Zinc in PDB 3vpe: Crystal Structure of Metallo-Beta-Lactamase Smb-1

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

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1, PDB code: 3vpe 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)	27.83 / 1.60
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	67.829, 67.829, 48.670, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 20

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 (pdb code 3vpe). 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, PDB code: 3vpe:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.6 occ:1.00 O A:HOH701 2.0 13.9 1.0 NE2 A:HIS150 2.0 12.5 1.0 NE2 A:HIS72 2.1 12.5 1.0 ND1 A:HIS74 2.1 13.0 1.0 CD2 A:HIS150 2.9 12.8 1.0 CD2 A:HIS72 3.0 13.0 1.0 CE1 A:HIS74 3.0 13.5 1.0 CE1 A:HIS72 3.0 13.3 1.0 CE1 A:HIS150 3.1 12.3 1.0 O A:HOH702 3.1 15.9 1.0 CG A:HIS74 3.1 13.0 1.0 CB A:HIS74 3.4 13.3 1.0 ZN A:ZN302 3.5 14.2 1.0 O2 A:GOL309 3.5 22.2 1.0 NE2 A:GLN113 3.9 18.0 1.0 CD2 A:HIS77 4.1 12.9 1.0 OD1 A:ASP76 4.1 14.6 1.0 ND1 A:HIS72 4.1 13.5 1.0 CG A:HIS150 4.1 12.8 1.0 CG A:HIS72 4.1 12.9 1.0 NE2 A:HIS77 4.1 12.4 1.0 NE2 A:HIS74 4.1 13.5 1.0 ND1 A:HIS150 4.2 13.2 1.0 CD2 A:HIS74 4.2 13.7 1.0 C2 A:GOL309 4.7 28.0 1.0 OD2 A:ASP76 4.7 14.3 1.0 CD1 A:LEU117 4.8 19.6 1.0 CG A:ASP76 4.8 15.0 1.0 OG A:SER175 4.8 14.7 1.0 CA A:HIS74 4.8 13.9 1.0 O A:HOH725 5.0 14.9 1.0 CD A:GLN113 5.0 19.0 1.0 CB A:SER175 5.0 12.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.2 occ:1.00 NE2 A:HIS77 2.1 12.4 1.0 NE2 A:HIS215 2.1 15.8 1.0 O A:HOH701 2.1 13.9 1.0 OD2 A:ASP76 2.1 14.3 1.0 O A:HOH702 2.2 15.9 1.0 CD2 A:HIS77 3.0 12.9 1.0 CG A:ASP76 3.0 15.0 1.0 CD2 A:HIS215 3.0 14.5 1.0 CE1 A:HIS215 3.1 15.6 1.0 CE1 A:HIS77 3.1 12.7 1.0 OD1 A:ASP76 3.3 14.6 1.0 ZN A:ZN301 3.5 13.6 1.0 O2 A:GOL309 3.7 22.2 1.0 C1 A:GOL309 3.8 34.4 1.0 C2 A:GOL309 3.8 28.0 1.0 NE2 A:HIS72 4.1 12.5 1.0 CG A:HIS77 4.1 12.7 1.0 CG A:HIS215 4.2 15.2 1.0 ND1 A:HIS215 4.2 15.1 1.0 ND1 A:HIS77 4.2 12.8 1.0 CE1 A:HIS72 4.2 13.3 1.0 OG A:SER175 4.3 14.7 1.0 CB A:ASP76 4.3 14.5 1.0 O A:HOH709 4.4 17.4 1.0 NE2 A:HIS150 4.6 12.5 1.0 CD1 A:ILE26 4.8 15.7 1.0 O1 A:GOL309 4.9 35.4 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