Sodium 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:

Zinc

(Zn)

4 atoms

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

Sodium binding site 1 out of 2 in the Metallo-Beta-Lactamase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3 b:11.3 occ:1.00 O A:ASP103 2.2 9.8 1.0 O A:HOH255 2.3 8.8 1.0 O A:ASN55 2.4 11.8 1.0 OD2 A:ASP69 2.5 6.6 1.0 O A:HOH263 2.5 9.2 1.0 CG A:ASP69 3.3 5.8 1.0 CB A:ASP69 3.3 8.0 1.0 C A:ASP103 3.4 10.5 1.0 C A:ASN55 3.5 12.4 1.0 N A:ASN55 3.9 13.3 1.0 O A:HOH254 4.0 7.4 1.0 O A:THR70 4.2 9.6 1.0 CB A:ASP103 4.2 8.4 1.0 CB A:SER54 4.3 18.0 1.0 OD2 A:ASP103 4.3 8.4 1.0 CA A:ASN55 4.3 12.6 1.0 N A:CYS104 4.4 10.7 1.0 CA A:ASP103 4.4 9.5 1.0 O A:GLY222 4.4 10.4 1.0 CA A:CYS104 4.4 9.9 1.0 OD1 A:ASP69 4.4 6.9 1.0 N A:GLY56 4.5 10.8 1.0 CZ A:PHE178 4.6 9.0 1.0 CG A:ASP103 4.6 8.2 1.0 C A:SER54 4.6 15.6 1.0 SG A:CYS104 4.6 7.6 1.0 OH A:TYR40 4.7 11.4 1.0 CA A:GLY56 4.7 11.8 1.0 CA A:ASP69 4.7 8.9 1.0 OG A:SER54 4.9 24.4 1.0 CA A:SER54 4.9 17.2 1.0

Sodium binding site 2 out of 2 in the Metallo-Beta-Lactamase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3 b:10.0 occ:1.00 O B:HOH255 2.2 8.7 1.0 O B:ASN55 2.3 8.0 1.0 O B:ASP103 2.4 9.4 1.0 OD2 B:ASP69 2.5 11.1 1.0 O B:HOH264 2.6 11.8 1.0 CG B:ASP69 3.3 10.8 1.0 CB B:ASP69 3.4 10.1 1.0 C B:ASN55 3.4 9.3 1.0 C B:ASP103 3.5 9.4 1.0 N B:ASN55 3.9 10.8 1.0 O B:HOH254 4.0 8.4 1.0 CB B:ASP103 4.2 8.1 1.0 CA B:ASN55 4.2 9.7 1.0 CB B:SER54 4.3 15.1 1.0 O B:GLY222 4.3 9.5 1.0 OD2 B:ASP103 4.4 9.9 1.0 OG B:SER54 4.4 19.6 1.0 O B:THR70 4.4 10.8 1.0 CA B:ASP103 4.4 8.4 1.0 N B:GLY56 4.4 9.9 1.0 OD1 B:ASP69 4.5 9.2 1.0 N B:CYS104 4.5 7.9 1.0 CA B:CYS104 4.5 9.0 1.0 CZ B:PHE178 4.5 7.9 1.0 CG B:ASP103 4.6 9.5 1.0 C B:SER54 4.7 12.3 1.0 CA B:GLY56 4.7 10.9 1.0 SG B:CYS104 4.7 10.1 1.0 CA B:ASP69 4.7 10.0 1.0 OH B:TYR40 4.8 13.4 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