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

The structure of N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium, PDB code: 4xlz 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)	31.16 / 1.51
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	93.895, 93.880, 93.877, 74.69, 74.68, 74.68
R / Rfree (%)	15.2 / 16.7

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

Chlorine

(Cl)

24 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Cadmium atom in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium (pdb code 4xlz). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium, PDB code: 4xlz:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:14.7 occ:1.00 NE2 A:HIS151 2.3 11.3 1.0 N A:TRS313 2.3 18.2 1.0 OD2 A:ASP43 2.3 13.7 1.0 ND1 A:HIS40 2.3 11.9 1.0 O1 A:TRS313 2.5 21.6 1.0 O A:HOH637 2.6 23.5 1.0 OD1 A:ASP43 2.6 14.1 1.0 CG A:ASP43 2.9 14.9 1.0 CE1 A:HIS151 3.1 12.2 1.0 C A:TRS313 3.2 18.3 1.0 CE1 A:HIS40 3.3 13.3 1.0 C1 A:TRS313 3.4 18.6 1.0 CG A:HIS40 3.4 12.4 1.0 CD2 A:HIS151 3.4 12.6 1.0 C3 A:TRS313 3.6 22.4 1.0 CB A:HIS40 3.6 13.3 1.0 O3 A:TRS313 3.9 29.7 1.0 NE2 C:HIS259 4.1 15.9 1.0 CB A:ASP43 4.3 13.3 1.0 N A:HIS40 4.3 13.4 1.0 O A:HOH493 4.4 24.9 1.0 ND1 A:HIS151 4.4 13.2 1.0 CE1 C:HIS259 4.4 15.1 1.0 NE2 A:HIS40 4.4 12.5 1.0 CG A:HIS151 4.5 11.8 1.0 CD2 A:HIS40 4.5 14.3 1.0 CB A:PRO39 4.5 12.3 1.0 OD1 A:ASP42 4.6 18.2 1.0 C2 A:TRS313 4.6 20.0 1.0 CA A:HIS40 4.6 13.7 1.0 O A:HOH541 4.7 30.3 1.0 CG A:PRO39 4.9 11.5 1.0

Cadmium binding site 2 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:19.9 occ:1.00 OE1 A:GLU225 2.4 18.3 1.0 OE2 A:GLU225 2.5 20.6 1.0 CL A:CL317 2.5 20.2 1.0 CL A:CL316 2.6 22.4 1.0 CL A:CL318 2.6 21.2 1.0 CD A:GLU225 2.8 18.4 1.0 SE C:MSE1 2.9 21.1 1.0 CE C:MSE1 3.6 22.6 1.0 CG C:MSE1 3.7 20.3 1.0 CG A:GLU225 4.3 17.9 1.0 O A:HOH403 4.6 29.4 1.0

Cadmium binding site 3 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:19.7 occ:0.50 OD1 A:ASP265 2.1 21.5 1.0 O A:HOH547 2.3 43.0 1.0 O A:HOH520 2.3 32.4 1.0 NE2 B:HIS193 2.3 14.7 0.5 O A:HOH627 2.4 21.6 1.0 OD2 A:ASP265 2.6 30.2 1.0 CG A:ASP265 2.7 22.2 1.0 CE1 B:HIS193 3.3 14.7 0.5 CD2 B:HIS193 3.3 15.0 0.5 CD2 A:LEU266 4.0 24.5 1.0 CB A:ASP265 4.3 17.9 1.0 CG A:LEU266 4.4 19.7 1.0 O A:HOH422 4.4 17.9 1.0 ND1 B:HIS193 4.4 17.9 0.5 CG B:HIS193 4.5 14.4 0.5 ND1 B:HIS193 4.5 23.6 0.5 O B:HOH512 4.5 29.6 1.0 O A:PRO262 4.8 22.4 1.0 C A:ASP265 4.9 19.3 1.0 O B:HOH546 4.9 45.2 1.0 CA A:ASP265 5.0 16.8 1.0 N A:LEU266 5.0 17.7 1.0

Cadmium binding site 4 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:19.8 occ:0.50 OD1 C:ASP265 2.2 21.3 1.0 O C:HOH524 2.2 33.2 1.0 NE2 A:HIS193 2.2 15.1 0.5 O C:HOH539 2.3 42.7 1.0 O A:HOH420 2.4 21.2 1.0 OD2 C:ASP265 2.6 28.4 1.0 CG C:ASP265 2.8 22.2 1.0 CE1 A:HIS193 3.1 15.3 0.5 CD2 A:HIS193 3.3 16.4 0.5 CD2 C:LEU266 4.0 24.7 1.0 CB C:ASP265 4.3 19.0 1.0 ND1 A:HIS193 4.3 18.9 0.5 O C:HOH424 4.4 18.5 1.0 O A:HOH522 4.4 28.9 1.0 CG A:HIS193 4.4 13.7 0.5 CG C:LEU266 4.4 19.4 1.0 O C:HOH606 4.5 41.2 1.0 ND1 A:HIS193 4.6 20.9 0.5 C C:ASP265 4.8 20.9 1.0 O C:PRO262 4.8 23.2 1.0 C5 A:HEZ310 4.9 54.9 1.0 CA C:ASP265 5.0 18.4 1.0

Cadmium binding site 5 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:14.8 occ:1.00 NE2 B:HIS151 2.3 12.4 1.0 OD2 B:ASP43 2.3 13.6 1.0 ND1 B:HIS40 2.3 12.8 1.0 N B:TRS311 2.4 15.3 1.0 O1 B:TRS311 2.5 19.9 1.0 O B:HOH619 2.6 26.8 1.0 OD1 B:ASP43 2.6 13.7 1.0 CG B:ASP43 2.8 13.3 1.0 CE1 B:HIS151 3.2 12.7 1.0 C B:TRS311 3.2 18.5 1.0 CE1 B:HIS40 3.3 12.6 1.0 C1 B:TRS311 3.3 17.5 1.0 CG B:HIS40 3.3 12.2 1.0 CD2 B:HIS151 3.4 12.8 1.0 CB B:HIS40 3.6 13.6 1.0 C3 B:TRS311 3.7 22.2 1.0 O3 B:TRS311 4.0 32.0 1.0 NE2 A:HIS259 4.1 16.2 1.0 N B:HIS40 4.3 13.1 1.0 CB B:ASP43 4.4 14.8 1.0 ND1 B:HIS151 4.4 13.1 1.0 O B:HOH486 4.4 25.9 1.0 CE1 A:HIS259 4.4 15.6 1.0 NE2 B:HIS40 4.4 12.7 1.0 CG B:HIS151 4.5 12.6 1.0 CD2 B:HIS40 4.5 13.3 1.0 CB B:PRO39 4.5 12.9 1.0 OD1 B:ASP42 4.6 19.0 1.0 O B:HOH485 4.6 28.5 1.0 C2 B:TRS311 4.7 19.7 1.0 CA B:HIS40 4.7 12.5 1.0 CG B:PRO39 4.9 13.3 1.0

Cadmium binding site 6 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:19.9 occ:1.00 OE1 B:GLU225 2.4 20.6 1.0 OE2 B:GLU225 2.4 20.0 1.0 CL B:CL312 2.5 19.6 1.0 CL A:CL315 2.5 22.0 1.0 CL B:CL313 2.6 21.5 1.0 CD B:GLU225 2.7 19.2 1.0 SE A:MSE1 2.9 21.1 1.0 CE A:MSE1 3.6 23.6 1.0 CG A:MSE1 3.7 19.1 1.0 CG B:GLU225 4.3 18.8 1.0 O B:HOH404 4.6 30.9 1.0 O B:HOH414 4.6 38.0 1.0

Cadmium binding site 7 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd303 b:19.7 occ:0.50 OD1 B:ASP265 2.2 21.3 1.0 O B:HOH618 2.2 48.1 1.0 NE2 C:HIS193 2.3 16.7 0.5 O B:HOH606 2.5 21.8 1.0 OD2 B:ASP265 2.6 29.2 1.0 CG B:ASP265 2.8 24.1 1.0 CE1 C:HIS193 3.3 16.5 0.5 CD2 C:HIS193 3.3 14.3 0.5 CD2 B:LEU266 4.0 25.4 1.0 CB B:ASP265 4.3 18.1 1.0 O B:HOH425 4.4 18.5 1.0 ND1 C:HIS193 4.4 24.2 0.5 ND1 C:HIS193 4.4 18.2 0.5 O C:HOH487 4.4 27.3 1.0 CG C:HIS193 4.5 12.7 0.5 CG B:LEU266 4.5 20.6 1.0 O B:HOH583 4.5 39.0 1.0 O B:PRO262 4.8 22.7 1.0 C B:ASP265 4.8 19.7 1.0 CA B:ASP265 4.9 17.0 1.0 O C:HOH525 4.9 44.0 1.0 CE1 C:HIS193 5.0 21.5 0.5

Cadmium binding site 8 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd301 b:14.8 occ:1.00 NE2 C:HIS151 2.3 13.2 1.0 ND1 C:HIS40 2.3 12.5 1.0 OD2 C:ASP43 2.3 13.7 1.0 N C:TRS309 2.3 16.9 1.0 O2 C:TRS309 2.5 21.2 1.0 O C:HOH640 2.5 24.3 1.0 OD1 C:ASP43 2.6 14.8 1.0 CG C:ASP43 2.9 14.6 1.0 CE1 C:HIS151 3.1 12.8 1.0 C C:TRS309 3.2 20.4 1.0 CE1 C:HIS40 3.3 14.6 1.0 CG C:HIS40 3.3 12.3 1.0 C2 C:TRS309 3.4 18.6 1.0 CD2 C:HIS151 3.4 12.2 1.0 C1 C:TRS309 3.6 23.8 1.0 CB C:HIS40 3.7 13.7 1.0 O1 C:TRS309 3.9 29.8 1.0 NE2 B:HIS259 4.1 15.5 1.0 ND1 C:HIS151 4.3 13.4 1.0 N C:HIS40 4.3 12.9 1.0 CB C:ASP43 4.4 14.9 1.0 CE1 B:HIS259 4.4 15.0 1.0 O C:HOH476 4.4 25.2 1.0 NE2 C:HIS40 4.4 12.9 1.0 CG C:HIS151 4.5 12.0 1.0 CB C:PRO39 4.5 12.6 1.0 CD2 C:HIS40 4.5 13.4 1.0 OD1 C:ASP42 4.6 18.1 1.0 C3 C:TRS309 4.6 21.1 1.0 CA C:HIS40 4.6 13.4 1.0 O C:HOH508 4.7 29.0 1.0 CG C:PRO39 4.9 13.1 1.0

Cadmium binding site 9 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 9 of N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd302 b:20.1 occ:1.00 OE1 C:GLU225 2.3 19.6 1.0 CL C:CL310 2.5 19.9 1.0 OE2 C:GLU225 2.5 19.8 1.0 CL C:CL311 2.6 21.1 1.0 CL B:CL314 2.6 21.9 1.0 CD C:GLU225 2.8 18.4 1.0 SE B:MSE1 2.9 20.9 1.0 CE B:MSE1 3.5 26.0 1.0 CG B:MSE1 3.6 18.6 1.0 CG C:GLU225 4.4 18.1 1.0 O C:HOH405 4.6 29.9 1.0

Cadmium binding site 10 out of 18 in the N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) 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 10 of N,N'-Diacetylchitobiose Deacetylase (Semet Derivative) From Pyrococcus Furiosus in the Presence of Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd301 b:14.8 occ:1.00 ND1 D:HIS40 2.3 11.6 1.0 NE2 D:HIS151 2.3 11.6 1.0 OD2 D:ASP43 2.3 13.8 1.0 N D:TRS314 2.3 16.8 1.0 O D:HOH633 2.5 23.5 1.0 O1 D:TRS314 2.5 19.3 1.0 OD1 D:ASP43 2.6 14.4 1.0 CG D:ASP43 2.8 15.3 1.0 CE1 D:HIS151 3.2 12.9 1.0 C D:TRS314 3.2 19.2 1.0 CE1 D:HIS40 3.2 12.2 1.0 CG D:HIS40 3.3 12.1 1.0 C1 D:TRS314 3.4 19.4 1.0 CD2 D:HIS151 3.4 13.7 1.0 C3 D:TRS314 3.6 21.6 1.0 CB D:HIS40 3.6 13.6 1.0 O3 D:TRS314 4.0 30.8 1.0 NE2 F:HIS259 4.1 15.7 1.0 N D:HIS40 4.3 12.5 1.0 O D:HOH463 4.3 24.3 1.0 CB D:ASP43 4.3 14.2 1.0 ND1 D:HIS151 4.4 12.7 1.0 NE2 D:HIS40 4.4 13.2 1.0 CE1 F:HIS259 4.4 15.4 1.0 CD2 D:HIS40 4.5 13.7 1.0 CG D:HIS151 4.5 12.0 1.0 CB D:PRO39 4.5 13.0 1.0 OD1 D:ASP42 4.6 18.3 1.0 O D:HOH497 4.6 28.3 1.0 CA D:HIS40 4.6 12.9 1.0 C2 D:TRS314 4.7 19.9 1.0 CG D:PRO39 5.0 12.8 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