Cadmium in PDB 7ooj: Structure of D-THR53 Ubiquitin

The structure of Structure of D-THR53 Ubiquitin, PDB code: 7ooj was solved by S.Becker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.17 / 2.60
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	105.479, 105.479, 105.479, 90, 90, 90
R / Rfree (%)	24.1 / 26.9

The binding sites of Cadmium atom in the Structure of D-THR53 Ubiquitin (pdb code 7ooj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Structure of D-THR53 Ubiquitin, PDB code: 7ooj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in the Structure of D-THR53 Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of D-THR53 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:82.1 occ:1.00 OE2 A:GLU18 2.3 64.6 1.0 OE1 A:GLU18 2.8 68.4 1.0 CD A:GLU18 2.9 64.6 1.0 O A:HOH202 3.3 42.2 0.3 CG A:GLU18 4.4 60.8 1.0

Cadmium binding site 2 out of 8 in the Structure of D-THR53 Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of D-THR53 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd102 b:65.6 occ:0.69 O A:HOH204 2.0 39.6 1.0 OE1 A:GLU64 2.2 68.4 1.0 OE2 A:GLU64 2.3 64.6 1.0 O A:HOH201 2.3 66.9 1.0 CD A:GLU64 2.5 65.2 1.0 NZ A:LYS63 3.6 87.1 1.0 CE A:LYS63 3.8 81.9 1.0 CG A:GLU64 4.0 64.5 1.0 CD A:LYS63 4.2 81.5 1.0 CB A:GLU64 4.9 64.8 1.0

Cadmium binding site 3 out of 8 in the Structure of D-THR53 Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of D-THR53 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd103 b:67.8 occ:0.67 OE1 A:GLU16 2.2 73.1 1.0 OE2 A:GLU16 2.5 70.0 1.0 N A:MET1 2.6 64.8 1.0 CD A:GLU16 2.7 70.6 1.0 O A:MET1 2.9 59.9 1.0 C A:MET1 3.1 62.7 1.0 CA A:MET1 3.3 64.5 1.0 N A:GLN2 4.1 62.9 1.0 CG A:GLU16 4.2 66.1 1.0 O A:VAL17 4.3 57.8 1.0 CB A:MET1 4.7 66.4 1.0 CG A:GLN2 4.8 76.9 1.0

Cadmium binding site 4 out of 8 in the Structure of D-THR53 Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of D-THR53 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd104 b:102.0 occ:0.56 OD2 A:ASP58 2.7 56.9 1.0 OD1 A:ASP58 3.0 63.7 1.0 CG A:ASP58 3.2 59.4 1.0 OG1 A:THR55 4.7 52.3 1.0 CB A:ASP58 4.7 58.3 1.0 CG2 A:THR55 4.9 51.3 1.0

Cadmium binding site 5 out of 8 in the Structure of D-THR53 Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of D-THR53 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd101 b:70.5 occ:0.84 OE1 B:GLU18 2.2 79.4 1.0 CD B:GLU18 2.9 79.4 1.0 OE2 B:GLU18 2.9 80.0 1.0 CG B:GLU18 4.3 75.9 1.0

Cadmium binding site 6 out of 8 in the Structure of D-THR53 Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of D-THR53 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd102 b:74.8 occ:0.52 OE1 B:GLU16 2.4 82.5 1.0 N B:MET1 2.7 92.7 1.0 OE2 B:GLU16 2.7 80.8 1.0 CD B:GLU16 2.9 81.9 1.0 O B:MET1 3.0 98.2 1.0 CA B:MET1 3.0 92.5 1.0 C B:MET1 3.0 96.5 1.0 N B:GLN2 3.9 95.8 1.0 CG B:GLN2 4.2 102.6 1.0 CG B:GLU16 4.4 81.9 1.0 CB B:MET1 4.5 87.3 1.0 O B:VAL17 4.7 67.6 1.0 CA B:GLN2 4.8 94.2 1.0 NZ B:LYS63 4.9 105.1 1.0 NE2 B:GLN2 4.9 106.8 1.0

Cadmium binding site 7 out of 8 in the Structure of D-THR53 Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of D-THR53 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd103 b:121.9 occ:0.55 OE2 B:GLU64 2.3 129.9 1.0 OE1 B:GLU64 2.7 119.3 1.0 CD B:GLU64 2.8 119.1 1.0 CG B:GLU64 4.3 109.9 1.0 CB B:GLU64 4.9 103.2 1.0

Cadmium binding site 8 out of 8 in the Structure of D-THR53 Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of D-THR53 Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd104 b:95.4 occ:0.42 OD2 B:ASP58 2.7 81.4 1.0 OD1 B:ASP58 3.1 86.4 1.0 CG B:ASP58 3.3 82.1 1.0 OG1 B:THR55 4.5 62.5 1.0 CG2 B:THR55 4.6 67.7 1.0 CB B:ASP58 4.8 82.0 1.0

K.S.Chakrabarti, S.Olsson, S.Pratihar, K.Giller, K.Overkamp, K.O.Lee, V.Gapsys, K.S.Ryu, B.L.De Groot, F.Noe, S.Becker, D.Lee, T.R.Weikl, C.Griesinger. A Litmus Test For Classifying Recognition Mechanisms of Transiently Binding Proteins. Nat Commun V. 13 3792 2022.
ISSN: ESSN 2041-1723
PubMed: 35778416
DOI: 10.1038/S41467-022-31374-5