Sodium in PDB 1hlk: Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor

All present enzymatic activity of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor:
3.5.2.6;

The structure of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor, PDB code: 1hlk was solved by D.J.Payne, J.A.Hueso-Rodriguez, H.Boyd, N.O.Concha, C.A.Janson, M.Gilpin, J.H.Bateson, C.Chever, N.L.Niconovich, S.Pearson, S.Rittenhouse, D.Tew, E.Diez, P.Perez, J.De La Fuente, M.Rees, A.Rivera-Sagredo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.800, 44.200, 58.500, 92.80, 95.30, 98.00
R / Rfree (%)	16.5 / 22.8

The structure of Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor (pdb code 1hlk). 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 From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor, PDB code: 1hlk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor


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 From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2001 b:32.0 occ:1.00 O A:HOH2016 2.7 19.6 1.0 O A:ASP103 2.9 23.1 1.0 O A:THR70 2.9 24.3 1.0 O A:ASN55 3.1 22.9 1.0 OH A:TYR40 3.2 18.0 1.0 C A:THR70 3.6 23.5 1.0 CB A:ASP69 3.7 15.6 1.0 C A:ASP103 3.8 24.3 1.0 C A:ASN55 3.8 24.5 1.0 CB A:SER54 3.9 30.2 1.0 CZ A:TYR40 4.1 18.6 1.0 N A:THR70 4.1 18.9 1.0 N A:PRO71 4.2 25.3 1.0 CE1 A:TYR40 4.2 20.1 1.0 C A:SER54 4.2 28.2 1.0 CA A:PRO71 4.2 27.1 1.0 O A:SER54 4.2 25.7 1.0 OD2 A:ASP69 4.3 15.7 1.0 C A:ASP69 4.4 18.0 1.0 N A:ASN55 4.4 27.0 1.0 CA A:THR70 4.4 22.4 1.0 CA A:ASP103 4.4 26.1 1.0 N A:GLY56 4.4 23.9 1.0 CG A:ASP69 4.5 16.2 1.0 CA A:GLY56 4.6 22.8 1.0 CB A:ASP103 4.6 28.7 1.0 CA A:ASN55 4.6 25.8 1.0 CA A:ASP69 4.6 16.2 1.0 OG A:SER42 4.7 36.4 1.0 N A:CYS104 4.7 22.6 1.0 CA A:SER54 4.7 31.1 1.0 C A:PRO71 4.9 27.5 1.0 O A:ASP69 4.9 15.6 1.0 OG A:SER54 4.9 31.7 1.0 CA A:CYS104 4.9 21.5 1.0

Sodium binding site 2 out of 2 in the Metallo-Beta-Lactamase From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor


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 From Bacteroides Fragilis in Complex with A Tricyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2002 b:22.8 occ:1.00 O B:ASP103 2.5 17.2 1.0 O B:ASN55 2.7 19.0 1.0 O B:HOH2019 3.2 24.6 1.0 C B:ASN55 3.4 19.2 1.0 OD2 B:ASP69 3.5 6.0 1.0 O B:THR70 3.6 20.4 1.0 C B:ASP103 3.6 16.7 1.0 CB B:SER54 3.7 22.0 1.0 N B:ASN55 3.7 21.2 1.0 CB B:ASP69 3.7 8.9 1.0 C B:SER54 4.0 22.4 1.0 CG B:ASP69 4.1 8.0 1.0 CA B:ASN55 4.1 18.8 1.0 N B:GLY56 4.2 18.8 1.0 CB B:ASP103 4.4 15.9 1.0 OH B:TYR40 4.4 9.8 1.0 CA B:ASP103 4.4 17.9 1.0 O B:SER54 4.4 21.9 1.0 CA B:SER54 4.4 23.6 1.0 CA B:GLY56 4.5 18.6 1.0 N B:CYS104 4.5 18.9 1.0 C B:THR70 4.6 16.6 1.0 OG B:SER54 4.6 24.4 1.0 N B:THR70 4.7 16.4 1.0 CA B:CYS104 4.7 19.0 1.0 OD2 B:ASP103 4.9 17.4 1.0 C B:ASP69 4.9 14.4 1.0 CA B:ASP69 4.9 12.0 1.0 CE1 B:TYR40 5.0 9.1 1.0 O B:GLY222 5.0 17.8 1.0

D.J.Payne, J.A.Hueso-Rodriguez, H.Boyd, N.O.Concha, C.A.Janson, M.Gilpin, J.H.Bateson, C.Chever, N.L.Niconovich, S.Pearson, S.Rittenhouse, D.Tew, E.Diez, P.Perez, J.De La Fuente, M.Rees, A.Rivera-Sagredo. Identification of A Series of Tricyclic Natural Products As Potent Broad Spectrum Inhibitors of Metallo-Beta-Lactamases Antimicrob.Agents Chemother. V. 46 1880 2002.
ISSN: ISSN 0066-4804
PubMed: 12019104
DOI: 10.1128/AAC.46.6.1880-1886.2002