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

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor, PDB code: 4zum 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)	38.89 / 1.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.119, 121.351, 64.295, 90.00, 96.76, 90.00
R / Rfree (%)	13.3 / 15.3

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

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

The binding sites of Sodium atom in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor (pdb code 4zum). 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 Trifluoromethylketone Inhibitor, PDB code: 4zum:
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 Trifluoromethylketone 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 Trifluoromethylketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:11.8 occ:1.00 O A:HOH708 2.2 10.8 1.0 O A:ARG209 2.3 9.8 1.0 O A:VAL212 2.4 10.6 1.0 OG1 A:THR243 2.4 12.7 1.0 O A:PHE206 2.5 8.0 1.0 CB A:THR243 3.3 10.7 1.0 C A:ARG209 3.4 8.7 1.0 O A:HOH540 3.5 10.2 1.0 C A:VAL212 3.6 9.4 1.0 C A:PHE206 3.6 7.2 1.0 O A:THR243 3.8 9.0 1.0 CB A:PHE206 3.9 8.0 1.0 N A:ARG209 4.1 8.1 1.0 CA A:ARG209 4.2 8.7 1.0 CG2 A:THR243 4.2 13.8 1.0 C A:THR243 4.3 7.6 1.0 CA A:PHE206 4.3 7.1 1.0 O A:HOH641 4.4 8.4 1.0 CB A:ARG209 4.4 9.2 1.0 CA A:GLY240 4.4 9.4 1.0 CA A:THR243 4.4 8.9 1.0 N A:VAL212 4.4 8.7 1.0 CA A:VAL212 4.4 9.2 1.0 N A:GLY210 4.5 9.6 1.0 N A:PHE213 4.5 8.9 1.0 O A:GLY240 4.6 8.8 1.0 O A:TYR207 4.6 9.0 1.0 CA A:PHE213 4.6 7.9 1.0 N A:TYR207 4.6 6.9 1.0 C A:TYR207 4.6 7.3 1.0 CB A:VAL212 4.7 9.3 1.0 CA A:GLY210 4.7 11.7 1.0 CA A:TYR207 4.7 5.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone 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 Trifluoromethylketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:12.4 occ:1.00 O B:HOH725 2.1 11.4 1.0 O B:ARG209 2.3 10.7 1.0 OG1 B:THR243 2.3 13.5 1.0 O B:VAL212 2.3 10.6 1.0 O B:PHE206 2.5 8.8 1.0 CB B:THR243 3.3 11.7 1.0 C B:ARG209 3.5 9.5 1.0 O B:HOH554 3.5 11.3 1.0 C B:VAL212 3.6 9.5 1.0 C B:PHE206 3.6 7.0 1.0 O B:THR243 3.8 8.1 1.0 CB B:PHE206 3.9 7.0 1.0 N B:ARG209 4.2 9.7 1.0 CA B:ARG209 4.2 10.9 1.0 CG2 B:THR243 4.3 14.6 1.0 C B:THR243 4.3 8.0 1.0 O B:HOH676 4.3 8.6 1.0 CA B:PHE206 4.3 6.8 1.0 CB B:ARG209 4.4 12.0 1.0 CA B:GLY240 4.4 12.7 1.0 CA B:THR243 4.4 9.0 1.0 CA B:VAL212 4.4 9.1 1.0 N B:VAL212 4.5 8.8 1.0 N B:GLY210 4.5 10.9 1.0 N B:PHE213 4.5 8.8 1.0 O B:GLY240 4.5 9.6 1.0 CA B:PHE213 4.6 7.9 1.0 O B:TYR207 4.6 9.2 1.0 N B:TYR207 4.6 7.8 1.0 C B:TYR207 4.6 7.8 1.0 CA B:GLY210 4.7 13.5 1.0 CB B:VAL212 4.7 9.3 1.0 CA B:TYR207 4.8 8.4 1.0 C B:GLY240 5.0 10.3 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