Zinc in PDB 5ncd: Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide

The structure of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide, PDB code: 5ncd 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)	48.48 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.647, 117.438, 99.488, 90.00, 102.92, 90.00
R / Rfree (%)	22.6 / 29.2

The binding sites of Zinc atom in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide (pdb code 5ncd). 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 (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide, PDB code: 5ncd:
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 (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide


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 (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:49.6 occ:1.00 NE2 A:HIS130 2.0 35.7 1.0 OD1 A:ASP77 2.2 58.4 1.0 NE2 A:HIS126 2.2 57.9 1.0 O A:ACT301 2.3 50.9 1.0 OXT A:ACT301 2.4 63.4 1.0 C A:ACT301 2.7 65.6 1.0 CE1 A:HIS130 2.9 41.5 1.0 O A:HOH431 3.1 60.7 1.0 CE1 A:HIS126 3.1 59.2 1.0 CG A:ASP77 3.1 55.8 1.0 CD2 A:HIS130 3.2 42.9 1.0 CD2 A:HIS126 3.3 60.0 1.0 OD2 A:ASP77 3.3 50.7 1.0 ND1 A:HIS130 4.1 41.7 1.0 OD2 A:ASP76 4.1 48.8 1.0 CH3 A:ACT301 4.1 56.9 1.0 CB A:ASP76 4.2 55.1 1.0 CG A:HIS130 4.2 43.4 1.0 ND1 A:HIS126 4.3 65.5 1.0 CG A:HIS126 4.4 63.5 1.0 CA A:PRO166 4.5 44.8 1.0 CB A:ASP77 4.6 65.6 1.0 CG A:ASP76 4.7 54.6 1.0 NE2 A:HIS230 4.7 60.5 1.0 CB A:PRO166 4.8 48.4 1.0 CD2 A:HIS230 4.8 69.0 1.0 N A:TYR167 5.0 53.8 1.0 N A:ASP77 5.0 43.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide


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 (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:79.1 occ:1.00 NE2 B:HIS130 2.1 36.7 1.0 NE2 B:HIS126 2.2 57.7 1.0 O2 B:AHL301 2.2 53.4 1.0 OD1 B:ASP77 2.2 82.3 1.0 O1 B:AHL301 2.3 74.6 1.0 O B:HOH423 2.4 55.2 1.0 CD2 B:HIS130 3.0 37.1 1.0 N2 B:AHL301 3.0 55.1 1.0 C B:AHL301 3.0 65.3 1.0 CD2 B:HIS126 3.1 46.9 1.0 CE1 B:HIS130 3.1 41.9 1.0 CG B:ASP77 3.1 66.8 1.0 CE1 B:HIS126 3.2 37.6 1.0 OD2 B:ASP77 3.3 63.1 1.0 CG B:HIS130 4.1 37.7 1.0 ND1 B:HIS130 4.2 40.6 1.0 ND1 B:HIS126 4.3 47.9 1.0 CG B:HIS126 4.3 50.3 1.0 CA B:PRO166 4.3 54.4 1.0 NE2 B:HIS230 4.4 37.2 1.0 CA B:AHL301 4.5 60.5 1.0 CB B:PRO166 4.5 49.3 1.0 CB B:ASP76 4.6 51.2 1.0 CB B:ASP77 4.6 64.3 1.0 CD2 B:HIS230 4.7 45.0 1.0 OD2 B:ASP76 4.7 49.7 1.0 N B:TYR167 4.8 56.1 1.0 CB B:AHL301 4.9 63.4 1.0 N B:ASP77 5.0 54.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide


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 (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:79.5 occ:1.00 NE2 C:HIS130 2.1 46.3 1.0 NE2 C:HIS126 2.2 50.0 1.0 OD1 C:ASP77 2.2 74.9 1.0 O C:HOH415 2.3 68.8 1.0 OXT C:ACT301 2.3 60.6 1.0 O C:ACT301 2.5 55.5 1.0 C C:ACT301 2.8 59.4 1.0 CD2 C:HIS130 3.0 46.3 1.0 CG C:ASP77 3.1 65.0 1.0 CE1 C:HIS130 3.1 52.6 1.0 CE1 C:HIS126 3.2 44.5 1.0 CD2 C:HIS126 3.2 58.5 1.0 OD2 C:ASP77 3.3 68.1 1.0 OD2 C:ASP76 3.9 65.5 1.0 CG C:HIS130 4.2 55.3 1.0 ND1 C:HIS130 4.2 51.7 1.0 CH3 C:ACT301 4.2 44.4 1.0 CB C:ASP76 4.3 59.4 1.0 ND1 C:HIS126 4.3 49.7 1.0 CG C:HIS126 4.3 58.9 1.0 CG C:ASP76 4.5 65.2 1.0 CA C:PRO166 4.5 42.8 1.0 CB C:ASP77 4.6 63.9 1.0 NE2 C:HIS230 4.8 56.5 1.0 CB C:PRO166 4.8 44.0 1.0 CD2 C:HIS230 4.8 65.9 1.0 N C:ASP77 4.9 44.7 1.0 N C:TYR167 5.0 52.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide


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 (2S)-2-Amino-5- (Diaminomethylideneamino)-N-Hydroxypentanamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:76.2 occ:1.00 O D:HOH412 1.9 50.8 1.0 NE2 D:HIS130 2.1 36.2 1.0 NE2 D:HIS126 2.1 55.0 1.0 OD1 D:ASP77 2.2 75.5 1.0 O D:ACT301 2.4 54.8 1.0 OXT D:ACT301 2.5 63.5 1.0 C D:ACT301 2.8 60.1 1.0 CE1 D:HIS130 3.0 39.4 1.0 CE1 D:HIS126 3.0 46.6 1.0 CD2 D:HIS130 3.1 36.0 1.0 CD2 D:HIS126 3.2 48.2 1.0 CG D:ASP77 3.2 61.0 1.0 OD2 D:ASP77 3.4 63.9 1.0 CB D:ASP76 4.1 50.4 1.0 CH3 D:ACT301 4.1 52.4 1.0 ND1 D:HIS130 4.1 39.6 1.0 ND1 D:HIS126 4.2 48.6 1.0 OD2 D:ASP76 4.2 51.4 1.0 CG D:HIS130 4.2 41.9 1.0 CG D:HIS126 4.3 45.5 1.0 CA D:PRO166 4.3 50.4 1.0 CB D:PRO166 4.5 46.0 1.0 NE2 D:HIS230 4.6 39.4 1.0 CB D:ASP77 4.6 56.5 1.0 CD2 D:HIS230 4.6 44.2 1.0 CG D:ASP76 4.6 54.4 1.0 N D:ASP77 4.7 49.5 1.0 N D:TYR167 4.8 55.8 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