:HIS74 3.1 5.2 1.0 CE1 A:HIS150 3.2 5.2 1.0 OAI A:DQM313 3.2 12.7 1.0 OAE A:DQM313 3.4 8.2 1.0 CB A:HIS74 3.5 5.3 1.0 ZN A:ZN302 3.6 6.1 1.0 CD2 A:HIS77 4.0 5.5 1.0 OD1 A:ASP76 4.1 5.9 1.0 ND1 A:HIS72 4.1 5.5 1.0 NE2 A:HIS74 4.1 5.5 1.0 CG A:HIS72 4.1 5.2 1.0 NE2 A:HIS77 4.2 5.9 1.0 CAR A:DQM313 4.2 10.2 1.0 CD2 A:HIS74 4.2 5.6 1.0 CG A:HIS150 4.2 4.8 1.0 NAN A:DQM313 4.3 11.3 1.0 ND1 A:HIS150 4.3 5.4 1.0 CAT A:DQM313 4.4 13.7 1.0 NE2 A:GLN113 4.4 7.5 1.0 CAA A:DQM313 4.5 15.6 1.0 CAS A:DQM313 4.5 11.7 1.0 OD2 A:ASP76 4.8 5.3 1.0 CA A:HIS74 4.9 4.8 1.0 CG A:ASP76 4.9 5.6 1.0

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


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 Doripenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:6.1 occ:1.00 O A:HOH425 2.1 7.2 1.0 OD2 A:ASP76 2.1 5.3 1.0 NE2 A:HIS215 2.1 6.2 1.0 NE2 A:HIS77 2.1 5.9 1.0 OAE A:DQM313 2.2 8.2 1.0 NAN A:DQM313 2.3 11.3 1.0 CAR A:DQM313 3.0 10.2 1.0 CG A:ASP76 3.0 5.6 1.0 CAS A:DQM313 3.0 11.7 1.0 CE1 A:HIS215 3.1 5.7 1.0 CD2 A:HIS77 3.1 5.5 1.0 CE1 A:HIS77 3.1 5.7 1.0 CD2 A:HIS215 3.1 5.6 1.0 OD1 A:ASP76 3.3 5.9 1.0 CAY A:DQM313 3.6 13.5 1.0 ZN A:ZN301 3.6 5.7 1.0 OAI A:DQM313 3.9 12.7 1.0 CAX A:DQM313 3.9 14.0 1.0 OAH A:DQM313 4.2 9.7 1.0 ND1 A:HIS215 4.2 6.0 1.0 ND1 A:HIS77 4.2 5.5 1.0 CG A:HIS77 4.3 5.2 1.0 CG A:HIS215 4.3 5.6 1.0 CB A:ASP76 4.4 5.7 1.0 CAT A:DQM313 4.4 13.7 1.0 NE2 A:HIS72 4.4 5.7 1.0 CE1 A:HIS72 4.4 5.6 1.0 OG A:SER175 4.4 4.7 0.5 CAZ A:DQM313 4.5 12.9 1.0 CAU A:DQM313 4.7 14.3 1.0 NE2 A:HIS150 4.8 4.8 1.0 CAA A:DQM313 4.8 15.6 1.0 CD1 A:ILE26 5.0 6.9 1.0

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