Cadmium in PDB 3h1u: Structure of Ubiquitin in Complex with Cd Ions

The structure of Structure of Ubiquitin in Complex with Cd Ions, PDB code: 3h1u was solved by I.A.Qureshi, F.Ferron, P.Cheung, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 3.00
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	105.231, 105.231, 105.231, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 25.7

The binding sites of Cadmium atom in the Structure of Ubiquitin in Complex with Cd Ions (pdb code 3h1u). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of Ubiquitin in Complex with Cd Ions, PDB code: 3h1u:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Structure of Ubiquitin in Complex with Cd Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Ubiquitin in Complex with Cd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd77 b:86.7 occ:1.00 OE1 A:GLU64 2.2 62.0 1.0 OE2 A:GLU64 2.7 56.8 1.0 CD A:GLU64 2.8 63.3 1.0 O A:HOH98 3.0 53.3 1.0 O A:HOH85 3.9 38.0 1.0 NZ A:LYS63 4.2 63.6 1.0 CG A:GLU64 4.3 64.2 1.0 CB A:GLU64 4.9 65.2 1.0

Cadmium binding site 2 out of 5 in the Structure of Ubiquitin in Complex with Cd Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Ubiquitin in Complex with Cd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd78 b:55.6 occ:1.00 OE2 A:GLU16 2.4 47.9 1.0 N A:MET1 2.5 58.8 1.0 OE1 A:GLU16 2.6 50.7 1.0 CD A:GLU16 2.9 48.4 1.0 O A:MET1 3.2 61.1 1.0 C A:MET1 3.4 61.8 1.0 CA A:MET1 3.4 60.5 1.0 N A:GLN2 4.3 64.3 1.0 CG A:GLU16 4.4 49.4 1.0 CB A:MET1 4.7 61.5 1.0 CB A:GLN2 4.8 65.1 1.0 CA A:GLN2 5.0 63.9 1.0

Cadmium binding site 3 out of 5 in the Structure of Ubiquitin in Complex with Cd Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Ubiquitin in Complex with Cd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd79 b:53.5 occ:1.00 OE2 A:GLU18 2.4 53.0 1.0 OD1 A:ASP21 2.7 47.6 1.0 OD2 A:ASP21 2.7 45.6 1.0 NZ A:LYS29 2.8 44.2 1.0 O A:HOH80 2.9 22.6 1.0 CG A:ASP21 3.0 45.9 1.0 CD A:GLU18 3.0 53.5 1.0 OE1 A:GLU18 3.4 59.5 1.0 CE A:LYS29 3.9 44.4 1.0 CG A:GLU18 4.1 48.8 1.0 ND2 A:ASN25 4.1 47.4 1.0 CB A:GLU18 4.3 47.8 1.0 CB A:ASP21 4.4 44.1 1.0 N A:GLU18 4.5 44.5 1.0 CA A:ASP21 5.0 44.1 1.0 CG A:ASN25 5.0 46.6 1.0

Cadmium binding site 4 out of 5 in the Structure of Ubiquitin in Complex with Cd Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Ubiquitin in Complex with Cd Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd77 b:70.1 occ:1.00 OE2 B:GLU18 2.4 72.6 1.0 OD1 B:ASP21 2.5 52.6 1.0 OE1 B:GLU18 2.7 69.8 1.0 CD B:GLU18 2.8 69.4 1.0 NZ B:LYS29 2.9 59.7 1.0 OD2 B:ASP21 3.0 50.6 1.0 O B:HOH80 3.1 32.3 1.0 CG B:ASP21 3.1 51.5 1.0 CE B:LYS29 3.7 59.6 1.0 CG B:GLU18 4.2 64.0 1.0 CB B:ASP21 4.5 49.5 1.0 OD1 B:ASN25 4.6 61.3 1.0 CB B:GLU18 4.8 61.0 1.0 CB B:ASN25 4.9 63.2 1.0 N B:GLU18 5.0 56.8 1.0

Cadmium binding site 5 out of 5 in the Structure of Ubiquitin in Complex with Cd Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Ubiquitin in Complex with Cd Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd78 b:82.9 occ:1.00 N B:MET1 2.6 85.2 1.0 O B:MET1 2.7 86.5 1.0 OE1 B:GLU16 2.7 69.0 1.0 OE2 B:GLU16 2.7 66.9 1.0 CD B:GLU16 3.0 69.0 1.0 C B:MET1 3.4 85.1 1.0 CA B:MET1 3.6 84.4 1.0 CG B:GLU16 4.5 68.3 1.0 N B:GLN2 4.6 85.1 1.0 CB B:MET1 4.8 83.5 1.0 O B:VAL17 4.8 57.5 1.0 CB B:GLN2 4.9 86.9 1.0

I.A.Qureshi, F.Ferron, C.C.Seh, P.Cheung, J.Lescar. Crystallographic Structure of Ubiquitin in Complex with Cadmium Ions Bmc Res Notes V. 2 251 2009.
ISSN: ESSN 1756-0500
PubMed: 20003470
DOI: 10.1186/1756-0500-2-251