Zinc in PDB 3n30: Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct

The structure of Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct, PDB code: 3n30 was solved by D.Siliqi, R.Caliandro, F.Arnesano, G.Natile, G.Falini, S.Fermani, B.D.Belviso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.17 / 3.00
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	104.890, 104.890, 104.890, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 31.8

The binding sites of Zinc atom in the Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct (pdb code 3n30). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct, PDB code: 3n30:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:80.6 occ:0.95 NE2 A:HIS68 2.2 71.0 1.0 O A:HOH204 2.9 75.7 1.0 CD2 A:HIS68 3.0 60.6 1.0 CE1 A:HIS68 3.3 74.2 1.0 CG A:HIS68 4.3 68.0 1.0 ND1 A:HIS68 4.3 73.5 1.0 O A:THR66 4.4 64.0 1.0 CG2 A:THR66 4.6 64.9 1.0 CB A:THR66 4.9 62.1 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:63.8 occ:0.84 OD1 A:ASP21 2.3 53.2 1.0 OD2 A:ASP21 2.5 52.7 1.0 CG A:ASP21 2.7 50.3 1.0 OE2 A:GLU18 2.9 61.3 1.0 O A:HOH202 3.2 63.5 0.5 NZ A:LYS29 3.7 62.8 1.0 CD A:GLU18 4.0 68.2 1.0 CE A:LYS29 4.0 58.4 1.0 CB A:GLU18 4.2 59.7 1.0 CB A:ASP21 4.2 47.6 1.0 N A:GLU18 4.4 56.5 1.0 CG A:GLU18 4.5 61.8 1.0 OD1 A:ASN25 4.5 57.4 1.0 CA A:GLU18 4.9 57.3 1.0 CA A:ASP21 4.9 50.7 1.0 C A:VAL17 5.0 60.5 1.0 OE1 A:GLU18 5.0 64.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:76.3 occ:0.99 OD2 A:ASP32 2.6 77.3 1.0 CB A:ASP32 2.7 72.7 1.0 CG A:ASP32 2.9 88.5 1.0 OD1 A:ASP32 4.1 89.9 1.0 CA A:ASP32 4.2 79.7 1.0 O A:ASP32 4.5 76.9 1.0 O A:ALA28 4.7 69.7 1.0 N A:ASP32 4.8 76.5 1.0 C A:ASP32 4.9 75.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:71.8 occ:0.94 OD2 B:ASP21 2.6 65.6 1.0 OD1 B:ASP21 2.7 60.4 1.0 CG B:ASP21 3.0 58.7 1.0 OE2 B:GLU18 3.7 72.2 1.0 CE B:LYS29 4.4 65.6 1.0 CB B:ASP21 4.5 48.4 1.0 N B:GLU18 4.5 54.7 1.0 CB B:GLU18 4.6 66.0 1.0 NZ B:LYS29 4.6 69.2 1.0 CD B:GLU18 4.7 67.3 1.0 CG B:GLU18 4.9 65.3 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:84.4 occ:0.93 OD1 B:ASP32 2.5 79.1 1.0 OD2 B:ASP32 2.9 73.0 1.0 CG B:ASP32 3.0 74.3 1.0 CB B:ASP32 4.5 67.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Cubic ZN3-Hub (Human Ubiquitin) Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn106 b:0.4 occ:0.82 NE2 B:HIS68 2.5 0.8 1.0 CE1 B:HIS68 3.1 99.6 1.0 CD2 B:HIS68 3.7 92.2 1.0 CD B:LYS6 3.8 90.9 1.0 CE B:LYS6 4.0 92.4 1.0 ND1 B:HIS68 4.3 98.9 1.0 CG B:HIS68 4.7 90.6 1.0 NZ B:LYS6 5.0 89.0 1.0

F.Arnesano, B.D.Belviso, R.Caliandro, G.Falini, S.Fermani, G.Natile, D.Siliqi. Crystallographic Analysis of Metal-Ion Binding to Human Ubiquitin. Chemistry V. 17 1569 2011.
ISSN: ISSN 0947-6539
PubMed: 21268159
DOI: 10.1002/CHEM.201001617