Zinc in PDB 3znb: Metallo-Beta-Lactamase (Zn, Hg-Bound Form)

All present enzymatic activity of Metallo-Beta-Lactamase (Zn, Hg-Bound Form):
3.5.2.6;

The structure of Metallo-Beta-Lactamase (Zn, Hg-Bound Form), PDB code: 3znb 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 / 2.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.200, 78.200, 140.600, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 26.8

The structure of Metallo-Beta-Lactamase (Zn, Hg-Bound Form) also contains other interesting chemical elements:

Mercury	(Hg)	2 atoms
Sodium	(Na)	2 atoms

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

Zinc binding site 1 out of 2 in the Metallo-Beta-Lactamase (Zn, Hg-Bound Form)


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 (Zn, Hg-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:14.2 occ:1.00 ND1 A:HIS101 2.2 4.5 1.0 NE2 A:HIS162 2.3 8.6 1.0 NE2 A:HIS99 2.4 17.7 1.0 CG A:HIS101 3.1 2.0 1.0 CE1 A:HIS99 3.1 13.6 1.0 CD2 A:HIS162 3.1 8.2 1.0 CE1 A:HIS101 3.2 3.9 1.0 CB A:HIS101 3.3 2.0 1.0 CE1 A:HIS162 3.3 12.5 1.0 CD2 A:HIS99 3.6 9.5 1.0 OD1 A:ASP103 3.9 19.1 1.0 CD2 A:HIS101 4.2 2.0 1.0 NE2 A:HIS101 4.3 2.0 1.0 CG A:HIS162 4.3 5.8 1.0 ND1 A:HIS99 4.4 7.9 1.0 ND1 A:HIS162 4.4 9.1 1.0 O A:HOH257 4.5 2.0 1.0 CG A:HIS99 4.6 11.3 1.0 CB A:CYS181 4.6 12.2 1.0 OD2 A:ASP103 4.7 23.6 1.0 SG A:CYS181 4.8 18.0 1.0 CA A:HIS101 4.8 7.3 1.0 CG A:ASP103 4.8 16.2 1.0 HG A:HG2 4.8 32.5 1.0

Zinc binding site 2 out of 2 in the Metallo-Beta-Lactamase (Zn, Hg-Bound Form)


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 (Zn, Hg-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:15.0 occ:1.00 ND1 B:HIS101 2.2 2.8 1.0 NE2 B:HIS99 2.3 15.9 1.0 NE2 B:HIS162 2.4 12.1 1.0 CE1 B:HIS99 2.9 10.3 1.0 CG B:HIS101 3.0 4.4 1.0 CD2 B:HIS162 3.2 5.6 1.0 CB B:HIS101 3.2 6.7 1.0 CE1 B:HIS101 3.2 2.0 1.0 CE1 B:HIS162 3.4 16.1 1.0 CD2 B:HIS99 3.5 7.6 1.0 OD1 B:ASP103 3.9 21.5 1.0 ND1 B:HIS99 4.2 7.8 1.0 CD2 B:HIS101 4.2 3.1 1.0 NE2 B:HIS101 4.3 3.6 1.0 CG B:HIS162 4.4 7.7 1.0 CG B:HIS99 4.5 11.1 1.0 ND1 B:HIS162 4.5 13.9 1.0 CB B:CYS181 4.6 8.8 1.0 O B:HOH258 4.6 2.0 1.0 CA B:HIS101 4.7 8.6 1.0 OD2 B:ASP103 4.7 20.0 1.0 CG B:ASP103 4.7 16.1 1.0 SG B:CYS104 4.9 12.1 1.0 SG B:CYS181 4.9 5.2 1.0 HG B:HG2 4.9 35.4 1.0

N.O.Concha, B.A.Rasmussen, K.Bush, O.Herzberg. Crystal Structures of the Cadmium- and Mercury-Substituted Metallo-Beta-Lactamase From Bacteroides Fragilis. Protein Sci. V. 6 2671 1997.
ISSN: ISSN 0961-8368
PubMed: 9416622