Zinc in PDB 5nc9: Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (2S)-2,6-Diamino-N-Hydroxyhexanamide

The structure of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (2S)-2,6-Diamino-N-Hydroxyhexanamide, PDB code: 5nc9 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)	48.61 / 2.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.767, 117.835, 99.059, 90.00, 102.38, 90.00
R / Rfree (%)	22 / 27.9

The binding sites of Zinc atom in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with (2S)-2,6-Diamino-N-Hydroxyhexanamide (pdb code 5nc9). 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)-2,6-Diamino-N-Hydroxyhexanamide, PDB code: 5nc9:
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)-2,6-Diamino-N-Hydroxyhexanamide


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)-2,6-Diamino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:88.6 occ:1.00 NE2 A:HIS130 2.1 44.5 1.0 O02 A:8SZ301 2.1 60.1 1.0 OD1 A:ASP77 2.2 75.3 1.0 NE2 A:HIS126 2.2 64.0 1.0 O01 A:8SZ301 2.3 83.2 1.0 N05 A:8SZ301 2.6 78.5 1.0 C11 A:8SZ301 2.7 82.5 1.0 CE1 A:HIS130 2.9 51.8 1.0 CG A:ASP77 3.1 68.0 1.0 CD2 A:HIS130 3.1 50.3 1.0 CD2 A:HIS126 3.2 55.3 1.0 CE1 A:HIS126 3.2 41.5 1.0 OD2 A:ASP77 3.3 67.3 1.0 C07 A:8SZ301 3.4 78.1 1.0 C08 A:8SZ301 4.0 79.0 1.0 C06 A:8SZ301 4.1 81.4 1.0 ND1 A:HIS130 4.1 52.8 1.0 CG A:HIS130 4.2 50.5 1.0 ND1 A:HIS126 4.3 53.2 1.0 CG A:HIS126 4.3 58.0 1.0 CB A:ASP76 4.3 52.5 1.0 OD2 A:ASP76 4.3 60.2 1.0 CA A:PRO166 4.5 40.6 1.0 C09 A:8SZ301 4.5 70.8 1.0 CB A:ASP77 4.5 64.8 1.0 CB A:PRO166 4.7 46.4 1.0 NE2 A:HIS230 4.8 61.1 1.0 N A:ASP77 4.8 53.9 1.0 CG A:ASP76 4.9 56.8 1.0 CD2 A:HIS230 4.9 63.5 1.0 N03 A:8SZ301 5.0 73.2 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)-2,6-Diamino-N-Hydroxyhexanamide


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)-2,6-Diamino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:71.7 occ:1.00 NE2 B:HIS130 2.1 40.2 1.0 NE2 B:HIS126 2.1 56.8 1.0 O02 B:8SZ301 2.2 64.7 1.0 OD1 B:ASP77 2.2 72.4 1.0 O B:HOH417 2.3 49.4 1.0 O01 B:8SZ301 2.3 57.8 1.0 N05 B:8SZ301 2.7 69.9 1.0 C11 B:8SZ301 2.7 66.6 1.0 CD2 B:HIS130 3.1 40.7 1.0 CD2 B:HIS126 3.1 47.5 1.0 CG B:ASP77 3.1 61.4 1.0 CE1 B:HIS130 3.1 45.1 1.0 CE1 B:HIS126 3.1 46.7 1.0 OD2 B:ASP77 3.3 58.9 1.0 C08 B:8SZ301 4.0 65.5 1.0 ND1 B:HIS130 4.2 51.1 1.0 ND1 B:HIS126 4.2 47.3 1.0 CG B:HIS130 4.3 42.7 1.0 CG B:HIS126 4.3 46.7 1.0 C06 B:8SZ301 4.3 66.3 1.0 CA B:PRO166 4.4 59.2 1.0 CB B:ASP76 4.4 50.4 1.0 OD2 B:ASP76 4.5 49.7 1.0 CB B:ASP77 4.6 54.4 1.0 NE2 B:HIS230 4.6 52.2 1.0 CB B:PRO166 4.6 56.4 1.0 CD2 B:HIS230 4.7 54.6 1.0 C07 B:8SZ301 4.7 70.5 1.0 N B:TYR167 4.8 57.2 1.0 N B:ASP77 4.9 47.4 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)-2,6-Diamino-N-Hydroxyhexanamide


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)-2,6-Diamino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:70.5 occ:1.00 NE2 C:HIS130 2.1 40.6 1.0 O02 C:8SZ301 2.1 55.0 1.0 OD1 C:ASP77 2.2 72.1 1.0 NE2 C:HIS126 2.2 54.3 1.0 O01 C:8SZ301 2.3 79.7 1.0 N05 C:8SZ301 2.6 76.9 1.0 C11 C:8SZ301 2.7 81.7 1.0 CD2 C:HIS130 3.1 52.3 1.0 CE1 C:HIS130 3.1 47.3 1.0 CG C:ASP77 3.1 66.1 1.0 CD2 C:HIS126 3.2 56.1 1.0 CE1 C:HIS126 3.2 47.7 1.0 OD2 C:ASP77 3.2 69.5 1.0 C07 C:8SZ301 3.6 80.1 1.0 C08 C:8SZ301 4.0 78.0 1.0 C06 C:8SZ301 4.1 81.3 1.0 ND1 C:HIS130 4.2 46.1 1.0 CG C:HIS130 4.2 50.3 1.0 CB C:ASP76 4.2 61.2 1.0 OD2 C:ASP76 4.3 67.4 1.0 ND1 C:HIS126 4.3 54.5 1.0 CG C:HIS126 4.4 58.0 1.0 CB C:ASP77 4.5 63.0 1.0 CA C:PRO166 4.5 39.7 1.0 C09 C:8SZ301 4.6 72.2 1.0 NE2 C:HIS230 4.6 64.7 1.0 CD2 C:HIS230 4.7 68.6 1.0 N C:ASP77 4.8 54.2 1.0 CG C:ASP76 4.8 64.1 1.0 CB C:PRO166 4.9 40.3 1.0 N C:TYR167 4.9 56.3 1.0 N03 C:8SZ301 5.0 70.7 1.0 CA C:ASP77 5.0 58.7 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)-2,6-Diamino-N-Hydroxyhexanamide


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)-2,6-Diamino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:50.3 occ:1.00 NE2 D:HIS130 2.1 39.5 1.0 O02 D:8SZ301 2.1 71.2 1.0 NE2 D:HIS126 2.1 39.5 1.0 OD1 D:ASP77 2.2 51.1 1.0 O01 D:8SZ301 2.2 60.8 1.0 O D:HOH412 2.3 34.7 1.0 N05 D:8SZ301 2.8 69.1 1.0 C11 D:8SZ301 2.8 65.3 1.0 CG D:ASP77 3.1 50.3 1.0 CD2 D:HIS130 3.1 46.9 1.0 CD2 D:HIS126 3.1 40.1 1.0 CE1 D:HIS130 3.1 44.9 1.0 CE1 D:HIS126 3.2 39.7 1.0 OD2 D:ASP77 3.2 58.9 1.0 ND1 D:HIS130 4.2 47.9 1.0 CG D:HIS130 4.2 45.4 1.0 CG D:HIS126 4.2 43.1 1.0 C08 D:8SZ301 4.2 70.6 1.0 ND1 D:HIS126 4.2 43.5 1.0 CB D:ASP76 4.3 56.5 1.0 C07 D:8SZ301 4.4 70.0 1.0 CA D:PRO166 4.4 48.5 1.0 OD2 D:ASP76 4.4 56.4 1.0 NE2 D:HIS230 4.5 44.3 1.0 CB D:ASP77 4.5 55.7 1.0 CB D:PRO166 4.7 45.9 1.0 CD2 D:HIS230 4.7 46.9 1.0 N D:ASP77 4.8 53.5 1.0 C06 D:8SZ301 4.8 68.2 1.0 CG D:ASP76 4.9 58.5 1.0 N D:TYR167 4.9 52.9 1.0 CA D:ASP77 5.0 55.4 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