Zinc in PDB 4xm2: N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium

The structure of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium, PDB code: 4xm2 was solved by T.Nakamura, M.Niiyama, W.Hashimoto, K.Ida, K.Uegaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.57 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.634, 121.825, 92.133, 90.00, 113.88, 90.00
R / Rfree (%)	20.9 / 27.6

The binding sites of Zinc atom in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium (pdb code 4xm2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium, PDB code: 4xm2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium


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 Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:50.2 occ:1.00 OD2 A:ASP43 2.0 42.0 1.0 NE2 A:HIS151 2.3 38.6 1.0 ND1 A:HIS40 2.3 37.7 1.0 CG A:ASP43 2.8 38.9 1.0 OD1 A:ASP43 2.9 40.2 1.0 CE1 A:HIS151 3.2 36.0 1.0 CE1 A:HIS40 3.2 38.1 1.0 CD2 A:HIS151 3.3 37.8 1.0 CG A:HIS40 3.4 38.8 1.0 CB A:HIS40 3.7 38.6 1.0 NE2 C:HIS259 3.9 47.3 1.0 CE1 C:HIS259 4.2 49.1 1.0 N A:HIS40 4.2 37.9 1.0 ND1 A:HIS151 4.3 36.0 1.0 CB A:ASP43 4.3 40.0 1.0 CB A:PRO39 4.3 35.6 1.0 NE2 A:HIS40 4.3 39.0 1.0 CG A:HIS151 4.4 36.3 1.0 OD1 A:ASP42 4.4 51.7 1.0 CD2 A:HIS40 4.4 40.4 1.0 CA A:HIS40 4.6 38.6 1.0 CG A:PRO39 4.8 32.6 1.0

Zinc binding site 2 out of 6 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium


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 Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:54.8 occ:1.00 NE2 B:HIS151 2.2 36.9 1.0 ND1 B:HIS40 2.2 35.6 1.0 OD2 B:ASP43 2.2 42.1 1.0 O B:HOH401 2.7 59.4 1.0 OD1 B:ASP43 2.9 39.5 1.0 CG B:ASP43 2.9 41.0 1.0 CE1 B:HIS40 3.1 36.7 1.0 CD2 B:HIS151 3.1 39.7 1.0 CE1 B:HIS151 3.2 41.6 1.0 CG B:HIS40 3.2 34.0 1.0 CB B:HIS40 3.5 34.7 1.0 NE2 A:HIS259 4.1 49.2 1.0 N B:HIS40 4.2 34.3 1.0 NE2 B:HIS40 4.2 35.2 1.0 ND1 B:HIS151 4.3 41.0 1.0 CG B:HIS151 4.3 38.1 1.0 CD2 B:HIS40 4.3 37.3 1.0 CB B:PRO39 4.3 30.3 1.0 CE1 A:HIS259 4.3 47.2 1.0 CB B:ASP43 4.4 39.3 1.0 CA B:HIS40 4.4 35.4 1.0 OD1 B:ASP42 4.6 46.3 1.0 CG B:PRO39 4.8 29.6 1.0

Zinc binding site 3 out of 6 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium


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 Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:62.9 occ:1.00 NE2 C:HIS151 2.2 40.9 1.0 ND1 C:HIS40 2.2 44.7 1.0 OD2 C:ASP43 2.3 46.5 1.0 OD1 C:ASP43 3.0 45.6 1.0 CG C:ASP43 3.0 45.9 1.0 CD2 C:HIS151 3.2 42.4 1.0 CE1 C:HIS40 3.2 45.7 1.0 CE1 C:HIS151 3.2 42.1 1.0 CG C:HIS40 3.3 43.5 1.0 O B:HOH402 3.5 53.3 1.0 CB C:HIS40 3.6 41.8 1.0 NE2 B:HIS259 3.9 66.5 1.0 N C:HIS40 4.3 41.1 1.0 NE2 C:HIS40 4.3 46.6 1.0 ND1 C:HIS151 4.3 40.8 1.0 CG C:HIS151 4.3 40.1 1.0 CE1 B:HIS259 4.4 65.1 1.0 CD2 C:HIS40 4.4 45.7 1.0 CA C:HIS40 4.5 42.1 1.0 CB C:ASP43 4.5 45.2 1.0 CB C:PRO39 4.6 40.4 1.0 OD1 C:ASP42 4.7 50.5 1.0 CG C:PRO39 4.9 39.7 1.0 O C:HIS40 4.9 42.4 1.0

Zinc binding site 4 out of 6 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:47.2 occ:1.00 O F:HOH402 2.1 49.8 1.0 ND1 D:HIS40 2.2 38.0 1.0 NE2 D:HIS151 2.3 26.6 1.0 O D:HOH401 2.4 39.7 1.0 OD2 D:ASP43 2.4 46.7 1.0 OD1 D:ASP43 2.9 41.3 1.0 CG D:ASP43 3.0 41.5 1.0 CE1 D:HIS40 3.1 39.9 1.0 CG D:HIS40 3.2 38.9 1.0 CE1 D:HIS151 3.2 31.8 1.0 CD2 D:HIS151 3.3 27.8 1.0 CB D:HIS40 3.6 35.9 1.0 NE2 F:HIS259 4.0 35.1 1.0 N D:HIS40 4.2 35.4 1.0 CE1 F:HIS259 4.2 36.6 1.0 NE2 D:HIS40 4.3 38.3 1.0 CB D:PRO39 4.3 33.7 1.0 CD2 D:HIS40 4.3 39.1 1.0 ND1 D:HIS151 4.4 29.0 1.0 CB D:ASP43 4.4 39.3 1.0 CG D:HIS151 4.4 30.5 1.0 OD1 D:ASP42 4.5 41.1 1.0 CA D:HIS40 4.5 36.0 1.0 CG D:PRO39 4.7 33.7 1.0 C D:PRO39 4.8 34.7 1.0

Zinc binding site 5 out of 6 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:53.5 occ:1.00 O E:HOH401 1.9 40.2 1.0 ND1 E:HIS40 2.2 44.6 1.0 OD2 E:ASP43 2.2 43.9 1.0 NE2 E:HIS151 2.3 38.2 1.0 OD1 E:ASP43 2.9 40.9 1.0 CG E:ASP43 2.9 44.4 1.0 O D:HOH402 3.1 59.1 1.0 CG E:HIS40 3.1 45.1 1.0 CE1 E:HIS40 3.2 44.5 1.0 CE1 E:HIS151 3.2 35.6 1.0 CD2 E:HIS151 3.3 38.7 1.0 CB E:HIS40 3.4 43.1 1.0 NE2 D:HIS259 4.0 46.4 1.0 N E:HIS40 4.1 42.2 1.0 NE2 E:HIS40 4.3 45.3 1.0 CD2 E:HIS40 4.3 44.9 1.0 ND1 E:HIS151 4.3 36.3 1.0 CA E:HIS40 4.4 43.5 1.0 CE1 D:HIS259 4.4 46.0 1.0 CB E:ASP43 4.4 46.4 1.0 OD1 E:ASP42 4.4 53.1 1.0 CG E:HIS151 4.4 36.0 1.0 CG E:PRO39 4.4 38.3 1.0 CB E:PRO39 4.4 38.8 1.0 C E:PRO39 5.0 40.7 1.0 O E:HIS40 5.0 45.4 1.0

Zinc binding site 6 out of 6 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:47.3 occ:1.00 O F:HOH401 1.9 33.0 1.0 OD2 F:ASP43 2.2 38.0 1.0 NE2 F:HIS151 2.2 33.6 1.0 ND1 F:HIS40 2.3 29.0 1.0 OD1 F:ASP43 2.7 29.4 1.0 CG F:ASP43 2.8 33.9 1.0 O E:HOH402 2.9 54.0 1.0 CG F:HIS40 3.1 30.8 1.0 CE1 F:HIS151 3.2 37.3 1.0 CD2 F:HIS151 3.2 34.1 1.0 CB F:HIS40 3.3 32.1 1.0 CE1 F:HIS40 3.4 33.5 1.0 NE2 E:HIS259 4.1 43.9 1.0 N F:HIS40 4.2 31.0 1.0 CB F:PRO39 4.2 26.8 1.0 CB F:ASP43 4.3 37.1 1.0 ND1 F:HIS151 4.3 36.5 1.0 CA F:HIS40 4.3 32.1 1.0 CG F:HIS151 4.3 34.4 1.0 CD2 F:HIS40 4.3 35.6 1.0 NE2 F:HIS40 4.4 34.8 1.0 CE1 E:HIS259 4.5 42.9 1.0 OD1 F:ASP42 4.6 46.9 1.0 CG F:PRO39 4.6 27.7 1.0 O F:HIS40 4.8 33.4 1.0 CD F:PRO39 4.9 26.1 1.0 C F:PRO39 4.9 30.0 1.0 C F:HIS40 5.0 33.3 1.0

T.Nakamura, M.Niiyama, W.Hashimoto, K.Ida, M.Abe, J.Morita, K.Uegaki. Multiple Crystal Forms of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus Acta Crystallogr.,Sect.F V. 71 657 2015.
ISSN: ESSN 2053-230X
DOI: 10.1107/S2053230X15005695