Sodium in PDB 5aya: Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril:
3.5.2.6;

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril, PDB code: 5aya was solved by J.Wachino, Y.Arakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.02
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	68.097, 68.097, 49.110, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 28.2

The structure of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril (pdb code 5aya). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril, PDB code: 5aya:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:34.4 occ:1.00 O A:GLN160 2.6 22.1 1.0 O A:HOH478 2.7 36.1 1.0 OD1 A:ASN17 2.9 21.3 1.0 O A:HOH499 3.3 36.6 1.0 ND2 A:ASN17 3.4 19.9 1.0 CG A:ASN17 3.6 23.4 1.0 CD2 A:LEU140 3.7 30.1 1.0 C A:GLN160 3.8 31.2 1.0 CD1 A:LEU31 3.8 26.3 1.0 OG A:SER161 3.9 27.0 1.0 O A:HOH459 4.3 30.9 1.0 CG A:LEU31 4.3 25.1 1.0 CA A:SER161 4.3 25.0 1.0 CD1 A:TRP159 4.4 24.0 1.0 CD2 A:LEU31 4.4 26.1 1.0 O A:HOH435 4.5 20.9 1.0 N A:SER161 4.5 21.4 1.0 CB A:SER161 4.7 25.6 1.0 N A:GLN160 4.8 28.5 1.0 CA A:GLN160 4.9 27.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:38.4 occ:1.00 O A:THR71 2.7 22.1 1.0 O A:HOH440 2.9 27.5 1.0 O A:SER70 2.9 30.6 1.0 O A:GLY153 2.9 30.8 1.0 N A:GLY95 3.1 30.7 1.0 CG1 A:ILE155 3.4 26.6 1.0 C A:THR71 3.6 31.1 1.0 CA A:ALA94 3.7 32.4 1.0 C A:SER70 3.7 21.2 1.0 N A:ILE155 3.8 24.2 1.0 CB A:ILE155 3.8 27.7 1.0 CB A:ALA94 3.8 32.1 1.0 C A:ALA94 3.9 33.8 1.0 C A:GLY153 4.0 31.1 1.0 OG A:SER70 4.0 24.7 1.0 CA A:GLY95 4.0 32.9 1.0 ND2 A:ASN98 4.1 31.1 1.0 C A:GLY154 4.2 25.7 1.0 CA A:THR71 4.3 23.1 1.0 CB A:SER70 4.3 25.5 1.0 CA A:GLY154 4.3 27.6 1.0 N A:HIS72 4.4 30.1 1.0 CA A:ILE155 4.4 26.6 1.0 N A:THR71 4.4 20.6 1.0 CA A:HIS72 4.4 32.4 1.0 CA A:SER70 4.6 21.1 1.0 N A:GLY154 4.6 27.9 1.0 CB A:ASN98 4.7 32.6 1.0 CD1 A:ILE155 4.8 30.4 1.0 CG A:ASN98 4.9 36.2 1.0 O A:GLY95 4.9 33.1 1.0 CZ2 A:TRP157 5.0 26.8 1.0 N A:ALA94 5.0 32.3 1.0

J.Wachino, Y.Arakawa. Crystal Structure of Metallo-Beta-Lactamase Smb-1 Bound to L-Captopril To Be Published.