Cadmium in PDB 3eec: X-Ray Structure of Human Ubiquitin Cd(II) Adduct

The structure of X-Ray Structure of Human Ubiquitin Cd(II) Adduct, PDB code: 3eec was solved by G.Falini, S.Fermani, G.Tosi, F.Arnesano, G.Natile, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.43 / 3.00
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	105.253, 105.253, 105.253, 90.00, 90.00, 90.00
R / Rfree (%)	27.9 / 30

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct (pdb code 3eec). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct, PDB code: 3eec:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:67.1 occ:0.70 OE1 A:GLU64 2.3 68.1 1.0 O A:HOH108 2.5 62.9 0.7 OE2 A:GLU64 2.5 66.6 1.0 O A:HOH107 2.6 86.0 0.7 CD A:GLU64 2.8 67.8 1.0 CE A:LYS63 4.1 70.6 1.0 CG A:GLU64 4.3 67.1 1.0 CD A:LYS63 4.8 70.4 1.0

Cadmium binding site 2 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd102 b:59.4 occ:0.85 OE1 A:GLU16 2.3 65.6 1.0 O A:MET1 2.5 72.6 1.0 OE2 A:GLU16 2.5 61.7 1.0 N A:MET1 2.7 70.4 1.0 CD A:GLU16 2.7 60.8 1.0 C A:MET1 3.1 71.6 1.0 CA A:MET1 3.4 71.8 1.0 CG A:GLU16 4.2 59.3 1.0 N A:GLN2 4.3 71.2 1.0 CB A:MET1 4.7 74.6 1.0

Cadmium binding site 3 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd103 b:58.4 occ:0.85 OE2 A:GLU18 2.3 43.9 1.0 OE1 A:GLU18 2.7 45.4 1.0 CD A:GLU18 2.8 45.7 1.0 CG A:GLU18 4.3 46.2 1.0

Cadmium binding site 4 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd104 b:69.1 occ:0.30 OD1 A:ASP58 2.6 67.4 1.0 OD2 A:ASP58 2.7 68.1 1.0 CG A:ASP58 3.0 66.8 1.0 OG1 A:THR55 4.2 61.9 1.0 CB A:ASP58 4.5 65.0 1.0 CG2 A:THR55 4.8 60.0 1.0 N A:THR55 4.9 61.9 1.0

Cadmium binding site 5 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd105 b:69.2 occ:0.75 OE1 A:GLU24 2.4 61.1 1.0 OD2 A:ASP52 2.4 68.9 1.0 CD A:GLU24 3.2 60.8 1.0 OE2 A:GLU24 3.2 63.1 1.0 CG A:ASP52 3.3 68.9 1.0 OD1 A:ASP39 3.7 63.9 1.0 CB A:ASP52 3.8 68.7 1.0 CD A:CD106 4.0 64.1 0.5 OD1 A:ASP52 4.3 69.7 1.0 CG A:GLU24 4.6 58.7 1.0 CG A:ASP39 4.8 63.9 1.0

Cadmium binding site 6 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd106 b:64.1 occ:0.50 OD1 A:ASP39 2.5 63.9 1.0 OD2 A:ASP39 2.8 64.6 1.0 CG A:ASP39 3.0 63.9 1.0 CD A:CD105 4.0 69.2 0.8 CB A:ASP39 4.4 64.1 1.0

Cadmium binding site 7 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd201 b:63.9 occ:0.20 NE2 B:HIS68 2.3 91.8 1.0 CD2 B:HIS68 3.0 90.4 1.0 CE1 B:HIS68 3.3 92.4 1.0 CG B:HIS68 4.1 89.5 1.0 ND1 B:HIS68 4.2 91.3 1.0

Cadmium binding site 8 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd202 b:64.5 occ:0.45 O B:HOH207 2.3 47.6 0.5 OE2 B:GLU16 2.4 82.4 1.0 OE1 B:GLU16 2.5 81.3 1.0 O B:MET1 2.6 84.1 1.0 CD B:GLU16 2.8 82.4 1.0 N B:MET1 2.8 84.0 1.0 CA B:MET1 3.2 84.2 1.0 C B:MET1 3.2 83.8 1.0 CG B:GLU16 4.3 82.3 1.0 N B:GLN2 4.3 83.2 1.0 CB B:MET1 4.5 84.8 1.0 CB B:GLN2 5.0 83.2 1.0 O B:VAL17 5.0 73.3 1.0

Cadmium binding site 9 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd203 b:61.1 occ:0.75 OD2 B:ASP21 2.5 59.9 1.0 O B:HOH209 2.5 25.3 0.8 OD1 B:ASP21 2.6 61.1 1.0 O B:HOH208 2.9 33.3 0.8 CG B:ASP21 2.9 60.7 1.0 OE1 B:GLU18 3.0 77.9 1.0 NZ B:LYS29 3.1 72.5 1.0 CD B:GLU18 3.9 76.1 1.0 CG B:GLU18 4.1 74.2 1.0 CE B:LYS29 4.2 72.1 1.0 CB B:GLU18 4.2 72.0 1.0 CB B:ASP21 4.4 60.6 1.0 ND2 B:ASN25 4.5 66.0 1.0 N B:GLU18 4.7 72.2 1.0

Cadmium binding site 10 out of 12 in the X-Ray Structure of Human Ubiquitin Cd(II) Adduct


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of X-Ray Structure of Human Ubiquitin Cd(II) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd204 b:63.5 occ:0.30 OD2 B:ASP58 2.6 80.4 1.0 OD1 B:ASP58 2.6 80.3 1.0 CG B:ASP58 3.0 79.3 1.0 CB B:ASP58 4.5 78.6 1.0 OG1 B:THR55 4.5 77.2 1.0 CG2 B:THR55 4.5 77.2 1.0

G.Falini, S.Fermani, G.Tosi, F.Arnesano, G.Natile. Structural Probing of Zn(II), Cd(II) and Hg(II) Binding to Human Ubiquitin. Chem.Commun.(Camb.) V. 45 5960 2008.
ISSN: ISSN 1359-7345
PubMed: 19030552
DOI: 10.1039/B813463D