Sodium 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:

Cadmium

(Cd)

4 atoms

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

Sodium binding site 1 out of 2 in the Metallo-Beta-Lactamase (Cadmium-Bound Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Metallo-Beta-Lactamase (Cadmium-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3 b:20.4 occ:1.00 O A:HOH255 2.1 18.0 1.0 O A:ASN55 2.4 13.9 1.0 O A:ASP103 2.4 16.2 1.0 OD2 A:ASP69 2.5 12.1 1.0 O A:HOH261 2.7 11.9 1.0 CG A:ASP69 3.3 10.2 1.0 CB A:ASP69 3.4 13.2 1.0 C A:ASN55 3.5 14.2 1.0 C A:ASP103 3.6 15.3 1.0 O A:HOH256 3.6 10.0 1.0 N A:ASN55 4.0 18.0 1.0 CA A:ASN55 4.3 15.1 1.0 OD2 A:ASP103 4.3 17.8 1.0 CB A:ASP103 4.3 15.0 1.0 O A:GLY222 4.4 9.5 1.0 CB A:SER54 4.4 19.9 1.0 OD1 A:ASP69 4.5 12.0 1.0 N A:CYS104 4.5 13.8 1.0 CG A:ASP103 4.5 14.8 1.0 CA A:CYS104 4.6 9.5 1.0 CA A:ASP103 4.6 14.3 1.0 N A:GLY56 4.6 13.8 1.0 O A:THR70 4.6 15.0 1.0 CZ A:PHE178 4.6 9.2 1.0 C A:SER54 4.7 20.5 1.0 SG A:CYS104 4.7 12.8 1.0 CA A:GLY56 4.8 12.9 1.0 CA A:ASP69 4.8 11.9 1.0 OG A:SER54 4.9 22.7 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Metallo-Beta-Lactamase (Cadmium-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3 b:24.7 occ:1.00 O B:ASN55 2.2 15.4 1.0 O B:HOH267 2.4 15.3 1.0 OD2 B:ASP69 2.4 16.2 1.0 O B:ASP103 2.5 22.6 1.0 O B:HOH300 2.7 31.1 1.0 CG B:ASP69 3.2 15.1 1.0 CB B:ASP69 3.3 12.0 1.0 C B:ASN55 3.3 17.5 1.0 C B:ASP103 3.7 20.0 1.0 O B:HOH286 3.7 20.2 1.0 N B:ASN55 4.0 19.8 1.0 CA B:ASN55 4.3 18.6 1.0 CB B:ASP103 4.3 16.0 1.0 N B:GLY56 4.3 17.4 1.0 O B:GLY222 4.3 13.8 1.0 OD1 B:ASP69 4.4 22.6 1.0 OD2 B:ASP103 4.4 16.2 1.0 OG B:SER54 4.5 24.9 1.0 CB B:SER54 4.5 19.3 1.0 CA B:GLY56 4.5 17.4 1.0 CA B:CYS104 4.5 17.9 1.0 N B:CYS104 4.5 18.4 1.0 CZ B:PHE178 4.6 19.7 1.0 CA B:ASP103 4.6 19.2 1.0 CG B:ASP103 4.6 16.4 1.0 O B:THR70 4.6 15.6 1.0 C B:SER54 4.6 19.3 1.0 SG B:CYS104 4.7 15.1 1.0 CA B:ASP69 4.8 12.0 1.0 OH B:TYR40 4.9 24.8 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