Sodium in PDB 7afy: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306, PDB code: 7afy was solved by J.Brem, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.18 / 1.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.648, 68.015, 40.236, 90, 92.94, 90
R / Rfree (%)	12.6 / 14.5

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306 (pdb code 7afy). 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 VIM1 with 1306, PDB code: 7afy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306


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 VIM1 with 1306 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:13.6 occ:1.00 H A:ASP117 2.3 10.2 1.0 HD21 A:ASN148 2.3 15.1 1.0 O A:HOH514 2.6 25.5 1.0 HA A:HIS116 2.9 9.7 1.0 HB2 A:ASP117 3.0 12.0 1.0 N A:ASP117 3.1 8.5 1.0 O A:HOH673 3.1 17.5 1.0 ND2 A:ASN148 3.2 12.6 1.0 H012 A:RBW301 3.2 12.9 0.7 H012 A:RBW301 3.2 12.9 0.3 HD2 A:HIS116 3.4 12.2 1.0 HB3 A:HIS116 3.5 10.3 1.0 CA A:HIS116 3.6 8.1 1.0 HD22 A:ASN148 3.6 15.1 1.0 HG2 A:GLU146 3.7 23.3 1.0 H033 A:RBW301 3.7 13.3 0.3 H033 A:RBW301 3.7 14.1 0.7 CB A:ASP117 3.8 10.0 1.0 H031 A:RBW301 3.8 13.3 0.3 H031 A:RBW301 3.8 14.1 0.7 C A:HIS116 3.8 8.3 1.0 HB3 A:ASP117 3.9 12.0 1.0 CD2 A:HIS116 3.9 10.2 1.0 CB A:HIS116 3.9 8.6 1.0 CA A:ASP117 4.0 8.6 1.0 C01 A:RBW301 4.1 10.8 0.7 C01 A:RBW301 4.1 10.7 0.3 CG A:ASN148 4.1 11.8 1.0 CG A:HIS116 4.2 8.8 1.0 H011 A:RBW301 4.2 12.9 0.7 C03 A:RBW301 4.2 11.1 0.3 C03 A:RBW301 4.2 11.7 0.7 OD1 A:ASN148 4.2 13.6 1.0 H011 A:RBW301 4.2 12.9 0.3 O A:HOH702 4.5 24.5 1.0 HA A:ASP117 4.5 10.4 1.0 CG A:GLU146 4.5 19.4 1.0 HE2 A:PHE62 4.6 17.9 1.0 HG3 A:GLU146 4.6 23.3 1.0 OE2 A:GLU146 4.6 24.8 1.0 O A:HOH593 4.7 36.3 1.0 C02 A:RBW301 4.7 10.0 0.7 C02 A:RBW301 4.8 10.4 0.3 H013 A:RBW301 4.8 12.9 0.7 O A:PHE115 4.8 7.9 1.0 H013 A:RBW301 4.8 12.9 0.3 HB2 A:HIS116 4.8 10.3 1.0 N A:HIS116 4.9 7.3 1.0 H A:ASP118 4.9 9.0 1.0 CD A:GLU146 5.0 22.5 1.0 NE2 A:HIS116 5.0 10.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 1306


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 VIM1 with 1306 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:17.9 occ:1.00 H A:ASP213 2.1 17.0 1.0 HE1 A:HIS116 2.6 11.3 1.0 O A:HIS179 2.8 10.5 1.0 O A:ASN210 2.9 13.5 1.0 HB2 A:ASP213 2.9 18.5 1.0 N A:ASP213 2.9 14.2 1.0 HA A:VAL211 3.2 18.6 1.0 H A:ALA214 3.4 15.7 1.0 CE1 A:HIS179 3.5 9.4 1.0 H A:ALA212 3.5 18.9 1.0 N A:ALA214 3.5 13.1 1.0 CA A:ASP213 3.5 14.2 1.0 CE1 A:HIS116 3.5 9.4 1.0 HB2 A:ALA214 3.5 17.6 1.0 HE1 A:HIS179 3.5 11.3 1.0 N A:ALA212 3.5 15.8 1.0 C A:VAL211 3.6 15.2 1.0 C A:ASP213 3.6 12.8 1.0 CB A:ASP213 3.6 15.4 1.0 ND1 A:HIS179 3.8 9.7 1.0 NE2 A:HIS179 3.8 9.9 1.0 CA A:VAL211 3.8 15.5 1.0 C A:ASN210 3.8 13.4 1.0 HD1 A:HIS179 4.0 11.7 1.0 C A:HIS179 4.0 10.0 1.0 C A:ALA212 4.0 15.9 1.0 O A:VAL211 4.1 16.8 1.0 N A:VAL211 4.2 14.7 1.0 HB3 A:ALA212 4.2 22.3 1.0 HA A:ALA214 4.2 15.9 1.0 HE2 A:HIS116 4.2 12.9 1.0 CA A:ALA214 4.2 13.2 1.0 CD2 A:HIS179 4.2 8.7 1.0 CG A:HIS179 4.3 9.3 1.0 CB A:ALA214 4.3 14.7 1.0 CA A:ALA212 4.3 17.6 1.0 NE2 A:HIS116 4.3 10.8 1.0 HB3 A:ASP213 4.3 18.5 1.0 HB3 A:SER180 4.4 11.4 1.0 O A:ASP213 4.4 13.6 1.0 HA A:ASP213 4.4 17.0 1.0 ND1 A:HIS116 4.5 8.7 1.0 CG A:ASP213 4.5 16.3 1.0 HA A:HIS179 4.5 12.2 1.0 HB3 A:ALA214 4.6 17.6 1.0 OD1 A:ASN210 4.6 15.9 1.0 OD2 A:ASP213 4.6 15.2 1.0 HA A:SER180 4.7 12.1 1.0 HB3 A:ASN210 4.7 15.6 1.0 CB A:ALA212 4.8 18.6 1.0 CA A:HIS179 4.8 10.2 1.0 HD2 A:HIS179 4.8 10.4 1.0 ZN A:ZN305 5.0 8.7 1.0 N A:SER180 5.0 9.5 1.0 H A:VAL211 5.0 17.6 1.0

J.Brem, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139 To Be Published.