Sodium in PDB 3vqz: Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid:
3.5.2.6;

The structure of Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid, PDB code: 3vqz was solved by J.Wachino, Y.Yamaguchi, S.Mori, Y.Arakawa, K.Shibayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.02 / 2.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	67.029, 67.029, 46.792, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 22.4

The structure of Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid 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, in A Complex with Mercaptoacetic Acid (pdb code 3vqz). 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, in A Complex with Mercaptoacetic Acid, PDB code: 3vqz:
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, in A Complex with Mercaptoacetic Acid


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, in A Complex with Mercaptoacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:24.6 occ:1.00 O A:SER70 2.6 22.1 1.0 O A:THR71 2.7 25.3 1.0 O A:HOH505 2.7 19.1 1.0 O A:GLY153 2.9 25.5 1.0 N A:GLY95 3.0 27.4 1.0 C A:THR71 3.5 24.7 1.0 C A:SER70 3.5 22.1 1.0 CG1 A:ILE155 3.6 19.8 1.0 CA A:ALA94 3.7 26.8 1.0 N A:ILE155 3.7 21.7 1.0 CB A:ILE155 3.8 20.4 1.0 CB A:ALA94 3.8 26.9 1.0 C A:ALA94 3.8 27.1 1.0 CA A:GLY95 4.0 28.7 1.0 C A:GLY153 4.0 26.0 1.0 CA A:THR71 4.1 23.1 1.0 OG A:SER70 4.2 21.9 1.0 ND2 A:ASN98 4.2 27.8 1.0 N A:THR71 4.2 22.7 1.0 C A:GLY154 4.3 23.1 1.0 N A:HIS72 4.3 24.3 1.0 CA A:ILE155 4.3 20.4 1.0 CB A:SER70 4.4 22.3 1.0 CA A:GLY154 4.4 22.5 1.0 CA A:HIS72 4.5 24.1 1.0 CA A:SER70 4.5 21.8 1.0 N A:GLY154 4.6 24.9 1.0 CB A:ASN98 4.8 29.5 1.0 CZ2 A:TRP157 4.8 20.5 1.0 CG A:ASN98 4.9 29.1 1.0 O A:GLY95 4.9 28.5 1.0 CD1 A:ILE155 5.0 20.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Metallo-Beta-Lactamase, Smb-1, in A Complex with Mercaptoacetic Acid


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, in A Complex with Mercaptoacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:29.0 occ:1.00 O A:HOH498 2.6 30.9 1.0 OD1 A:ASN54 2.7 20.8 1.0 O A:HOH529 2.9 29.2 1.0 N A:GLN9 3.1 25.0 1.0 O A:GLN9 3.1 23.6 1.0 O A:HOH467 3.5 25.8 1.0 C A:GLN9 3.5 23.6 1.0 CG A:ASN54 3.6 21.3 1.0 CG1 A:VAL50 3.6 21.4 1.0 CA A:PRO8 3.7 25.7 1.0 ND2 A:ASN54 3.8 20.9 1.0 CB A:PRO8 3.8 25.5 1.0 C A:PRO8 3.9 26.1 1.0 CA A:GLN9 4.0 24.5 1.0 N A:GLN10 4.3 23.1 1.0 O A:HOH524 4.4 37.0 1.0 O A:VAL50 4.6 21.5 1.0 CB A:VAL50 4.6 22.5 1.0 CA A:GLN10 4.7 24.0 1.0 CG2 A:VAL50 4.8 23.2 1.0 CA A:VAL50 4.8 22.6 1.0 CG A:PRO8 5.0 25.8 1.0 CB A:GLN9 5.0 23.8 1.0

J.Wachino, Y.Yamaguchi, S.Mori, H.Kurosaki, Y.Arakawa, K.Shibayama. Structural Insights Into the Subclass B3 Metallo-Beta-Lactamase Smb-1 and the Mode of Inhibition By the Common Metallo- -Lactamase Inhibitor Mercaptoacetate Antimicrob.Agents Chemother. V. 57 101 2013.
ISSN: ISSN 0066-4804
PubMed: 23070156
DOI: 10.1128/AAC.01264-12