Cadmium in PDB 2znb: Metallo-Beta-Lactamase (Cadmium-Bound Form)

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

The structure of Metallo-Beta-Lactamase (Cadmium-Bound Form), PDB code: 2znb 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 / 2.15
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.086, 78.086, 139.746, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 25.9

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

Sodium

(Na)

2 atoms

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

Cadmium binding site 1 out of 4 in the Metallo-Beta-Lactamase (Cadmium-Bound Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Metallo-Beta-Lactamase (Cadmium-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1 b:30.6 occ:1.00 O A:HOH250 2.0 20.2 1.0 NE2 A:HIS162 2.1 12.4 1.0 ND1 A:HIS101 2.2 9.2 1.0 NE2 A:HIS99 2.2 12.7 1.0 CD2 A:HIS162 3.0 10.6 1.0 CG A:HIS101 3.0 7.3 1.0 CE1 A:HIS99 3.1 11.0 1.0 CE1 A:HIS101 3.2 8.4 1.0 CE1 A:HIS162 3.2 12.7 1.0 CD2 A:HIS99 3.2 8.8 1.0 CB A:HIS101 3.3 7.2 1.0 O A:HOH302 3.5 25.1 1.0 CD A:CD2 3.7 23.5 1.0 OD1 A:ASP103 3.9 17.4 1.0 O A:HOH251 4.1 15.8 1.0 CD2 A:HIS101 4.2 8.3 1.0 CG A:HIS162 4.2 13.0 1.0 ND1 A:HIS99 4.2 11.7 1.0 NE2 A:HIS101 4.2 9.7 1.0 ND1 A:HIS162 4.3 11.4 1.0 CG A:HIS99 4.3 12.9 1.0 CB A:CYS181 4.3 10.6 1.0 SG A:CYS181 4.3 15.5 1.0 OD2 A:ASP103 4.6 17.8 1.0 CA A:HIS101 4.7 9.7 1.0 CG A:ASP103 4.7 14.8 1.0 N A:HIS101 5.0 10.7 1.0

Cadmium binding site 2 out of 4 in the Metallo-Beta-Lactamase (Cadmium-Bound Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Metallo-Beta-Lactamase (Cadmium-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2 b:23.5 occ:1.00 O A:HOH250 2.1 20.2 1.0 O A:HOH251 2.3 15.8 1.0 OD2 A:ASP103 2.3 17.8 1.0 SG A:CYS181 2.5 15.5 1.0 NE2 A:HIS223 2.6 13.5 1.0 CD2 A:HIS223 3.3 11.2 1.0 CG A:ASP103 3.4 14.8 1.0 CB A:CYS181 3.4 10.6 1.0 CE1 A:HIS223 3.7 13.8 1.0 CD A:CD1 3.7 30.6 1.0 OD1 A:ASP103 3.7 17.4 1.0 O A:HOH302 3.9 25.1 1.0 O A:HOH255 4.0 18.0 1.0 NE2 A:HIS162 4.1 12.4 1.0 CE1 A:HIS162 4.5 12.7 1.0 CG A:HIS223 4.5 11.9 1.0 CA A:CYS181 4.6 10.8 1.0 ND1 A:HIS223 4.7 11.9 1.0 CB A:ASP103 4.7 15.0 1.0 CE1 A:HIS99 4.8 11.0 1.0 CD2 A:HIS162 4.8 10.6 1.0 NE2 A:HIS99 4.9 12.7 1.0

Cadmium binding site 3 out of 4 in the Metallo-Beta-Lactamase (Cadmium-Bound Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Metallo-Beta-Lactamase (Cadmium-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1 b:34.9 occ:1.00 NE2 B:HIS162 2.1 7.1 1.0 O B:HOH250 2.1 16.1 1.0 ND1 B:HIS101 2.2 13.3 1.0 NE2 B:HIS99 2.3 12.0 1.0 CD2 B:HIS162 2.9 9.2 1.0 CG B:HIS101 3.0 7.2 1.0 CB B:HIS101 3.2 10.2 1.0 CE1 B:HIS162 3.2 7.8 1.0 CD2 B:HIS99 3.2 12.7 1.0 CE1 B:HIS99 3.3 10.1 1.0 CE1 B:HIS101 3.3 9.7 1.0 O B:HOH272 3.5 18.6 1.0 CD B:CD2 3.7 24.0 1.0 OD1 B:ASP103 4.0 17.7 1.0 CG B:HIS162 4.1 12.3 1.0 ND1 B:HIS162 4.2 13.4 1.0 CD2 B:HIS101 4.2 9.9 1.0 O B:HOH251 4.3 12.7 1.0 SG B:CYS181 4.3 14.5 1.0 CB B:CYS181 4.3 11.0 1.0 ND1 B:HIS99 4.3 12.6 1.0 NE2 B:HIS101 4.3 11.2 1.0 CG B:HIS99 4.3 12.0 1.0 OD2 B:ASP103 4.6 16.2 1.0 CA B:HIS101 4.6 10.4 1.0 CG B:ASP103 4.7 16.4 1.0 CB B:ALA163 4.9 9.4 1.0 N B:HIS101 5.0 10.6 1.0

Cadmium binding site 4 out of 4 in the Metallo-Beta-Lactamase (Cadmium-Bound Form)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Metallo-Beta-Lactamase (Cadmium-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd2 b:24.0 occ:1.00 O B:HOH251 2.2 12.7 1.0 OD2 B:ASP103 2.2 16.2 1.0 NE2 B:HIS223 2.4 11.6 1.0 SG B:CYS181 2.5 14.5 1.0 O B:HOH250 2.8 16.1 1.0 CG B:ASP103 3.3 16.4 1.0 CD2 B:HIS223 3.3 7.3 1.0 CE1 B:HIS223 3.3 14.0 1.0 CB B:CYS181 3.3 11.0 1.0 OD1 B:ASP103 3.7 17.7 1.0 CD B:CD1 3.7 34.9 1.0 O B:HOH267 4.0 15.3 1.0 NE2 B:HIS162 4.1 7.1 1.0 O B:HOH272 4.2 18.6 1.0 O B:HOH317 4.3 28.7 1.0 ND1 B:HIS223 4.4 13.8 1.0 CG B:HIS223 4.5 10.8 1.0 CE1 B:HIS162 4.5 7.8 1.0 CB B:ASP103 4.5 16.0 1.0 CA B:CYS181 4.6 15.3 1.0 NE2 B:HIS99 4.7 12.0 1.0 CE1 B:HIS99 4.8 10.1 1.0 CD2 B:HIS162 4.9 9.2 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