Zinc in PDB 6h8n: Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis - Mutant D285S

The structure of Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis - Mutant D285S, PDB code: 6h8n was solved by M.A.Sainz-Polo, L.Grifoll-Romero, D.Albesa-Jove, A.Planas, M.E.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.12 / 1.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.420, 61.800, 130.990, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 17.5

The binding sites of Zinc atom in the Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis - Mutant D285S (pdb code 6h8n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis - Mutant D285S, PDB code: 6h8n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis - Mutant D285S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis - Mutant D285S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:10.2 occ:1.00 O3 A:PO4502 1.9 9.9 1.0 OD1 A:ASP261 2.0 10.0 1.0 NE2 A:HIS315 2.0 11.1 1.0 NE2 A:HIS311 2.1 9.7 1.0 CG A:ASP261 2.9 10.3 1.0 CD2 A:HIS315 2.9 12.9 1.0 P A:PO4502 3.0 9.6 1.0 CD2 A:HIS311 3.0 8.9 1.0 CE1 A:HIS311 3.1 10.0 1.0 CE1 A:HIS315 3.1 11.9 1.0 O4 A:PO4502 3.1 10.3 1.0 OD2 A:ASP261 3.2 11.8 1.0 NH1 B:ARG446 3.8 11.2 1.0 O1 A:PO4502 3.9 10.8 1.0 CB A:SER260 4.0 9.2 1.0 CG A:HIS315 4.1 10.2 1.0 O2 A:PO4502 4.1 10.1 1.0 ND1 A:HIS315 4.1 11.8 1.0 ND1 A:HIS311 4.2 10.2 1.0 CG A:HIS311 4.2 9.1 1.0 CB A:ASP261 4.3 9.8 1.0 CD2 A:HIS402 4.4 10.4 1.0 O A:HOH655 4.4 11.1 1.0 CA A:ASP261 4.6 9.2 1.0 N A:ASP261 4.6 8.9 1.0 OG A:SER260 4.8 9.3 1.0 NE2 A:HIS402 4.8 10.5 1.0 C A:SER260 4.8 8.5 1.0 C3 B:GOL501 4.9 26.3 1.0 O A:HOH642 4.9 11.4 1.0 CZ B:ARG446 5.0 10.2 1.0

Zinc binding site 2 out of 2 in the Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis - Mutant D285S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis - Mutant D285S within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:11.4 occ:1.00 O1 B:PO4503 1.9 11.1 1.0 OD1 B:ASP261 2.0 13.3 1.0 NE2 B:HIS315 2.0 11.1 1.0 NE2 B:HIS311 2.0 10.6 1.0 CG B:ASP261 2.9 12.9 1.0 CD2 B:HIS315 2.9 11.2 1.0 P B:PO4503 3.0 10.3 1.0 CD2 B:HIS311 3.0 10.3 1.0 CE1 B:HIS311 3.1 11.0 1.0 CE1 B:HIS315 3.1 12.4 1.0 O2 B:PO4503 3.1 12.3 1.0 OD2 B:ASP261 3.3 15.1 1.0 NH1 A:ARG446 3.8 13.8 1.0 O4 B:PO4503 3.9 12.6 1.0 CB B:SER260 4.0 10.7 1.0 O3 B:PO4503 4.1 12.4 1.0 CG B:HIS315 4.1 10.9 1.0 ND1 B:HIS311 4.2 10.9 1.0 ND1 B:HIS315 4.2 12.5 1.0 CG B:HIS311 4.2 9.3 1.0 CB B:ASP261 4.3 10.9 1.0 O B:HOH643 4.3 12.3 1.0 CD2 B:HIS402 4.4 12.9 1.0 N B:ASP261 4.6 10.3 1.0 CA B:ASP261 4.6 11.1 1.0 OG B:SER260 4.7 11.3 1.0 C B:SER260 4.8 10.4 1.0 NE2 B:HIS402 4.8 11.5 1.0 O B:HOH624 4.9 12.2 1.0

L.Grifoll-Romero, M.A.Sainz-Polo, D.Albesa-Jove, M.E.Guerin, X.Biarnes, A.Planas. Structure of Peptidoglycan Deacetylase Pdac From Bacillus Subtilis with Dual N-Acetylmuramic and N-Acetylglucosamine Specificities To Be Published.