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

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor, PDB code: 4zuq 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)	41.80 / 1.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.917, 120.511, 64.408, 90.00, 96.89, 90.00
R / Rfree (%)	13.7 / 15.2

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

Potassium	(K)	2 atoms
Zinc	(Zn)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor (pdb code 4zuq). 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 Hydroxamate Inhibitor, PDB code: 4zuq:
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 Hydroxamate 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 Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:10.7 occ:1.00 O A:ARG209 2.2 10.8 1.0 O A:HOH705 2.2 10.4 1.0 O A:VAL212 2.3 9.1 1.0 OG1 A:THR243 2.4 10.8 1.0 O A:PHE206 2.5 7.9 1.0 CB A:THR243 3.3 10.1 1.0 C A:ARG209 3.3 10.5 1.0 C A:VAL212 3.5 7.6 1.0 C A:PHE206 3.6 6.6 1.0 O A:HOH554 3.7 9.8 1.0 CB A:PHE206 3.9 7.9 1.0 O A:THR243 4.0 8.1 1.0 N A:ARG209 4.0 9.8 1.0 CA A:ARG209 4.1 10.6 1.0 CG2 A:THR243 4.2 12.4 1.0 CB A:ARG209 4.3 12.1 1.0 CA A:PHE206 4.3 6.9 1.0 CA A:VAL212 4.4 8.4 1.0 N A:VAL212 4.4 8.6 1.0 N A:GLY210 4.4 10.6 1.0 C A:THR243 4.4 7.6 1.0 O A:HOH692 4.4 8.0 1.0 CA A:GLY240 4.4 11.2 1.0 CA A:THR243 4.5 8.5 1.0 N A:PHE213 4.5 7.8 1.0 O A:GLY240 4.6 9.4 1.0 CB A:VAL212 4.6 8.4 1.0 CA A:GLY210 4.6 11.8 1.0 N A:TYR207 4.6 6.8 1.0 CA A:PHE213 4.6 7.7 1.0 C A:TYR207 4.6 7.5 1.0 O A:TYR207 4.7 8.1 1.0 CA A:TYR207 4.8 7.6 1.0 C A:GLY210 5.0 10.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:10.0 occ:1.00 O B:ARG209 2.2 10.4 1.0 O B:HOH715 2.2 9.7 1.0 O B:VAL212 2.3 8.8 1.0 OG1 B:THR243 2.4 10.4 1.0 O B:PHE206 2.5 6.9 1.0 CB B:THR243 3.3 9.7 1.0 C B:ARG209 3.4 9.2 1.0 C B:VAL212 3.5 8.1 1.0 O B:HOH542 3.6 9.3 1.0 C B:PHE206 3.6 6.4 1.0 CB B:PHE206 3.9 7.5 1.0 O B:THR243 3.9 7.5 1.0 N B:ARG209 4.0 8.0 1.0 CA B:ARG209 4.1 8.9 1.0 CG2 B:THR243 4.2 12.5 1.0 CA B:PHE206 4.3 7.1 1.0 CB B:ARG209 4.3 10.6 1.0 CA B:VAL212 4.3 8.5 1.0 N B:VAL212 4.4 8.2 1.0 C B:THR243 4.4 7.0 1.0 CA B:GLY240 4.4 8.9 1.0 N B:GLY210 4.4 9.1 1.0 O B:HOH673 4.4 7.5 1.0 CA B:THR243 4.5 8.2 1.0 N B:PHE213 4.5 7.8 1.0 O B:GLY240 4.6 8.3 1.0 CB B:VAL212 4.6 8.5 1.0 O B:TYR207 4.6 7.7 1.0 N B:TYR207 4.6 6.7 1.0 C B:TYR207 4.6 7.3 1.0 CA B:GLY210 4.6 10.2 1.0 CA B:PHE213 4.7 7.6 1.0 CA B:TYR207 4.8 6.4 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