Zinc in PDB 5o6y: Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide

The structure of Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide, PDB code: 5o6y was solved by V.E.Fadouloglou, D.Kotsifaki, M.Kokkinidis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.52 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.042, 93.042, 243.868, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.4

The structure of Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	21 atoms

The binding sites of Zinc atom in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide (pdb code 5o6y). 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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide, PDB code: 5o6y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:19.7 occ:0.41 O2 B:5YA302 1.2 16.4 0.6 NE2 B:HIS131 2.2 3.2 1.0 N1 B:5YA302 2.3 25.3 0.6 OD1 B:ASP81 2.5 7.9 1.0 NE2 B:HIS135 2.7 28.6 1.0 O1 B:5YA302 2.9 11.8 0.6 C17 B:5YA302 2.9 24.7 0.6 CD2 B:HIS135 3.0 22.8 1.0 CD2 B:HIS131 3.1 10.1 1.0 CE1 B:HIS131 3.2 8.4 1.0 OA B:PXU171 3.3 13.8 1.0 CG B:ASP81 3.7 13.5 1.0 CE1 B:HIS135 4.0 27.3 1.0 OD2 B:ASP80 4.0 11.6 1.0 CB B:ASP80 4.1 12.8 1.0 OD2 B:ASP81 4.1 12.6 1.0 CG B:HIS131 4.3 11.2 1.0 ND1 B:HIS131 4.3 12.9 1.0 CG B:HIS135 4.3 25.6 1.0 C14 B:5YA302 4.4 31.0 0.6 CG B:ASP80 4.6 12.5 1.0 CA B:PXU171 4.6 4.4 1.0 O B:HOH498 4.6 34.3 1.0 N B:ASP81 4.6 21.0 1.0 CB B:PXU171 4.7 9.7 1.0 ND1 B:HIS135 4.8 28.4 1.0 CB B:ASP81 4.9 18.4 1.0 CA B:ASP81 4.9 20.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn306 b:26.3 occ:0.44 O2 C:5YA305 1.2 39.8 0.6 N1 C:5YA305 1.9 36.3 0.6 OD1 C:ASP81 2.3 8.0 1.0 NE2 C:HIS131 2.4 4.9 1.0 NE2 C:HIS135 2.8 31.8 1.0 CD2 C:HIS135 3.2 31.8 1.0 C17 C:5YA305 3.2 38.8 0.6 CD2 C:HIS131 3.2 4.8 1.0 CG C:ASP81 3.3 12.5 1.0 CE1 C:HIS131 3.4 5.0 1.0 OA C:PXU171 3.4 5.0 0.7 OD2 C:ASP81 3.6 13.4 1.0 O C:HOH436 3.7 46.1 1.0 O1 C:5YA305 3.8 25.1 0.6 CB C:ASP80 3.8 15.1 1.0 CE1 C:HIS135 4.0 29.7 1.0 O C:HOH413 4.1 30.0 0.8 OD1 C:ASP80 4.1 18.6 1.0 C14 C:5YA305 4.3 46.5 0.6 CG C:ASP80 4.4 14.8 1.0 CG C:HIS131 4.4 4.9 1.0 CG C:HIS135 4.4 29.6 1.0 ND1 C:HIS131 4.5 6.1 1.0 C13 C:5YA305 4.5 42.7 0.6 N C:ASP81 4.6 10.9 1.0 CB C:ASP81 4.7 8.6 1.0 CA C:PXU171 4.8 7.2 1.0 ND1 C:HIS135 4.8 31.3 1.0 CA C:ASP81 4.9 6.8 1.0 CD2 C:HIS225 4.9 11.6 1.0 CB C:PXU171 4.9 8.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn303 b:33.7 occ:0.42 O2 D:5YA302 0.9 34.5 0.6 N1 D:5YA302 2.1 35.0 0.6 OD1 D:ASP81 2.4 28.9 1.0 NE2 D:HIS131 2.5 8.5 1.0 O1 D:5YA302 2.7 26.4 0.6 NE2 D:HIS135 2.7 34.4 1.0 C17 D:5YA302 2.8 35.7 0.6 CG D:ASP81 3.1 27.3 1.0 OD2 D:ASP81 3.2 28.1 1.0 CD2 D:HIS135 3.3 33.1 1.0 CE1 D:HIS131 3.4 10.2 1.0 OA D:PXU171 3.5 14.7 1.0 CD2 D:HIS131 3.6 8.5 1.0 CB D:ASP80 3.8 20.9 1.0 CE1 D:HIS135 3.9 34.6 1.0 OD1 D:ASP80 4.1 25.6 1.0 C14 D:5YA302 4.3 47.3 0.6 CD2 D:HIS225 4.4 20.6 1.0 O D:HOH433 4.4 37.1 0.8 NE2 D:HIS225 4.4 18.0 1.0 CG D:ASP80 4.4 22.3 1.0 CB D:ASP81 4.5 19.7 1.0 N D:ASP81 4.6 23.3 1.0 ND1 D:HIS131 4.6 11.5 1.0 CG D:HIS135 4.6 31.8 1.0 CG D:HIS131 4.7 10.5 1.0 CA D:PXU171 4.8 12.9 1.0 ND1 D:HIS135 4.9 34.4 1.0 C15 D:5YA302 4.9 53.8 0.6 CA D:ASP81 4.9 19.1 1.0 CB D:PXU171 5.0 17.9 1.0 C D:ASP80 5.0 14.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide


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 BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn308 b:34.2 occ:1.00 ND1 D:HIS98 3.4 12.7 1.0 NZ D:LYS247 3.6 8.1 1.0 CD D:LYS247 3.9 7.8 1.0 CE1 D:HIS98 4.2 10.2 1.0 CE D:LYS247 4.3 7.9 1.0 CG D:HIS98 4.5 11.5 1.0 CB D:PRO244 4.5 20.1 1.0 CB D:HIS98 4.6 10.3 1.0 CA D:PRO244 4.7 24.1 1.0 CG2 D:ILE243 4.8 7.8 1.0 CA D:HIS98 4.9 17.6 1.0 N D:PRO244 5.0 21.4 1.0

V.E.Fadouloglou, D.Kotsifaki, M.Kokkinidis. Crystal Structure of the BC1960 Peptidoglycan N-Acetylglucosamine Deacetylase in Complex with 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide To Be Published.