Sodium in PDB 5n1p: Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide

The structure of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide, PDB code: 5n1p was solved by P.Giastas, A.Andreou, E.E.Eliopoulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	196.103, 44.347, 99.132, 90.00, 98.83, 90.00
R / Rfree (%)	16.1 / 18

The structure of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide (pdb code 5n1p). 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 the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide, PDB code: 5n1p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide


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 the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:36.3 occ:1.00 O C:HOH464 3.1 41.7 1.0 O C:HOH486 3.9 45.0 1.0 O C:HOH468 4.6 30.3 1.0 OE1 C:GLU85 4.9 59.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide


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 the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:32.5 occ:1.00 O D:GLY168 2.7 22.4 1.0 N D:GLY172 2.8 25.6 1.0 O D:HOH509 3.0 37.6 1.0 C D:MET170 3.2 22.6 1.0 O D:MET170 3.3 23.5 1.0 N D:PRO171 3.3 23.2 1.0 CA D:GLY172 3.4 26.8 1.0 CE2 D:PHE132 3.4 37.7 1.0 N D:MET170 3.5 22.1 1.0 C D:SER169 3.6 20.8 1.0 CD D:PRO171 3.7 29.4 1.0 C D:GLY168 3.8 20.7 1.0 O D:SER169 3.8 21.9 1.0 CA D:MET170 3.9 22.6 1.0 C D:PRO171 3.9 23.8 1.0 O D:TYR167 4.0 23.5 1.0 CZ D:PHE132 4.1 36.1 1.0 CA D:PRO171 4.2 23.5 1.0 O D:HOH421 4.2 25.5 1.0 CA D:SER169 4.3 18.0 1.0 CE2 D:TYR136 4.4 26.1 1.0 CD2 D:PHE132 4.4 37.2 1.0 N D:SER169 4.4 18.4 1.0 C D:TYR167 4.5 22.3 1.0 C D:GLY172 4.5 25.8 1.0 N D:LEU173 4.6 25.0 1.0 CB D:TYR167 4.6 23.2 1.0 CD2 D:TYR136 4.6 25.4 1.0 CZ D:TYR136 4.6 21.2 1.0 O D:HOH416 4.7 37.0 1.0 CG D:PRO171 4.8 30.2 1.0 O D:PRO166 4.8 21.8 1.0 CA D:GLY168 4.8 20.9 1.0 N D:GLY168 4.9 18.9 1.0

P.Giastas, A.Andreou, A.Papakyriakou, D.Koutsioulis, S.Balomenou, S.J.Tzartos, V.Bouriotis, E.E.Eliopoulos. Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase BC1974 and Its Complexes with Zinc Metalloenzyme Inhibitors. Biochemistry V. 57 753 2018.
ISSN: ISSN 1520-4995
PubMed: 29257674
DOI: 10.1021/ACS.BIOCHEM.7B00919