Sodium in PDB 6ol8: Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin

The structure of Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin, PDB code: 6ol8 was solved by J.E.Raczynska, B.Imiolczyk, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.65 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.469, 76.449, 130.906, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.7

The structure of Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin (pdb code 6ol8). 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 Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin, PDB code: 6ol8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin


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 Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:48.0 occ:1.00 OD2 A:ASP223 1.9 48.6 1.0 OE2 A:GLU152 2.3 39.2 1.0 CG A:ASP223 2.7 43.2 1.0 OE1 A:GLU152 2.9 35.8 1.0 CD A:GLU152 2.9 38.0 1.0 OD1 A:ASP223 3.0 48.4 1.0 NE2 A:HIS122 3.8 27.2 1.0 CB A:ASP223 4.2 37.4 1.0 O A:HOH490 4.3 34.8 1.0 CG A:GLU152 4.4 38.8 1.0 CD2 A:HIS122 4.5 26.3 1.0 CE1 A:HIS122 4.9 29.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin


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 Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:21.7 occ:1.00 O B:HOH450 1.9 33.2 1.0 OD2 B:ASP223 1.9 42.5 1.0 OE2 B:GLU152 2.3 43.2 1.0 OE1 B:GLU152 2.5 34.6 1.0 CG B:ASP223 2.7 44.9 1.0 CD B:GLU152 2.8 35.5 1.0 OD1 B:ASP223 2.9 39.8 1.0 NE2 B:HIS122 4.0 25.6 1.0 O B:HOH468 4.1 29.6 1.0 CB B:ASP223 4.2 40.3 1.0 CG B:GLU152 4.2 35.0 1.0 CD2 B:HIS122 4.6 25.8 1.0

J.E.Raczynska, J.Sliwiak, M.Komorowska, J.Czyrko, B.Imiolczyk, K.Brzezinski, M.Jaskolski. Flexible Loop of New Delhi Metall-Beta-Lactamase Modulates Its Activity Towards Different Substrates To Be Published.