Sodium 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
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Metallo-Beta-Lactamase (Zn, Hg-Bound Form) (pdb code 3znb). 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 (Zn, Hg-Bound Form), PDB code: 3znb:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na binding site number 1 of Metallo-Beta-Lactamase (Zn, Hg-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3 b:14.2 occ:1.00 O A:ASN55 2.3 11.8 1.0 O A:ASP103 2.8 12.4 1.0 O A:HOH258 2.9 4.1 1.0 CB A:ASP69 3.0 10.5 1.0 OD2 A:ASP69 3.2 16.4 1.0 C A:ASN55 3.3 11.2 1.0 O A:THR70 3.5 11.3 1.0 CG A:ASP69 3.5 16.8 1.0 OH A:TYR40 3.6 18.1 1.0 CA A:GLY56 4.0 9.6 1.0 N A:GLY56 4.0 7.9 1.0 C A:ASP103 4.0 9.8 1.0 N A:ASN55 4.1 14.0 1.0 CB A:SER54 4.1 22.1 1.0 O A:HOH262 4.2 15.5 1.0 CA A:ASP69 4.2 10.1 1.0 C A:ASP69 4.3 8.8 1.0 CA A:ASN55 4.3 12.3 1.0 N A:THR70 4.3 7.7 1.0 C A:SER54 4.4 17.2 1.0 CZ A:TYR40 4.4 12.7 1.0 C A:THR70 4.5 11.9 1.0 CA A:CYS104 4.7 8.5 1.0 OD1 A:ASP69 4.8 17.4 1.0 CE1 A:TYR40 4.8 10.6 1.0 N A:CYS104 4.8 12.1 1.0 CA A:SER54 4.9 19.3 1.0 HG A:HG2 4.9 32.5 1.0 O A:ASP69 4.9 9.1 1.0 O A:SER54 4.9 15.4 1.0 CA A:ASP103 5.0 10.3 1.0 CB A:ASP103 5.0 9.7 1.0

Sodium 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 Sodium with other atoms in the Na binding site number 2 of Metallo-Beta-Lactamase (Zn, Hg-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3 b:23.5 occ:1.00 O B:ASN55 2.3 11.2 1.0 O B:ASP103 2.5 14.2 1.0 O B:HOH259 2.9 16.2 1.0 OD2 B:ASP69 3.0 20.5 1.0 C B:ASN55 3.4 12.6 1.0 CB B:ASP69 3.5 9.5 1.0 CG B:ASP69 3.6 18.2 1.0 C B:ASP103 3.7 10.9 1.0 CB B:SER54 3.7 23.2 1.0 N B:ASN55 3.9 17.5 1.0 O B:THR70 3.9 16.6 1.0 C B:SER54 4.2 18.1 1.0 CA B:ASN55 4.3 13.8 1.0 N B:GLY56 4.3 7.8 1.0 HG B:HG2 4.3 35.4 1.0 OH B:TYR40 4.4 19.5 1.0 CA B:GLY56 4.5 8.3 1.0 CB B:ASP103 4.5 11.5 1.0 CA B:SER54 4.5 20.9 1.0 CA B:ASP103 4.6 13.4 1.0 N B:CYS104 4.7 11.2 1.0 CA B:CYS104 4.7 10.7 1.0 CA B:ASP69 4.8 11.4 1.0 O B:SER54 4.8 13.2 1.0 OG B:SER54 4.8 25.4 1.0 O B:GLY222 4.9 19.8 1.0 OD1 B:ASP69 4.9 25.6 1.0 N B:THR70 4.9 13.0 1.0 C B:ASP69 4.9 16.7 1.0 C B:THR70 5.0 16.2 1.0 SG B:CYS181 5.0 5.2 1.0 OD2 B:ASP103 5.0 20.0 1.0 CG B:ASP103 5.0 16.1 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