Zinc in PDB 3we7: Crystal Structure of Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii

The structure of Crystal Structure of Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii, PDB code: 3we7 was solved by S.Mine, T.Nakamura, Y.Fukuda, T.Inoue, K.Uegaki, T.Sato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.62 / 1.55
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.372, 77.372, 230.223, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.7

The structure of Crystal Structure of Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii (pdb code 3we7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii, PDB code: 3we7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of 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 Crystal Structure of Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.3 occ:1.00 OXT A:ACY303 1.9 30.6 1.0 ND1 A:HIS44 2.1 17.1 1.0 NE2 A:HIS155 2.1 17.6 1.0 OD2 A:ASP47 2.1 16.1 1.0 C A:ACY303 2.4 29.7 1.0 O A:ACY303 2.5 21.3 1.0 CG A:ASP47 2.7 16.1 1.0 OD1 A:ASP47 2.7 19.5 1.0 CE1 A:HIS155 3.0 18.1 1.0 CE1 A:HIS44 3.1 17.6 1.0 CG A:HIS44 3.1 17.5 1.0 CD2 A:HIS155 3.2 16.6 1.0 CB A:HIS44 3.5 19.4 1.0 CH3 A:ACY303 3.8 29.8 1.0 NE2 B:HIS264 4.0 21.9 1.0 CB A:PRO43 4.1 14.5 1.0 ND1 A:HIS155 4.2 18.1 1.0 CB A:ASP47 4.2 15.4 1.0 N A:HIS44 4.2 16.8 1.0 NE2 A:HIS44 4.2 16.9 1.0 CE1 B:HIS264 4.3 21.2 1.0 CG A:HIS155 4.3 16.6 1.0 CD2 A:HIS44 4.3 17.2 1.0 O2 A:GOL302 4.3 27.5 1.0 CA A:HIS44 4.5 17.9 1.0 OD1 A:ASP46 4.5 22.3 1.0 CG A:PRO43 4.6 17.1 1.0 C3 A:GOL302 4.8 27.5 1.0 CD A:PRO43 4.9 13.7 1.0 C A:PRO43 4.9 16.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of 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 Crystal Structure of Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:17.6 occ:1.00 OXT B:ACY304 2.0 28.2 1.0 OD2 B:ASP47 2.0 14.3 1.0 NE2 B:HIS155 2.0 12.1 1.0 ND1 B:HIS44 2.1 13.9 1.0 O B:ACY304 2.4 22.9 1.0 C B:ACY304 2.5 28.7 1.0 CG B:ASP47 2.7 15.4 1.0 OD1 B:ASP47 2.8 15.4 1.0 CE1 B:HIS155 2.9 14.1 1.0 CE1 B:HIS44 3.0 15.8 1.0 CD2 B:HIS155 3.1 14.6 1.0 CG B:HIS44 3.1 15.1 1.0 CB B:HIS44 3.4 15.5 1.0 CH3 B:ACY304 4.0 26.3 1.0 NE2 C:HIS264 4.0 19.4 1.0 ND1 B:HIS155 4.1 15.7 1.0 N B:HIS44 4.1 13.3 1.0 NE2 B:HIS44 4.2 15.9 1.0 CB B:PRO43 4.2 14.6 1.0 O2 B:GOL302 4.2 33.3 1.0 CB B:ASP47 4.2 15.8 1.0 CG B:HIS155 4.2 14.1 1.0 CD2 B:HIS44 4.2 17.4 1.0 CE1 C:HIS264 4.3 18.0 1.0 CA B:HIS44 4.5 15.7 1.0 OD1 B:ASP46 4.5 22.6 1.0 CG B:PRO43 4.6 17.2 1.0 CD B:PRO43 4.8 15.9 1.0 C1 B:GOL302 4.9 30.8 1.0 C B:PRO43 4.9 14.5 1.0 C2 B:GOL302 4.9 34.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of 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 Crystal Structure of Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:22.0 occ:1.00 OXT C:ACY302 1.9 28.0 1.0 OD2 C:ASP47 2.0 18.3 1.0 NE2 C:HIS155 2.0 15.9 1.0 ND1 C:HIS44 2.1 16.8 1.0 O C:ACY302 2.4 23.4 1.0 C C:ACY302 2.5 30.6 1.0 CG C:ASP47 2.7 17.0 1.0 OD1 C:ASP47 2.8 18.0 1.0 CE1 C:HIS155 2.9 16.7 1.0 CE1 C:HIS44 3.0 15.3 1.0 CG C:HIS44 3.1 15.9 1.0 CD2 C:HIS155 3.1 17.5 1.0 CB C:HIS44 3.5 15.7 1.0 CH3 C:ACY302 3.9 30.7 1.0 NE2 A:HIS264 4.0 23.8 1.0 N C:HIS44 4.1 17.5 1.0 NE2 C:HIS44 4.1 16.0 1.0 ND1 C:HIS155 4.1 17.4 1.0 CB C:PRO43 4.2 15.4 1.0 O2 C:GOL303 4.2 38.6 1.0 CB C:ASP47 4.2 18.2 1.0 CD2 C:HIS44 4.2 16.6 1.0 CG C:HIS155 4.2 16.7 1.0 CE1 A:HIS264 4.3 20.1 1.0 CA C:HIS44 4.4 17.2 1.0 OD1 C:ASP46 4.5 23.3 1.0 CG C:PRO43 4.6 16.1 1.0 C C:PRO43 4.8 17.2 1.0 C1 C:GOL303 4.8 39.0 1.0 CD C:PRO43 4.9 16.6 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