Zinc in PDB 5nl5: Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/1.3 Mm E16V Hub

The structure of Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/1.3 Mm E16V Hub, PDB code: 5nl5 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)	34.29 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.320, 50.460, 93.870, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 23.7

The binding sites of Zinc atom in the Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/1.3 Mm E16V Hub (pdb code 5nl5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/1.3 Mm E16V Hub, PDB code: 5nl5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 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 ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:14.1 occ:1.00 O2 C:EDO103 2.0 19.9 1.0 OD1 C:ASP21 2.0 8.6 1.0 OE1 A:GLU18 2.0 8.2 1.0 OXT C:ACT102 2.6 16.3 1.0 O1 C:EDO103 2.6 28.8 1.0 CD A:GLU18 2.7 8.5 1.0 OE2 A:GLU18 2.8 8.5 1.0 CG C:ASP21 2.8 8.4 1.0 OD2 C:ASP21 2.9 8.9 1.0 C1 C:EDO103 3.1 21.2 1.0 C2 C:EDO103 3.1 24.6 1.0 C C:ACT102 3.6 16.6 1.0 ND2 C:ASN25 3.9 4.6 1.0 CH3 C:ACT102 3.9 18.4 1.0 O A:HOH215 4.0 11.3 1.0 O C:HOH255 4.1 25.3 1.0 NZ C:LYS29 4.1 10.0 1.0 CG A:GLU18 4.2 7.5 1.0 CB C:ASP21 4.2 7.9 1.0 OE2 C:GLU18 4.3 7.5 1.0 CE C:LYS29 4.3 8.7 1.0 CG C:ASN25 4.6 5.0 1.0 CA C:ASP21 4.7 7.4 1.0 CB C:ASN25 4.8 5.4 1.0 O C:ACT102 4.8 18.3 1.0 CG C:GLU18 4.8 7.1 1.0 CB A:GLU18 4.8 7.2 1.0 O A:ACT104 4.9 27.5 1.0 CB C:GLU18 4.9 7.5 1.0 O A:HOH222 5.0 20.9 1.0 N C:GLU18 5.0 7.3 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 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 ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:11.1 occ:1.00 O A:HOH215 2.0 11.3 1.0 OXT A:ACT104 2.1 18.2 1.0 OD1 A:ASP21 2.1 5.6 1.0 CG A:ASP21 2.8 5.3 1.0 OD2 A:ASP21 2.8 5.2 1.0 C A:ACT104 3.0 24.4 1.0 CH3 C:ACT102 3.2 18.4 1.0 O A:ACT104 3.3 27.5 1.0 C C:ACT102 3.4 16.6 1.0 O C:ACT102 3.7 18.3 1.0 O A:HOH222 3.9 20.9 1.0 ND2 A:ASN25 4.0 5.5 1.0 NZ A:LYS29 4.1 11.6 1.0 OXT C:ACT102 4.1 16.3 1.0 O C:HOH225 4.2 24.1 1.0 CB A:ASP21 4.2 5.2 1.0 CH3 A:ACT104 4.4 20.7 1.0 OE1 A:GLU18 4.4 8.2 1.0 CE A:LYS29 4.5 9.2 1.0 CB A:GLU18 4.7 7.2 1.0 CA A:ASP21 4.7 5.1 1.0 OXT C:ACT101 4.8 11.6 1.0 CG A:ASN25 4.8 6.0 1.0 N A:GLU18 4.8 7.5 1.0 CB A:ASN25 4.9 5.8 1.0 CG A:GLU18 5.0 7.5 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 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 ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:29.4 occ:0.50 OD1 A:ASP39 2.3 21.3 1.0 CG A:ASP39 3.0 19.3 1.0 OD2 A:ASP39 3.0 19.9 1.0 O A:HOH269 4.0 12.1 1.0 O A:HOH292 4.2 46.8 1.0 O A:HOH252 4.3 22.6 1.0 CB A:ASP39 4.4 16.0 1.0 CB A:PRO37 4.5 9.8 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 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 ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:16.6 occ:1.00 NZ B:LYS6 1.9 18.0 1.0 NE2 A:HIS68 2.1 11.9 1.0 NE2 B:HIS68 2.1 13.3 1.0 O1 A:EDO106 2.3 26.9 1.0 CD2 B:HIS68 3.0 12.0 1.0 CD2 A:HIS68 3.0 12.2 1.0 CE1 A:HIS68 3.1 11.6 1.0 CE1 B:HIS68 3.2 14.4 1.0 CE B:LYS6 3.2 17.0 1.0 O2 A:EDO106 3.3 27.3 1.0 C1 A:EDO106 3.5 30.0 1.0 CD B:LYS6 3.6 15.1 1.0 C2 A:EDO106 3.6 27.3 1.0 CG B:HIS68 4.2 11.3 1.0 ND1 A:HIS68 4.2 11.2 1.0 CG A:HIS68 4.2 11.3 1.0 ND1 B:HIS68 4.2 11.8 1.0 O A:HOH235 4.9 13.5 1.0 CG B:LYS6 5.0 14.9 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 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 5 of Crystal Structure of ZN1.7-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:8.0 occ:1.00 OD1 B:ASP21 1.9 5.2 1.0 CG B:ASP21 2.6 5.5 1.0 OD2 B:ASP21 2.7 5.3 1.0 OD1 B:ASN25 4.0 5.7 1.0 CB B:ASP21 4.1 5.5 1.0 NZ B:LYS29 4.2 5.6 1.0 CE B:LYS29 4.3 5.5 1.0 OE1 B:GLU18 4.5 6.9 1.0 CA B:ASP21 4.7 5.4 1.0 CG B:ASN25 4.7 5.6 1.0 CB B:ASN25 4.9 5.4 1.0 N B:GLU18 4.9 6.0 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