Sodium in PDB 4bz3: Crystal Structure of the Metallo-Beta-Lactamase Vim-2

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Vim-2:
3.5.2.6;

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-2, PDB code: 4bz3 was solved by D.Zollman, J.Brem, M.A.Mcdonough, S.S.Vanberkel, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.844 / 1.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.955, 79.689, 68.171, 90.00, 130.56, 90.00
R / Rfree (%)	11.26 / 13.75

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-2 also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-2 (pdb code 4bz3). 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 the Metallo-Beta-Lactamase Vim-2, PDB code: 4bz3:
Jump to Sodium binding site number: 1; 2;

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


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 the Metallo-Beta-Lactamase Vim-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na300 b:23.2 occ:0.90 OE1 A:GLU171 2.1 19.0 1.0 NE2 A:HIS229 2.2 22.5 1.0 O A:HOH2177 2.3 26.8 1.0 O A:HOH2176 2.4 25.8 1.0 OE2 A:GLU171 2.6 21.0 1.0 CD A:GLU171 2.7 17.7 1.0 CD2 A:HIS229 2.9 20.7 1.0 CE1 A:HIS229 3.3 21.9 1.0 CG A:HIS229 4.1 17.4 1.0 OH A:TYR230 4.1 15.0 1.0 CG A:GLU171 4.2 14.2 1.0 CE1 A:TYR230 4.2 12.1 1.0 ND1 A:HIS229 4.3 21.3 1.0 CZ A:TYR230 4.5 12.6 1.0 CB A:ALA164 4.5 14.7 1.0 O A:HOH2235 4.5 21.3 1.0 O A:HOH2178 4.9 30.3 1.0

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


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 the Metallo-Beta-Lactamase Vim-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na300 b:23.1 occ:0.80 O B:HOH2152 2.1 23.8 1.0 OE1 B:GLU171 2.1 16.0 1.0 NE2 B:HIS229 2.1 20.8 1.0 O B:HOH2153 2.2 21.7 1.0 O B:HOH2214 2.6 27.9 1.0 CD B:GLU171 2.8 13.9 1.0 OE2 B:GLU171 2.8 18.5 1.0 CD2 B:HIS229 2.9 17.9 1.0 O B:HOH2155 3.2 38.5 1.0 CE1 B:HIS229 3.2 19.8 1.0 O B:HOH2236 3.2 28.6 1.0 CG B:HIS229 4.1 15.0 1.0 OH B:TYR230 4.1 13.3 1.0 CE1 B:TYR230 4.1 11.1 1.0 ND1 B:HIS229 4.2 19.1 1.0 CG B:GLU171 4.2 10.9 1.0 O B:HOH2212 4.3 17.1 1.0 O B:HOH2211 4.3 31.8 1.0 CB B:ALA164 4.4 11.7 1.0 CZ B:TYR230 4.4 11.1 1.0 O B:HIS229 4.9 12.1 1.0

J.Brem, S.S.Vanberkel, D.Zollman, C.J.Schofield. B1 Mbl Inhibitor Structures. To Be Published.