Zinc in PDB 5nc6: Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide

The structure of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide, PDB code: 5nc6 was solved by P.Giastas, A.Andreou, S.Balomenou, V.Bouriotis, E.E.Eliopoulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.35 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.358, 118.012, 98.618, 90.00, 102.28, 90.00
R / Rfree (%)	22 / 28

The binding sites of Zinc atom in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide (pdb code 5nc6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide, PDB code: 5nc6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:85.7 occ:1.00 NE2 A:HIS130 2.1 46.8 1.0 NE2 A:HIS126 2.2 73.6 1.0 OD1 A:ASP77 2.2 71.2 1.0 O A:ACT301 2.4 57.7 1.0 OXT A:ACT301 2.4 66.0 1.0 O A:HOH403 2.6 61.8 1.0 OD2 A:ASP77 2.7 68.9 1.0 CG A:ASP77 2.8 63.7 1.0 C A:ACT301 2.8 62.5 1.0 CD2 A:HIS130 3.0 33.5 1.0 CE1 A:HIS126 3.1 59.8 1.0 CD2 A:HIS126 3.2 57.0 1.0 CE1 A:HIS130 3.2 39.0 1.0 OD2 A:ASP76 3.5 48.1 1.0 CB A:ASP76 3.9 55.5 1.0 CG A:HIS130 4.2 34.5 1.0 ND1 A:HIS126 4.2 58.0 1.0 CG A:ASP76 4.2 55.3 1.0 ND1 A:HIS130 4.3 36.1 1.0 CG A:HIS126 4.3 52.2 1.0 CH3 A:ACT301 4.3 49.9 1.0 CB A:ASP77 4.3 51.0 1.0 CA A:PRO166 4.5 36.5 1.0 NE2 A:HIS230 4.6 51.5 1.0 N A:ASP77 4.7 43.4 1.0 CD2 A:HIS230 4.7 55.7 1.0 CB A:PRO166 4.8 50.9 1.0 O D:HOH413 4.9 34.0 1.0 CA A:ASP77 4.9 34.4 1.0 N A:TYR167 5.0 33.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:60.4 occ:1.00 NE2 B:HIS130 2.1 57.9 1.0 O02 B:8SQ301 2.1 66.8 1.0 NE2 B:HIS126 2.1 66.3 1.0 O B:HOH410 2.2 55.2 1.0 OD1 B:ASP77 2.2 75.1 1.0 O01 B:8SQ301 2.3 71.2 1.0 OD2 B:ASP77 2.8 89.0 1.0 CD2 B:HIS130 2.8 34.7 1.0 C13 B:8SQ301 2.8 70.0 1.0 CG B:ASP77 2.9 69.3 1.0 N01 B:8SQ301 2.9 67.2 1.0 CD2 B:HIS126 3.0 65.3 1.0 CE1 B:HIS126 3.1 59.7 1.0 CE1 B:HIS130 3.3 35.0 1.0 CG B:HIS130 4.1 44.1 1.0 C12 B:8SQ301 4.1 59.5 1.0 ND1 B:HIS126 4.1 58.1 1.0 CG B:HIS126 4.1 56.5 1.0 ND1 B:HIS130 4.2 36.0 1.0 CB B:ASP76 4.3 59.1 1.0 CB B:ASP77 4.4 52.0 1.0 CA B:PRO166 4.4 58.2 1.0 CB B:PRO166 4.6 51.0 1.0 OD2 B:ASP76 4.6 45.5 1.0 CD2 B:HIS230 4.7 47.2 1.0 NE2 B:HIS230 4.8 42.9 1.0 N B:TYR167 4.9 59.8 1.0 N B:ASP77 4.9 56.9 1.0 O B:HOH427 5.0 32.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:57.2 occ:1.00 CE1 C:HIS130 1.9 76.1 1.0 OXT C:ACT301 2.2 94.7 1.0 NE2 C:HIS126 2.2 62.2 1.0 OD1 C:ASP77 2.3 85.8 1.0 O C:HOH408 2.4 60.4 1.0 OD2 C:ASP77 2.4 88.5 1.0 O C:ACT301 2.5 94.2 1.0 NE2 C:HIS130 2.5 55.5 1.0 CG C:ASP77 2.7 79.2 1.0 C C:ACT301 2.8 93.2 1.0 ND1 C:HIS130 3.2 65.1 1.0 CD2 C:HIS126 3.2 59.4 1.0 CE1 C:HIS126 3.2 57.3 1.0 CD2 C:HIS130 3.9 48.4 1.0 CG C:HIS130 4.1 50.6 1.0 OD2 C:ASP76 4.2 62.6 1.0 CB C:ASP76 4.2 66.7 1.0 CB C:ASP77 4.2 58.2 1.0 CH3 C:ACT301 4.2 84.4 1.0 ND1 C:HIS126 4.3 56.4 1.0 CG C:HIS126 4.3 56.6 1.0 CA C:PRO166 4.6 41.5 1.0 CE1 C:HIS230 4.6 97.1 1.0 CG C:ASP76 4.7 65.2 1.0 CB C:PRO166 4.7 42.9 1.0 N C:ASP77 4.8 38.7 1.0 CA C:ASP77 4.9 39.1 1.0 ND1 C:HIS230 5.0 99.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (E)-N-Hydroxy-3-(Naphthalen-1-Yl) Prop-2-Enamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:44.0 occ:1.00 CE1 D:HIS130 1.5 59.7 1.0 O D:HOH401 2.0 56.2 1.0 O01 D:8SQ301 2.1 61.4 0.9 O02 D:8SQ301 2.2 48.8 0.9 OD1 D:ASP77 2.2 71.1 1.0 NE2 D:HIS130 2.3 41.1 1.0 NE2 D:HIS126 2.4 54.5 1.0 CE1 D:HIS126 2.5 57.8 1.0 ND1 D:HIS130 2.7 42.5 1.0 C13 D:8SQ301 2.9 50.9 0.9 CG D:ASP77 3.0 55.8 1.0 N01 D:8SQ301 3.0 48.4 0.9 OD2 D:ASP77 3.2 60.9 1.0 CD2 D:HIS130 3.5 32.2 1.0 ND1 D:HIS126 3.6 50.4 1.0 CD2 D:HIS126 3.6 46.0 1.0 CG D:HIS130 3.7 35.5 1.0 C12 D:8SQ301 4.2 51.3 0.9 CG D:HIS126 4.2 47.9 1.0 CA D:PRO166 4.3 37.3 1.0 CB D:ASP77 4.4 52.8 1.0 CB D:PRO166 4.5 32.2 1.0 C11 D:8SQ301 4.6 57.0 0.9 N D:TYR167 4.9 59.7 1.0 N D:ASP77 4.9 39.4 1.0 CB D:ASP76 4.9 42.9 1.0 CA D:ASP77 4.9 52.5 1.0 CG D:PRO166 4.9 32.5 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