Zinc in PDB 5nl4: Crystal Structure of ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub

The structure of Crystal Structure of ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub, PDB code: 5nl4 was solved by S.Fermani, G.Falini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.92 / 1.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.170, 50.330, 93.850, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.3

The binding sites of Zinc atom in the Crystal Structure of ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub (pdb code 5nl4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub, PDB code: 5nl4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub


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 ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:11.7 occ:0.67 O A:HOH248 1.9 23.5 1.0 O C:HOH237 1.9 18.8 1.0 OE1 A:GLU18 2.0 17.8 1.0 O A:HOH204 2.0 22.9 1.0 OD1 C:ASP21 2.0 12.4 1.0 CD A:GLU18 2.7 15.6 1.0 OE2 A:GLU18 2.7 15.5 1.0 CG C:ASP21 2.8 10.0 1.0 OD2 C:ASP21 2.9 11.2 1.0 O A:HOH266 3.3 20.7 1.0 O C:HOH245 3.4 30.0 1.0 ND2 C:ASN25 3.7 9.2 1.0 O A:HOH208 3.9 19.4 1.0 CG A:GLU18 4.1 13.6 1.0 CB C:ASP21 4.2 10.3 1.0 O A:HOH274 4.2 31.1 1.0 NZ C:LYS29 4.3 20.3 1.0 OE1 C:GLU18 4.4 10.9 1.0 CE C:LYS29 4.4 15.5 1.0 CG C:ASN25 4.5 7.8 1.0 CB C:ASN25 4.7 8.3 1.0 CA C:ASP21 4.7 11.6 1.0 CB A:GLU18 4.8 10.3 1.0 CG C:GLU18 4.8 8.9 1.0 OXT A:ACT103 5.0 28.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub


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 ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:7.3 occ:0.79 OD1 A:ASP21 2.0 8.9 1.0 O A:ACT103 2.0 14.3 1.0 O A:HOH208 2.1 19.4 1.0 CG A:ASP21 2.9 8.6 1.0 C A:ACT103 2.9 22.3 1.0 OD2 A:ASP21 2.9 9.8 1.0 OXT A:ACT103 3.0 28.0 1.0 O A:HOH266 3.4 20.7 1.0 O A:HOH252 3.9 28.2 1.0 ND2 A:ASN25 4.0 8.5 1.0 NZ A:LYS29 4.2 15.3 1.0 CB A:ASP21 4.2 8.1 1.0 CH3 A:ACT103 4.3 21.7 1.0 CE A:LYS29 4.4 12.2 1.0 OE1 A:GLU18 4.5 17.8 1.0 CA A:ASP21 4.7 7.4 1.0 CG A:ASN25 4.8 7.2 1.0 CG A:GLU18 4.8 13.6 1.0 CB A:ASN25 4.9 7.4 1.0 N A:GLU18 4.9 8.3 1.0 CB A:GLU18 4.9 10.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub


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 ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:11.2 occ:0.79 O2 B:EDO105 1.9 19.9 1.0 NE2 B:HIS68 2.0 10.4 1.0 NE2 A:HIS68 2.0 9.5 1.0 NZ B:LYS6 2.4 20.5 1.0 C2 B:EDO105 2.5 14.2 1.0 C1 B:EDO105 2.8 15.9 1.0 CE1 A:HIS68 2.9 10.3 1.0 CE1 B:HIS68 3.0 12.8 1.0 CD2 B:HIS68 3.0 10.7 1.0 CD2 A:HIS68 3.1 9.7 1.0 CE B:LYS6 3.2 19.9 1.0 CD B:LYS6 3.7 18.1 1.0 ND1 A:HIS68 4.1 11.1 1.0 ND1 B:HIS68 4.1 12.1 1.0 O1 B:EDO105 4.1 32.7 1.0 CG B:HIS68 4.1 11.0 1.0 CG A:HIS68 4.2 9.9 1.0 O B:HOH265 4.3 47.6 1.0 CG2 A:THR66 4.9 12.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub


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 ZN1.3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:7.7 occ:0.80 O B:HOH238 1.9 14.3 1.0 OD1 B:ASP21 2.0 8.5 1.0 O B:ACT103 2.0 12.0 1.0 CG B:ASP21 2.8 8.9 1.0 C B:ACT103 2.8 14.0 1.0 OD2 B:ASP21 2.8 9.9 1.0 OXT B:ACT103 2.9 22.0 1.0 OD1 B:ASN25 3.9 11.4 1.0 O B:HOH256 3.9 22.5 1.0 O B:HOH240 3.9 26.3 1.0 NZ B:LYS29 4.2 13.1 1.0 CB B:ASP21 4.2 8.3 1.0 CH3 B:ACT103 4.3 18.2 1.0 CE B:LYS29 4.3 10.6 1.0 OE1 B:GLU18 4.5 15.0 1.0 O B:HOH266 4.5 29.8 1.0 CG B:ASN25 4.7 8.2 1.0 CA B:ASP21 4.7 7.8 1.0 CB B:ASN25 4.8 8.1 1.0

S.Fermani, M.Calvaresi, V.Mangini, G.Falini, A.Bottoni, G.Natile, F.Arnesano. Aggregation Pathways of Native-Like Ubiquitin Promoted By Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium. Chemistry V. 24 4140 2018.
ISSN: ISSN 1521-3765
PubMed: 29266436
DOI: 10.1002/CHEM.201705543