Sodium in PDB 4zun: Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor, PDB code: 4zun was solved by C.Decroos, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.78 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.859, 120.993, 64.710, 90.00, 97.03, 90.00
R / Rfree (%)	14.6 / 16.4

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Zinc	(Zn)	6 atoms

The binding sites of Sodium atom in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor (pdb code 4zun). 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 Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor, PDB code: 4zun:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor


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 Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:16.5 occ:1.00 O A:ARG209 2.2 16.3 1.0 O A:HOH706 2.2 15.9 1.0 O A:VAL212 2.3 15.2 1.0 OG1 A:THR243 2.3 19.1 1.0 O A:PHE206 2.6 13.8 1.0 CB A:THR243 3.3 16.2 1.0 C A:ARG209 3.4 15.1 1.0 C A:VAL212 3.5 14.4 1.0 O A:HOH551 3.6 16.5 1.0 C A:PHE206 3.7 13.2 1.0 O A:THR243 3.9 14.0 1.0 CB A:PHE206 4.0 12.5 1.0 N A:ARG209 4.1 13.7 1.0 CA A:ARG209 4.2 15.7 1.0 CG2 A:THR243 4.2 19.3 1.0 C A:THR243 4.3 14.3 1.0 CA A:VAL212 4.4 14.0 1.0 N A:VAL212 4.4 13.5 1.0 CA A:THR243 4.4 15.4 1.0 CA A:PHE206 4.4 11.3 1.0 CA A:GLY240 4.4 15.1 1.0 CB A:ARG209 4.4 16.9 1.0 O A:HOH684 4.4 13.2 1.0 N A:GLY210 4.4 16.1 1.0 N A:PHE213 4.5 14.3 1.0 O A:GLY240 4.5 15.2 1.0 CA A:PHE213 4.6 14.1 1.0 CB A:VAL212 4.6 13.2 1.0 CA A:GLY210 4.6 18.6 1.0 O A:TYR207 4.7 13.8 1.0 N A:TYR207 4.7 12.4 1.0 C A:TYR207 4.7 12.2 1.0 CA A:TYR207 4.8 11.3 1.0 C A:GLY210 5.0 18.5 1.0 C A:GLY240 5.0 14.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor


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 Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:19.7 occ:1.00 O B:ARG209 2.2 19.6 1.0 O B:HOH673 2.2 17.1 1.0 O B:VAL212 2.3 17.8 1.0 OG1 B:THR243 2.4 19.1 1.0 O B:PHE206 2.5 14.8 1.0 CB B:THR243 3.3 17.5 1.0 C B:ARG209 3.4 19.4 1.0 C B:VAL212 3.5 16.2 1.0 O B:HOH537 3.6 18.3 1.0 C B:PHE206 3.6 14.7 1.0 O B:THR243 3.9 15.0 1.0 CB B:PHE206 3.9 14.3 1.0 N B:ARG209 4.1 19.9 1.0 CA B:ARG209 4.1 20.9 1.0 CG2 B:THR243 4.2 20.0 1.0 CA B:PHE206 4.3 12.9 1.0 C B:THR243 4.3 15.1 1.0 CB B:ARG209 4.4 19.4 1.0 CA B:VAL212 4.4 16.4 1.0 N B:GLY210 4.4 21.9 1.0 N B:VAL212 4.4 16.9 1.0 O B:HOH625 4.4 15.1 1.0 CA B:GLY240 4.4 21.9 1.0 CA B:THR243 4.5 16.3 1.0 N B:PHE213 4.5 15.5 1.0 O B:GLY240 4.5 17.8 1.0 CB B:VAL212 4.6 15.5 1.0 CA B:PHE213 4.6 15.2 1.0 CA B:GLY210 4.6 22.3 1.0 N B:TYR207 4.7 14.6 1.0 C B:TYR207 4.7 14.1 1.0 O B:TYR207 4.7 15.8 1.0 CA B:TYR207 4.8 13.8 1.0 C B:GLY240 5.0 18.9 1.0

C.Decroos, D.W.Christianson. Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase. Biochemistry V. 54 4692 2015.
ISSN: ISSN 0006-2960
PubMed: 26200446
DOI: 10.1021/ACS.BIOCHEM.5B00536