Zinc in PDB 4xm0: N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium

The structure of N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium, PDB code: 4xm0 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)	50.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.006, 121.926, 92.271, 90.00, 114.21, 90.00
R / Rfree (%)	26.2 / 34.6

The binding sites of Zinc atom in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium (pdb code 4xm0). 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 (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium, PDB code: 4xm0:
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 (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:52.1 occ:1.00 ND1 A:HIS40 2.0 54.6 1.0 NE2 A:HIS151 2.3 42.0 1.0 OD2 A:ASP43 2.3 56.0 1.0 CE1 A:HIS40 2.5 54.2 1.0 OD1 A:ASP43 3.0 53.7 1.0 CG A:ASP43 3.0 56.6 1.0 O C:HOH402 3.2 40.5 1.0 CE1 A:HIS151 3.2 42.4 1.0 CD2 A:HIS151 3.3 40.2 1.0 CG A:HIS40 3.3 54.9 1.0 O C:HOH403 3.3 25.2 1.0 NE2 C:HIS259 3.7 66.0 1.0 NE2 A:HIS40 3.8 53.8 1.0 CB A:HIS40 4.0 55.7 1.0 CE1 C:HIS259 4.1 66.2 1.0 CD2 A:HIS40 4.1 53.5 1.0 ND1 A:HIS151 4.3 42.1 1.0 N A:HIS40 4.4 55.8 1.0 CG A:HIS151 4.4 40.7 1.0 CB A:ASP43 4.5 57.4 1.0 OD2 A:ASP42 4.5 61.6 1.0 CB A:PRO39 4.7 55.1 1.0 CA A:HIS40 4.8 56.1 1.0 CG A:PRO39 4.9 54.8 1.0 CD2 C:HIS259 4.9 66.8 1.0

Zinc binding site 2 out of 6 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:40.0 occ:1.00 ND1 B:HIS40 2.1 42.9 1.0 NE2 B:HIS151 2.4 37.0 1.0 O A:HOH402 2.5 42.5 1.0 OD2 B:ASP43 2.5 50.3 1.0 OD1 B:ASP43 2.6 52.1 1.0 CG B:ASP43 2.9 50.3 1.0 CE1 B:HIS40 2.9 42.5 1.0 O A:HOH401 3.1 44.8 1.0 CE1 B:HIS151 3.2 36.4 1.0 CG B:HIS40 3.3 45.0 1.0 CD2 B:HIS151 3.4 35.5 1.0 CB B:HIS40 3.8 45.6 1.0 NE2 A:HIS259 3.8 61.7 1.0 NE2 B:HIS40 4.1 42.1 1.0 CD2 B:HIS40 4.3 42.4 1.0 N B:HIS40 4.4 45.6 1.0 CB B:ASP43 4.4 50.1 1.0 ND1 B:HIS151 4.4 37.1 1.0 CE1 A:HIS259 4.4 61.8 1.0 CG B:HIS151 4.5 36.3 1.0 CB B:PRO39 4.6 44.6 1.0 CA B:HIS40 4.7 46.1 1.0 CG B:PRO39 4.9 44.8 1.0 ND1 B:HIS148 4.9 37.2 1.0 CD2 A:HIS259 5.0 60.7 1.0

Zinc binding site 3 out of 6 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:49.3 occ:1.00 ND1 C:HIS40 1.8 55.3 1.0 O B:HOH402 2.2 21.8 1.0 OD2 C:ASP43 2.3 59.7 1.0 NE2 C:HIS151 2.4 39.0 1.0 CE1 C:HIS40 2.5 55.0 1.0 O C:HOH401 2.8 32.8 1.0 CG C:HIS40 3.0 57.5 1.0 CG C:ASP43 3.1 59.7 1.0 OD1 C:ASP43 3.2 59.8 1.0 CE1 C:HIS151 3.3 40.1 1.0 CD2 C:HIS151 3.3 38.8 1.0 CB C:HIS40 3.7 58.6 1.0 NE2 C:HIS40 3.7 54.8 1.0 CD2 C:HIS40 4.0 55.9 1.0 NE2 B:HIS259 4.0 83.0 1.0 N C:HIS40 4.3 59.0 1.0 ND1 C:HIS151 4.4 39.6 1.0 CG C:HIS151 4.4 37.3 1.0 CB C:PRO39 4.5 59.8 1.0 CE1 B:HIS259 4.5 82.7 1.0 CB C:ASP43 4.6 58.6 1.0 CA C:HIS40 4.7 58.9 1.0

Zinc binding site 4 out of 6 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:40.6 occ:1.00 ND1 D:HIS40 2.2 45.6 1.0 NE2 D:HIS151 2.2 24.6 1.0 OD2 D:ASP43 2.3 51.8 1.0 OD1 D:ASP43 2.5 50.1 1.0 O D:HOH401 2.7 42.5 1.0 CG D:ASP43 2.7 52.2 1.0 O F:HOH401 2.8 33.2 1.0 CE1 D:HIS40 3.1 45.9 1.0 CE1 D:HIS151 3.1 27.3 1.0 CD2 D:HIS151 3.2 27.4 1.0 CG D:HIS40 3.2 46.9 1.0 CB D:HIS40 3.6 47.9 1.0 NE2 F:HIS259 4.0 56.1 1.0 N D:HIS40 4.2 48.0 1.0 CB D:ASP43 4.2 52.4 1.0 NE2 D:HIS40 4.2 45.8 1.0 ND1 D:HIS151 4.3 29.5 1.0 CD2 D:HIS40 4.3 45.9 1.0 CG D:HIS151 4.3 30.4 1.0 CE1 F:HIS259 4.3 56.8 1.0 OD1 D:ASP42 4.4 54.6 1.0 CB D:PRO39 4.5 47.0 1.0 CA D:HIS40 4.5 48.5 1.0 OD2 D:ASP42 4.8 54.4 1.0 C D:PRO39 4.9 47.3 1.0 CG D:PRO39 4.9 47.2 1.0 CA D:ASP43 5.0 52.2 1.0 CG D:ASP42 5.0 53.7 1.0

Zinc binding site 5 out of 6 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:50.1 occ:1.00 O E:HOH402 1.8 30.0 1.0 O D:HOH402 2.1 20.8 1.0 OD2 E:ASP43 2.2 59.5 1.0 NE2 E:HIS151 2.6 41.9 1.0 ND1 E:HIS40 2.6 66.1 1.0 CB E:HIS40 3.0 64.8 1.0 CG E:ASP43 3.0 62.5 1.0 CG E:HIS40 3.0 66.0 1.0 OD1 E:ASP43 3.1 60.9 1.0 CE1 E:HIS151 3.4 44.2 1.0 CD2 E:HIS151 3.5 43.1 1.0 N E:HIS40 3.6 63.7 1.0 CE1 E:HIS40 3.7 65.1 1.0 CA E:HIS40 3.9 64.7 1.0 CB E:PRO39 4.1 62.8 1.0 CD2 E:HIS40 4.1 66.6 1.0 NE2 D:HIS259 4.3 73.6 1.0 CG E:PRO39 4.3 62.4 1.0 CB E:ASP43 4.4 64.0 1.0 NE2 E:HIS40 4.4 66.1 1.0 OD1 E:ASP42 4.5 68.8 1.0 C E:PRO39 4.5 63.2 1.0 ND1 E:HIS151 4.5 44.8 1.0 CG E:HIS151 4.6 43.1 1.0 C E:HIS40 4.8 64.7 1.0 CD2 E:HIS148 4.9 45.9 1.0 CE1 D:HIS259 4.9 73.6 1.0 CA E:PRO39 4.9 63.0 1.0

Zinc binding site 6 out of 6 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Absence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:54.7 occ:1.00 OD2 F:ASP43 2.0 47.6 1.0 O E:HOH401 2.0 29.5 1.0 ND1 F:HIS40 2.4 45.9 1.0 NE2 F:HIS151 2.4 34.4 1.0 CG F:ASP43 2.8 47.4 1.0 OD1 F:ASP43 3.0 42.2 1.0 CG F:HIS40 3.3 47.0 1.0 CE1 F:HIS151 3.3 36.1 1.0 CE1 F:HIS40 3.4 43.7 1.0 CD2 F:HIS151 3.4 33.5 1.0 CB F:HIS40 3.5 47.8 1.0 O F:HOH402 3.9 31.8 1.0 N F:HIS40 3.9 48.3 1.0 NE2 E:HIS259 4.1 65.0 1.0 CB F:PRO39 4.2 48.2 1.0 CB F:ASP43 4.2 49.0 1.0 CA F:HIS40 4.3 48.0 1.0 ND1 F:HIS151 4.5 35.5 1.0 CD2 F:HIS40 4.5 43.9 1.0 NE2 F:HIS40 4.5 45.1 1.0 CG F:HIS151 4.5 33.4 1.0 CE1 E:HIS259 4.6 65.5 1.0 O F:HIS40 4.8 48.6 1.0 CG F:PRO39 4.8 48.4 1.0 OD2 F:ASP42 4.8 53.3 1.0 C F:HIS40 4.9 48.2 1.0 C F:PRO39 4.9 48.0 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