Zinc in PDB 3vqz: Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid:
3.5.2.6;

The structure of Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid, PDB code: 3vqz was solved by J.Wachino, Y.Yamaguchi, S.Mori, Y.Arakawa, K.Shibayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.02 / 2.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	67.029, 67.029, 46.792, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 22.4

The structure of Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid (pdb code 3vqz). 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, in A Complex with Mercaptoacetic Acid, PDB code: 3vqz:
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, in A Complex with Mercaptoacetic Acid


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, in A Complex with Mercaptoacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:24.0 occ:1.00 ND1 A:HIS74 2.0 24.7 1.0 NE2 A:HIS150 2.1 23.6 1.0 NE2 A:HIS72 2.1 21.0 1.0 S2 A:MCR305 2.2 25.1 1.0 CE1 A:HIS74 2.9 24.4 1.0 CD2 A:HIS150 3.0 23.4 1.0 CD2 A:HIS72 3.0 23.7 1.0 CG A:HIS74 3.1 24.1 1.0 CE1 A:HIS72 3.1 21.7 1.0 O2 A:MCR305 3.1 23.9 1.0 CE1 A:HIS150 3.1 23.8 1.0 C2 A:MCR305 3.3 24.6 1.0 C1 A:MCR305 3.5 26.6 1.0 CB A:HIS74 3.5 24.1 1.0 ZN A:ZN302 3.6 24.3 1.0 OE1 A:GLN113 4.0 44.5 1.0 NE2 A:HIS77 4.1 23.3 1.0 NE2 A:HIS74 4.1 24.2 1.0 ND1 A:HIS72 4.2 22.1 1.0 CG A:HIS72 4.2 22.9 1.0 NE2 A:GLN113 4.2 41.1 1.0 CG A:HIS150 4.2 24.2 1.0 CD2 A:HIS74 4.2 23.8 1.0 CD2 A:HIS77 4.2 22.4 1.0 ND1 A:HIS150 4.2 24.2 1.0 OD1 A:ASP76 4.3 21.8 1.0 CD A:GLN113 4.4 44.0 1.0 O1 A:MCR305 4.5 28.2 1.0 CA A:HIS74 4.9 24.8 1.0 OG A:SER175 4.9 26.0 1.0 OD2 A:ASP76 4.9 24.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid


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, in A Complex with Mercaptoacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:24.3 occ:1.00 NE2 A:HIS77 2.0 23.3 1.0 NE2 A:HIS215 2.0 22.3 1.0 OD2 A:ASP76 2.1 24.2 1.0 S2 A:MCR305 2.4 25.1 1.0 O2 A:MCR305 2.6 23.9 1.0 CE1 A:HIS77 2.9 22.3 1.0 CD2 A:HIS215 2.9 22.0 1.0 CG A:ASP76 2.9 23.1 1.0 C2 A:MCR305 3.0 24.6 1.0 CD2 A:HIS77 3.0 22.4 1.0 CE1 A:HIS215 3.1 22.4 1.0 C1 A:MCR305 3.1 26.6 1.0 OD1 A:ASP76 3.2 21.8 1.0 ZN A:ZN301 3.6 24.0 1.0 ND1 A:HIS77 4.0 21.9 1.0 CG A:HIS77 4.1 22.4 1.0 CG A:HIS215 4.1 21.5 1.0 ND1 A:HIS215 4.2 22.4 1.0 NE2 A:HIS72 4.2 21.0 1.0 O1 A:MCR305 4.2 28.2 1.0 CE1 A:HIS72 4.2 21.7 1.0 CB A:ASP76 4.3 23.2 1.0 CD1 A:ILE26 4.6 20.9 1.0 OG A:SER175 4.7 26.0 1.0

J.Wachino, Y.Yamaguchi, S.Mori, H.Kurosaki, Y.Arakawa, K.Shibayama. Structural Insights Into the Subclass B3 Metallo-Beta-Lactamase Smb-1 and the Mode of Inhibition By the Common Metallo- -Lactamase Inhibitor Mercaptoacetate Antimicrob.Agents Chemother. V. 57 101 2013.
ISSN: ISSN 0066-4804
PubMed: 23070156
DOI: 10.1128/AAC.01264-12