Sodium in PDB 8gpc: Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Ampicillin

The structure of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Ampicillin, PDB code: 8gpc was solved by X.Shi, Y.Dai, Q.Zhang, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.59 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.26, 79.11, 134.35, 90, 90, 90
R / Rfree (%)	13 / 16

The structure of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Ampicillin also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Ampicillin (pdb code 8gpc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Ampicillin, PDB code: 8gpc:

Sodium binding site 1 out of 1 in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) 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-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:8.1 occ:1.00 O A:HOH597 1.9 34.4 1.0 OD2 A:ASP223 2.1 15.8 1.0 OE2 A:GLU152 2.1 20.6 1.0 OE1 A:GLU152 2.7 16.6 1.0 CD A:GLU152 2.7 15.8 1.0 CG A:ASP223 2.9 17.6 1.0 OD1 A:ASP223 2.9 19.5 1.0 O A:HOH552 4.0 14.0 1.0 NE2 A:HIS122 4.0 11.8 1.0 CG A:GLU152 4.2 12.9 1.0 O A:HOH445 4.2 42.4 1.0 CB A:ASP223 4.3 14.2 1.0 O A:HOH536 4.5 33.0 1.0 CD2 A:HIS122 4.8 10.4 1.0

X.Shi, Y.Dai, Q.Zhang, W.Liu. Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Ampicillin To Be Published.