Cadmium in PDB 3wl4: N,N'-Diacetylchitobiose Deacetylase (Se-Derivative) From Pyrococcus Furiosus

The structure of N,N'-Diacetylchitobiose Deacetylase (Se-Derivative) From Pyrococcus Furiosus, PDB code: 3wl4 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)	26.40 / 1.54
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	113.894, 113.894, 201.029, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 16.9

The structure of N,N'-Diacetylchitobiose Deacetylase (Se-Derivative) From Pyrococcus Furiosus also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	8 atoms

The binding sites of Cadmium atom in the N,N'-Diacetylchitobiose Deacetylase (Se-Derivative) From Pyrococcus Furiosus (pdb code 3wl4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the N,N'-Diacetylchitobiose Deacetylase (Se-Derivative) From Pyrococcus Furiosus, PDB code: 3wl4:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the N,N'-Diacetylchitobiose Deacetylase (Se-Derivative) From Pyrococcus Furiosus


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 (Se-Derivative) From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:16.0 occ:1.00 N A:TAM309 2.3 16.5 1.0 NE2 A:HIS151 2.3 13.0 1.0 OD2 A:ASP43 2.3 15.2 1.0 ND1 A:HIS40 2.3 14.1 1.0 C5 A:TAM309 2.4 15.7 1.0 O4 A:TAM309 2.5 26.1 1.0 OD1 A:ASP43 2.6 14.9 1.0 CG A:ASP43 2.9 14.1 1.0 O5 A:TAM309 3.0 41.5 1.0 CE1 A:HIS151 3.1 13.3 1.0 CE1 A:HIS40 3.3 12.9 1.0 C A:TAM309 3.3 19.8 1.0 C2 A:TAM309 3.3 19.7 1.0 CG A:HIS40 3.4 12.7 1.0 CD2 A:HIS151 3.5 13.1 1.0 C4 A:TAM309 3.6 28.4 1.0 CB A:HIS40 3.6 14.3 1.0 C1 A:TAM309 3.7 24.8 1.0 N A:HIS40 4.3 14.6 1.0 ND1 A:HIS151 4.3 15.2 1.0 O A:HOH456 4.4 26.4 1.0 CB A:ASP43 4.4 15.0 1.0 NE2 A:HIS40 4.4 14.1 1.0 CG A:HIS151 4.5 13.8 1.0 CD2 A:HIS40 4.5 14.9 1.0 CB A:PRO39 4.5 13.8 1.0 OD1 A:ASP42 4.6 20.8 1.0 C3 A:TAM309 4.6 21.6 1.0 O A:HOH465 4.6 30.5 1.0 CA A:HIS40 4.7 15.0 1.0 CG A:PRO39 5.0 13.8 1.0

Cadmium binding site 2 out of 4 in the N,N'-Diacetylchitobiose Deacetylase (Se-Derivative) From Pyrococcus Furiosus


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 (Se-Derivative) From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:20.9 occ:1.00 OE2 A:GLU225 2.2 17.5 1.0 OE1 A:GLU225 2.5 22.3 1.0 CL A:CL305 2.5 20.4 1.0 CL A:CL306 2.6 22.5 1.0 CL A:CL307 2.6 23.3 1.0 CD A:GLU225 2.7 19.2 1.0 CG A:GLU225 4.4 18.7 1.0 O A:HOH479 4.6 32.5 1.0

Cadmium binding site 3 out of 4 in the N,N'-Diacetylchitobiose Deacetylase (Se-Derivative) From Pyrococcus Furiosus


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 (Se-Derivative) From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:16.1 occ:1.00 N B:TAM309 2.2 16.2 1.0 NE2 B:HIS151 2.3 13.5 1.0 OD2 B:ASP43 2.3 14.7 1.0 ND1 B:HIS40 2.3 13.1 1.0 O4 B:TAM309 2.4 22.2 1.0 O6 B:TAM309 2.5 25.6 1.0 OD1 B:ASP43 2.6 16.1 1.0 CG B:ASP43 2.9 14.5 1.0 C4 B:TAM309 3.1 33.7 1.0 CE1 B:HIS151 3.1 12.6 1.0 CE1 B:HIS40 3.2 13.2 1.0 C B:TAM309 3.3 20.6 1.0 CG B:HIS40 3.3 12.9 1.0 CD2 B:HIS151 3.4 13.4 1.0 C1 B:TAM309 3.5 19.7 1.0 C6 B:TAM309 3.5 30.3 1.0 CB B:HIS40 3.6 14.8 1.0 C3 B:TAM309 3.8 24.9 1.0 N B:HIS40 4.3 14.4 1.0 O B:HOH463 4.3 25.7 1.0 ND1 B:HIS151 4.4 14.9 1.0 CB B:ASP43 4.4 15.9 1.0 NE2 B:HIS40 4.4 14.1 1.0 CD2 B:HIS40 4.5 14.7 1.0 CB B:PRO39 4.5 14.8 1.0 CG B:HIS151 4.5 14.2 1.0 C2 B:TAM309 4.6 22.4 1.0 OD1 B:ASP42 4.6 21.4 1.0 CA B:HIS40 4.6 13.8 1.0 O B:HOH452 4.7 30.2 1.0 CG B:PRO39 5.0 14.2 1.0

Cadmium binding site 4 out of 4 in the N,N'-Diacetylchitobiose Deacetylase (Se-Derivative) From Pyrococcus Furiosus


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 (Se-Derivative) From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:20.9 occ:1.00 OE2 B:GLU225 2.2 17.7 1.0 OE1 B:GLU225 2.4 23.8 1.0 CL B:CL307 2.5 20.4 1.0 CL B:CL305 2.6 22.2 1.0 CL B:CL306 2.6 23.4 1.0 CD B:GLU225 2.7 17.9 1.0 CG B:GLU225 4.3 19.6 1.0 O B:HOH483 4.5 32.1 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