Zinc in PDB 1znb: Metallo-Beta-Lactamase

All present enzymatic activity of Metallo-Beta-Lactamase:
3.5.2.6;

The structure of Metallo-Beta-Lactamase, PDB code: 1znb was solved by N.O.Concha, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.298, 78.298, 140.916, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 24.1

The structure of Metallo-Beta-Lactamase also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

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

Zinc binding site 1 out of 4 in the Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:12.3 occ:1.00 O A:HOH250 1.9 8.0 1.0 ND1 A:HIS101 2.1 8.6 1.0 NE2 A:HIS162 2.1 8.3 1.0 NE2 A:HIS99 2.1 6.3 1.0 CG A:HIS101 3.0 8.2 1.0 CD2 A:HIS99 3.0 5.6 1.0 CD2 A:HIS162 3.0 5.8 1.0 CE1 A:HIS162 3.1 8.6 1.0 CE1 A:HIS101 3.1 8.8 1.0 CE1 A:HIS99 3.2 5.8 1.0 CB A:HIS101 3.3 5.5 1.0 ZN A:ZN2 3.5 11.4 1.0 O A:HOH252 3.5 12.4 1.0 OD1 A:ASP103 3.9 9.7 1.0 O A:HOH251 4.0 9.1 1.0 ND1 A:HIS162 4.1 7.1 1.0 CG A:HIS162 4.2 6.6 1.0 CD2 A:HIS101 4.2 8.0 1.0 NE2 A:HIS101 4.2 8.1 1.0 SG A:CYS181 4.2 8.6 1.0 CG A:HIS99 4.2 7.4 1.0 ND1 A:HIS99 4.2 5.0 1.0 CB A:CYS181 4.3 6.5 1.0 OD2 A:ASP103 4.5 8.4 1.0 CG A:ASP103 4.6 8.2 1.0 O A:HOH339 4.7 49.2 1.0 CA A:HIS101 4.8 7.7 1.0

Zinc binding site 2 out of 4 in the Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:11.4 occ:1.00 O A:HOH250 2.1 8.0 1.0 NE2 A:HIS223 2.1 9.7 1.0 OD2 A:ASP103 2.2 8.4 1.0 O A:HOH251 2.3 9.1 1.0 SG A:CYS181 2.3 8.6 1.0 CD2 A:HIS223 3.0 8.7 1.0 CE1 A:HIS223 3.1 9.3 1.0 CG A:ASP103 3.2 8.2 1.0 CB A:CYS181 3.4 6.5 1.0 ZN A:ZN1 3.5 12.3 1.0 OD1 A:ASP103 3.5 9.7 1.0 O A:HOH255 4.0 8.8 1.0 O A:HOH252 4.2 12.4 1.0 CG A:HIS223 4.2 9.9 1.0 ND1 A:HIS223 4.2 10.0 1.0 NE2 A:HIS162 4.2 8.3 1.0 O A:HOH298 4.4 11.6 1.0 CE1 A:HIS162 4.4 8.6 1.0 NE2 A:HIS99 4.4 6.3 1.0 CE1 A:HIS99 4.5 5.8 1.0 O A:HOH457 4.5 38.8 1.0 CB A:ASP103 4.5 8.4 1.0 CA A:CYS181 4.6 7.3 1.0 O A:HOH296 4.9 31.1 1.0 CD2 A:HIS162 5.0 5.8 1.0 O A:GLY222 5.0 10.4 1.0

Zinc binding site 3 out of 4 in the Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:13.1 occ:1.00 O B:HOH250 2.0 15.1 1.0 NE2 B:HIS162 2.0 7.3 1.0 ND1 B:HIS101 2.2 8.6 1.0 NE2 B:HIS99 2.2 9.7 1.0 CE1 B:HIS162 3.0 8.2 1.0 CD2 B:HIS162 3.0 8.3 1.0 CG B:HIS101 3.1 6.7 1.0 CD2 B:HIS99 3.1 8.1 1.0 CE1 B:HIS99 3.1 9.1 1.0 CE1 B:HIS101 3.2 6.3 1.0 CB B:HIS101 3.3 6.5 1.0 ZN B:ZN2 3.5 13.0 1.0 O B:HOH252 3.6 14.9 1.0 O B:HOH251 3.9 7.7 1.0 OD1 B:ASP103 4.0 8.1 1.0 ND1 B:HIS162 4.1 7.7 1.0 CG B:HIS162 4.1 9.3 1.0 SG B:CYS181 4.2 9.0 1.0 ND1 B:HIS99 4.2 8.7 1.0 CB B:CYS181 4.2 4.9 1.0 CG B:HIS99 4.2 7.9 1.0 CD2 B:HIS101 4.2 6.2 1.0 NE2 B:HIS101 4.3 6.3 1.0 OD2 B:ASP103 4.4 9.9 1.0 CG B:ASP103 4.7 9.5 1.0 CA B:HIS101 4.8 7.9 1.0

Zinc binding site 4 out of 4 in the Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:13.0 occ:1.00 O B:HOH250 2.1 15.1 1.0 OD2 B:ASP103 2.1 9.9 1.0 O B:HOH251 2.2 7.7 1.0 NE2 B:HIS223 2.2 12.7 1.0 SG B:CYS181 2.3 9.0 1.0 CD2 B:HIS223 3.0 9.6 1.0 CG B:ASP103 3.2 9.5 1.0 CE1 B:HIS223 3.3 11.1 1.0 CB B:CYS181 3.4 4.9 1.0 ZN B:ZN1 3.5 13.1 1.0 OD1 B:ASP103 3.5 8.1 1.0 O B:HOH255 3.9 8.7 1.0 O B:HOH252 4.0 14.9 1.0 NE2 B:HIS162 4.2 7.3 1.0 CG B:HIS223 4.2 10.2 1.0 ND1 B:HIS223 4.3 10.3 1.0 O B:HOH263 4.3 8.6 1.0 CE1 B:HIS162 4.3 8.2 1.0 CE1 B:HIS99 4.4 9.1 1.0 NE2 B:HIS99 4.4 9.7 1.0 CB B:ASP103 4.5 8.1 1.0 CA B:CYS181 4.7 7.6 1.0 CD2 B:HIS162 5.0 8.3 1.0

N.O.Concha, B.A.Rasmussen, K.Bush, O.Herzberg. Crystal Structure of the Wide-Spectrum Binuclear Zinc Beta-Lactamase From Bacteroides Fragilis. Structure V. 4 823 1996.
ISSN: ISSN 0969-2126
PubMed: 8805566
DOI: 10.1016/S0969-2126(96)00089-5