Zinc in PDB 3wl3: N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii

The structure of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii, PDB code: 3wl3 was solved by T.Nakamura, M.Niiyama, W.Hashimoto, K.Uegaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.24 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.561, 77.561, 229.114, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 27.4

The binding sites of Zinc atom in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii (pdb code 3wl3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii, PDB code: 3wl3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:31.3 occ:1.00 O1 A:PO4302 1.8 29.4 1.0 OD2 A:ASP47 2.0 16.9 1.0 NE2 A:HIS155 2.1 21.2 1.0 ND1 A:HIS44 2.1 27.5 1.0 CG A:ASP47 2.9 22.6 1.0 P A:PO4302 2.9 34.2 1.0 CE1 A:HIS44 3.0 28.7 1.0 OD1 A:ASP47 3.0 24.7 1.0 CE1 A:HIS155 3.0 25.7 1.0 CD2 A:HIS155 3.0 25.6 1.0 CG A:HIS44 3.1 19.1 1.0 O3 A:PO4302 3.2 30.3 1.0 CB A:HIS44 3.5 19.9 1.0 O4 A:PO4302 3.6 33.5 1.0 NE2 C:HIS264 3.8 29.8 1.0 N A:HIS44 4.1 20.0 1.0 CE1 C:HIS264 4.1 29.8 1.0 CB A:PRO43 4.1 18.9 1.0 O2 A:PO4302 4.1 34.9 1.0 NE2 A:HIS44 4.1 29.9 1.0 ND1 A:HIS155 4.1 26.5 1.0 CG A:HIS155 4.2 24.9 1.0 CD2 A:HIS44 4.2 24.4 1.0 CB A:ASP47 4.3 21.8 1.0 CA A:HIS44 4.4 20.6 1.0 CG A:PRO43 4.5 21.3 1.0 C3 A:GOL305 4.5 32.6 1.0 O3 A:GOL305 4.6 28.4 1.0 OD1 A:ASP46 4.7 26.7 1.0 C A:PRO43 4.9 19.5 1.0

Zinc binding site 2 out of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:31.9 occ:1.00 O2 B:PO4302 1.7 35.1 1.0 OD2 B:ASP47 2.0 25.1 1.0 ND1 B:HIS44 2.3 34.4 1.0 NE2 B:HIS155 2.3 31.8 1.0 CG B:ASP47 2.7 22.6 1.0 OD1 B:ASP47 2.7 17.2 1.0 P B:PO4302 2.8 38.9 1.0 O1 B:PO4302 3.1 37.0 1.0 CE1 B:HIS155 3.2 27.8 1.0 CE1 B:HIS44 3.2 37.4 1.0 CG B:HIS44 3.3 29.6 1.0 CD2 B:HIS155 3.3 29.2 1.0 CB B:HIS44 3.5 26.8 1.0 O4 B:PO4302 3.6 32.2 1.0 N B:HIS44 4.0 26.2 1.0 O3 B:PO4302 4.0 37.0 1.0 NE2 A:HIS264 4.0 34.8 1.0 CB B:ASP47 4.2 25.0 1.0 NE2 B:HIS44 4.3 33.3 1.0 ND1 B:HIS155 4.3 29.9 1.0 O1 B:GOL304 4.3 31.9 1.0 CA B:HIS44 4.3 26.4 1.0 CD2 B:HIS44 4.4 34.6 1.0 CE1 A:HIS264 4.4 30.1 1.0 CB B:PRO43 4.4 25.4 1.0 CG B:HIS155 4.4 27.5 1.0 CD B:PRO43 4.7 23.1 1.0 CG B:PRO43 4.7 26.0 1.0 OD1 B:ASP46 4.7 29.4 1.0 C3 B:GOL304 4.8 31.0 1.0 C B:PRO43 4.8 26.2 1.0

Zinc binding site 3 out of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:37.1 occ:1.00 ND1 C:HIS44 2.0 29.6 1.0 O3 C:PO4302 2.1 40.1 1.0 OD2 C:ASP47 2.1 37.3 1.0 NE2 C:HIS155 2.2 22.8 1.0 CG C:ASP47 2.9 33.8 1.0 CE1 C:HIS44 3.0 29.5 1.0 P C:PO4302 3.0 38.7 1.0 O2 C:PO4302 3.0 38.7 1.0 OD1 C:ASP47 3.1 28.4 1.0 CG C:HIS44 3.1 32.2 1.0 CE1 C:HIS155 3.2 21.6 1.0 CD2 C:HIS155 3.2 24.4 1.0 CB C:HIS44 3.5 27.3 1.0 O4 C:PO4302 3.7 40.0 1.0 NE2 B:HIS264 3.9 42.6 1.0 N C:HIS44 4.0 25.7 1.0 NE2 C:HIS44 4.1 33.5 1.0 CE1 B:HIS264 4.1 42.1 1.0 CD2 C:HIS44 4.2 32.3 1.0 O1 C:PO4302 4.3 42.9 1.0 ND1 C:HIS155 4.3 23.5 1.0 CB C:ASP47 4.3 32.2 1.0 CG C:HIS155 4.3 24.1 1.0 CA C:HIS44 4.3 27.0 1.0 CB C:PRO43 4.4 24.4 1.0 CG C:PRO43 4.7 23.4 1.0 CD C:PRO43 4.7 23.3 1.0 C C:PRO43 4.8 25.4 1.0 OD1 C:ASP46 4.8 36.1 1.0 O C:HIS44 5.0 25.2 1.0

S.Mine, M.Niiyama, W.Hashimoto, T.Ikegami, D.Koma, T.Ohmoto, Y.Fukuda, T.Inoue, Y.Abe, T.Ueda, J.Morita, K.Uegaki, T.Nakamura. Expression From Engineered Escherichia Coli Chromosome and Crystallographic Study of Archaeal N,N'-Diacetylchitobiose Deacetylase Febs J. V. 281 2584 2014.
ISSN: ISSN 1742-464X
PubMed: 24702737
DOI: 10.1111/FEBS.12805