Sodium in PDB 2bmi: Metallo-Beta-Lactamase

All present enzymatic activity of Metallo-Beta-Lactamase:
3.5.2.6;

The structure of Metallo-Beta-Lactamase, PDB code: 2bmi was solved by A.Carfi, E.Duee, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.256, 94.920, 111.420, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 26.2

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 2bmi). 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: 2bmi:
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:Na275 b:9.7 occ:1.00 O A:HOH493 2.2 9.0 1.0 O A:HOH494 2.4 8.6 1.0 O A:ASP86 2.4 9.9 1.0 O A:ASN38 2.4 7.0 1.0 OD2 A:ASP52 2.5 11.5 1.0 CG A:ASP52 3.3 8.4 1.0 CB A:ASP52 3.3 5.5 1.0 C A:ASN38 3.5 6.3 1.0 C A:ASP86 3.5 10.8 1.0 N A:ASN38 3.9 10.1 1.0 O A:HOH277 4.0 8.4 1.0 CB A:ASP86 4.2 7.8 1.0 CB A:SER37 4.2 12.0 1.0 CA A:ASN38 4.2 7.5 1.0 O A:GLY205 4.4 9.0 1.0 O A:THR53 4.4 7.6 1.0 CA A:ASP86 4.4 9.4 1.0 N A:CYS87 4.4 11.0 1.0 OD2 A:ASP86 4.5 6.1 1.0 N A:GLY39 4.5 7.7 1.0 OD1 A:ASP52 4.5 8.8 1.0 OH A:TYR23 4.5 8.4 1.0 C A:SER37 4.5 11.1 1.0 CA A:CYS87 4.6 10.6 1.0 OG A:SER37 4.6 17.6 1.0 CZ A:PHE161 4.6 10.2 1.0 CA A:GLY39 4.6 7.8 1.0 CA A:ASP52 4.7 5.8 1.0 CG A:ASP86 4.7 8.2 1.0 SG A:CYS87 4.7 7.7 1.0 CA A:SER37 4.9 12.5 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:Na275 b:9.3 occ:1.00 O B:HOH475 2.2 8.1 1.0 O B:ASN38 2.3 6.4 1.0 O B:ASP86 2.3 9.0 1.0 O B:HOH279 2.4 8.9 1.0 OD2 B:ASP52 2.6 8.7 1.0 CB B:ASP52 3.4 7.4 1.0 CG B:ASP52 3.4 5.0 1.0 C B:ASN38 3.4 6.5 1.0 C B:ASP86 3.5 9.1 1.0 N B:ASN38 3.9 6.9 1.0 O B:HOH280 4.0 7.5 1.0 CB B:ASP86 4.2 6.7 1.0 CB B:SER37 4.2 8.7 1.0 CA B:ASN38 4.2 7.2 1.0 OG B:SER37 4.3 14.8 1.0 O B:GLY205 4.3 8.7 1.0 O B:THR53 4.3 10.1 1.0 CA B:ASP86 4.4 7.7 1.0 N B:GLY39 4.4 8.6 1.0 CZ B:PHE161 4.5 2.8 1.0 N B:CYS87 4.5 9.8 1.0 C B:SER37 4.5 9.1 1.0 OD1 B:ASP52 4.5 5.2 1.0 OD2 B:ASP86 4.6 8.3 1.0 CA B:GLY39 4.6 10.6 1.0 CA B:CYS87 4.7 9.5 1.0 OH B:TYR23 4.7 11.3 1.0 SG B:CYS87 4.7 10.4 1.0 CG B:ASP86 4.7 9.4 1.0 CA B:ASP52 4.7 8.7 1.0 CA B:SER37 4.9 9.1 1.0

A.Carfi, E.Duee, R.Paul-Soto, M.Galleni, J.M.Frere, O.Dideberg. X-Ray Structure of the Znii Beta-Lactamase From Bacteroides Fragilis in An Orthorhombic Crystal Form. Acta Crystallogr.,Sect.D V. 54 45 1998.
ISSN: ISSN 0907-4449
PubMed: 9761816
DOI: 10.1107/S090744499700927X