Cadmium in PDB 4xm1: N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium

The structure of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium, PDB code: 4xm1 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)	41.13 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	74.353, 77.847, 93.511, 66.39, 84.70, 61.95
R / Rfree (%)	23.8 / 29

The structure of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Cadmium atom in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium (pdb code 4xm1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium, PDB code: 4xm1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:24.0 occ:1.00 NE2 A:HIS151 2.2 8.6 1.0 O2 A:GOL305 2.4 27.0 1.0 ND1 A:HIS40 2.5 16.0 1.0 OD2 A:ASP43 2.5 19.9 1.0 OD1 A:ASP43 2.8 21.7 1.0 O1 A:GOL305 2.8 26.4 1.0 CG A:ASP43 3.0 19.0 1.0 CD2 A:HIS151 3.1 10.8 1.0 C2 A:GOL305 3.3 28.4 1.0 C1 A:GOL305 3.3 37.4 1.0 CE1 A:HIS40 3.3 17.5 1.0 CE1 A:HIS151 3.3 27.8 1.0 CG A:HIS40 3.7 23.0 1.0 NE2 C:HIS259 3.9 28.1 1.0 CB A:HIS40 4.0 15.8 1.0 CG A:HIS151 4.4 19.6 1.0 ND1 A:HIS151 4.4 13.7 1.0 CE1 C:HIS259 4.4 22.8 1.0 CB A:PRO39 4.4 19.9 1.0 CB A:ASP43 4.5 24.2 1.0 N A:HIS40 4.5 18.5 1.0 C3 A:GOL305 4.5 30.4 1.0 NE2 A:HIS40 4.6 26.4 1.0 OD1 A:ASP42 4.6 34.3 1.0 CD2 A:HIS40 4.7 17.7 1.0 CA A:HIS40 4.9 20.6 1.0 CG A:PRO39 4.9 13.4 1.0

Cadmium binding site 2 out of 8 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:37.7 occ:1.00 CL C:CL304 2.3 43.0 1.0 CL A:CL304 2.5 35.4 1.0 OE1 A:GLU225 2.5 32.1 1.0 OE2 A:GLU225 2.6 32.3 1.0 CL C:CL303 2.7 34.0 1.0 CD A:GLU225 2.9 31.1 1.0 SD C:MET1 2.9 41.1 1.0 CG C:MET1 3.6 27.9 1.0 CE C:MET1 4.1 41.4 1.0 CG A:GLU225 4.4 34.2 1.0

Cadmium binding site 3 out of 8 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:30.3 occ:1.00 O B:HOH445 1.9 38.2 1.0 OD1 B:ASP43 2.1 22.4 1.0 ND1 B:HIS40 2.2 9.0 1.0 NE2 B:HIS151 2.3 23.1 1.0 OD2 B:ASP43 2.4 27.3 1.0 O B:HOH444 2.6 42.1 1.0 CG B:ASP43 2.7 30.9 1.0 O B:HOH447 2.7 33.7 1.0 CE1 B:HIS151 3.2 25.2 1.0 CG B:HIS40 3.2 19.9 1.0 CE1 B:HIS40 3.3 33.0 1.0 CD2 B:HIS151 3.4 22.5 1.0 CB B:HIS40 3.4 18.8 1.0 NE2 A:HIS259 4.1 38.6 1.0 CB B:ASP43 4.3 33.6 1.0 ND1 B:HIS151 4.4 29.7 1.0 N B:HIS40 4.4 24.9 1.0 CD2 B:HIS40 4.4 22.6 1.0 NE2 B:HIS40 4.4 19.8 1.0 CB B:PRO39 4.4 26.5 1.0 OD1 B:ASP42 4.4 42.2 1.0 CG B:HIS151 4.5 26.7 1.0 CA B:HIS40 4.5 23.9 1.0 CE1 A:HIS259 4.6 39.0 1.0 CG B:PRO39 4.9 27.3 1.0

Cadmium binding site 4 out of 8 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd301 b:31.1 occ:1.00 O B:HOH443 1.9 15.4 1.0 O B:HOH442 1.9 25.2 1.0 OD2 C:ASP43 2.3 25.9 1.0 NE2 C:HIS151 2.3 30.2 1.0 ND1 C:HIS40 2.5 25.5 1.0 O C:HOH459 2.7 40.2 1.0 OD1 C:ASP43 2.8 26.8 1.0 CG C:ASP43 2.9 27.6 1.0 CE1 C:HIS151 3.2 29.2 1.0 CG C:HIS40 3.3 29.4 1.0 CD2 C:HIS151 3.4 28.6 1.0 CB C:HIS40 3.4 28.2 1.0 CE1 C:HIS40 3.5 27.0 1.0 NE2 B:HIS259 4.0 30.6 1.0 N C:HIS40 4.3 26.1 1.0 CB C:PRO39 4.4 25.2 1.0 CB C:ASP43 4.4 31.7 1.0 ND1 C:HIS151 4.4 29.8 1.0 CE1 B:HIS259 4.4 32.9 1.0 CA C:HIS40 4.4 26.6 1.0 OD1 C:ASP42 4.5 37.9 1.0 CD2 C:HIS40 4.5 26.4 1.0 CG C:HIS151 4.5 25.8 1.0 CG C:PRO39 4.5 25.1 1.0 NE2 C:HIS40 4.6 31.5 1.0 O C:HIS40 5.0 28.0 1.0

Cadmium binding site 5 out of 8 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd301 b:27.5 occ:1.00 NE2 D:HIS151 2.2 17.7 1.0 OD2 D:ASP43 2.4 26.9 1.0 ND1 D:HIS40 2.5 17.9 1.0 O2 D:GOL305 2.6 26.4 1.0 O F:HOH446 2.7 37.4 1.0 O1 D:GOL305 2.8 32.4 1.0 OD1 D:ASP43 2.8 30.9 1.0 CG D:ASP43 2.9 28.3 1.0 C1 D:GOL305 3.1 37.3 1.0 CE1 D:HIS151 3.2 26.3 1.0 CD2 D:HIS151 3.2 16.1 1.0 C2 D:GOL305 3.2 33.0 1.0 CE1 D:HIS40 3.3 19.3 1.0 CG D:HIS40 3.5 23.6 1.0 CB D:HIS40 3.8 23.4 1.0 NE2 F:HIS259 4.0 33.5 1.0 ND1 D:HIS151 4.3 20.2 1.0 CG D:HIS151 4.4 25.3 1.0 CE1 F:HIS259 4.4 27.7 1.0 N D:HIS40 4.4 23.6 1.0 CB D:ASP43 4.4 27.9 1.0 CB D:PRO39 4.5 21.3 1.0 NE2 D:HIS40 4.5 25.0 1.0 CD2 D:HIS40 4.6 22.1 1.0 OD1 D:ASP42 4.6 27.1 1.0 C3 D:GOL305 4.7 32.9 1.0 CA D:HIS40 4.7 22.6 1.0 CG D:PRO39 5.0 19.3 1.0 O3 D:GOL305 5.0 33.9 1.0

Cadmium binding site 6 out of 8 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd302 b:31.7 occ:1.00 CL D:CL304 2.2 36.3 1.0 CL F:CL303 2.5 40.6 1.0 CL F:CL304 2.5 39.0 1.0 OE2 D:GLU225 2.5 14.6 1.0 OE1 D:GLU225 2.5 23.5 1.0 SD F:MET1 2.9 32.3 1.0 CD D:GLU225 2.9 11.1 1.0 CE F:MET1 3.3 27.8 1.0 CG F:MET1 3.8 27.4 1.0 CG D:GLU225 4.5 25.8 1.0 O D:HOH401 4.6 42.9 1.0

Cadmium binding site 7 out of 8 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ E:Cd301 b:36.8 occ:1.00 NE2 E:HIS151 2.2 32.6 1.0 ND1 E:HIS40 2.3 26.3 1.0 OD1 E:ASP43 2.3 34.9 1.0 OD2 E:ASP43 2.3 38.9 1.0 O E:HOH437 2.6 41.5 1.0 CG E:ASP43 2.7 38.7 1.0 CE1 E:HIS151 3.0 31.5 1.0 CG E:HIS40 3.2 33.7 1.0 CD2 E:HIS151 3.4 31.6 1.0 CE1 E:HIS40 3.4 38.2 1.0 CB E:HIS40 3.4 29.5 1.0 NE2 D:HIS259 4.0 41.1 1.0 CB E:ASP43 4.2 40.5 1.0 ND1 E:HIS151 4.2 33.8 1.0 CB E:PRO39 4.4 31.9 1.0 CD2 E:HIS40 4.4 31.9 1.0 CG E:HIS151 4.4 32.9 1.0 N E:HIS40 4.4 33.1 1.0 NE2 E:HIS40 4.4 28.8 1.0 CE1 D:HIS259 4.5 41.9 1.0 OD1 E:ASP42 4.5 41.9 1.0 CA E:HIS40 4.5 32.1 1.0 CG E:PRO39 4.8 32.1 1.0

Cadmium binding site 8 out of 8 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ F:Cd301 b:40.2 occ:1.00 OD2 F:ASP43 2.1 28.9 1.0 O E:HOH436 2.2 37.5 1.0 NE2 F:HIS151 2.3 33.7 1.0 ND1 F:HIS40 2.5 32.0 1.0 OD1 F:ASP43 2.8 29.9 1.0 CG F:ASP43 2.8 34.5 1.0 O E:HOH435 3.0 48.8 1.0 CE1 F:HIS151 3.2 33.8 1.0 CD2 F:HIS151 3.3 31.1 1.0 CE1 F:HIS40 3.4 31.8 1.0 CG F:HIS40 3.5 33.7 1.0 CB F:HIS40 3.8 30.8 1.0 NE2 E:HIS259 4.0 48.5 1.0 CB F:ASP43 4.3 35.9 1.0 ND1 F:HIS151 4.4 33.5 1.0 OD1 F:ASP42 4.4 47.4 1.0 CE1 E:HIS259 4.5 46.7 1.0 CG F:HIS151 4.5 29.2 1.0 N F:HIS40 4.5 31.0 1.0 NE2 F:HIS40 4.6 36.9 1.0 CD2 F:HIS40 4.7 32.4 1.0 CB F:PRO39 4.7 28.8 1.0 CA F:HIS40 4.7 31.8 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