Zinc in PDB 5nli: Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub

The structure of Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub, PDB code: 5nli 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)	26.61 / 1.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.450, 50.730, 93.760, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.2

The structure of Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub (pdb code 5nli). 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 ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub, PDB code: 5nli:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/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 ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:12.3 occ:0.99 O C:HOH228 1.9 15.0 1.0 OXT A:ACT109 2.0 14.2 1.0 OE1 A:GLU18 2.0 13.2 1.0 OD1 C:ASP21 2.0 11.5 1.0 CD A:GLU18 2.6 13.7 1.0 CG C:ASP21 2.8 12.5 1.0 OE2 A:GLU18 2.8 13.7 1.0 OD2 C:ASP21 2.8 14.5 1.0 C A:ACT109 2.9 19.8 1.0 O A:ACT109 3.2 19.9 1.0 ZN A:ZN105 3.3 15.4 0.6 O A:HOH240 3.8 16.1 1.0 O C:HOH264 3.8 30.1 1.0 ND2 C:ASN25 4.0 9.9 1.0 O A:HOH232 4.0 14.3 1.0 CG A:GLU18 4.1 11.2 1.0 NZ C:LYS29 4.2 18.1 1.0 CB C:ASP21 4.2 12.2 1.0 CH3 A:ACT109 4.2 20.6 1.0 OE2 C:GLU18 4.3 13.8 1.0 CE C:LYS29 4.4 16.5 1.0 CG C:ASN25 4.7 9.8 1.0 CA C:ASP21 4.8 11.0 1.0 O A:ACT101 4.8 25.2 1.0 O A:HOH243 4.8 36.0 1.0 CB C:ASN25 4.9 10.3 1.0 CG C:GLU18 4.9 11.2 1.0 CB A:GLU18 4.9 11.4 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/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 ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:12.5 occ:1.00 OXT A:ACT101 1.9 14.8 1.0 O A:HOH232 2.0 14.3 1.0 OD1 A:ASP21 2.1 11.3 1.0 C A:ACT101 2.8 20.2 1.0 CG A:ASP21 2.8 11.1 1.0 OD2 A:ASP21 2.9 12.5 1.0 O A:ACT101 3.1 25.2 1.0 ZN A:ZN105 3.3 15.4 0.6 O A:HOH240 3.8 16.1 1.0 O A:HOH257 3.8 25.9 1.0 ND2 A:ASN25 3.9 9.3 1.0 CB A:ASP21 4.2 10.3 1.0 NZ A:LYS29 4.2 19.6 1.0 CH3 A:ACT101 4.3 19.2 1.0 O C:HOH232 4.3 27.2 1.0 OE1 A:GLU18 4.4 13.2 1.0 CE A:LYS29 4.4 16.5 1.0 OXT C:ACT101 4.7 21.2 1.0 CA A:ASP21 4.7 9.3 1.0 CG A:ASN25 4.8 8.8 1.0 CG A:GLU18 4.9 11.2 1.0 CB A:ASN25 5.0 8.9 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/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 ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:15.4 occ:0.56 O A:HOH232 2.0 14.3 1.0 O A:HOH240 2.1 16.1 1.0 O C:HOH228 2.1 15.0 1.0 OE1 A:GLU18 3.1 13.2 1.0 OE2 C:GLU18 3.2 13.8 1.0 ZN A:ZN104 3.3 12.5 1.0 ZN A:ZN103 3.3 12.3 1.0 O A:HOH257 3.7 25.9 1.0 OXT C:ACT101 3.7 21.2 1.0 O A:ACT109 3.8 19.9 1.0 O C:HOH264 3.8 30.1 1.0 O A:ACT101 3.8 25.2 1.0 CD A:GLU18 4.3 13.7 1.0 O C:ACT101 4.4 13.9 1.0 OXT A:ACT109 4.5 14.2 1.0 OXT A:ACT101 4.5 14.8 1.0 CD C:GLU18 4.5 13.7 1.0 C A:ACT109 4.5 19.8 1.0 C C:ACT101 4.5 18.0 1.0 C A:ACT101 4.6 20.2 1.0 OD1 C:ASP21 4.8 11.5 1.0 OD1 A:ASP21 4.9 11.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/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 ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:24.2 occ:0.66 O A:ACT102 1.8 34.0 1.0 OD2 A:ASP39 2.0 27.9 1.0 O A:HOH251 2.1 33.7 1.0 C A:ACT102 2.8 40.6 1.0 CG A:ASP39 2.8 27.6 1.0 OD1 A:ASP39 2.9 30.1 1.0 OXT A:ACT102 3.1 33.0 1.0 CH3 A:ACT102 4.1 37.4 1.0 O A:HOH248 4.2 19.0 1.0 CB A:ASP39 4.2 20.8 1.0 O A:HOH268 4.4 30.5 1.0 CB A:PRO37 4.7 19.1 1.0 NE2 A:GLN40 5.0 36.4 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/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 ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn108 b:18.5 occ:1.00 OXT A:ACT107 2.0 24.0 1.0 NE2 B:HIS68 2.1 16.8 1.0 NE2 A:HIS68 2.1 13.0 1.0 NZ B:LYS6 2.4 29.8 1.0 C A:ACT107 2.7 21.6 1.0 O A:ACT107 2.9 31.2 1.0 CE1 A:HIS68 2.9 17.3 1.0 CE1 B:HIS68 3.0 19.7 1.0 CD2 B:HIS68 3.1 17.7 1.0 CD2 A:HIS68 3.1 14.6 1.0 CE B:LYS6 3.2 26.8 1.0 CD B:LYS6 3.7 24.7 1.0 O B:HOH265 3.7 41.7 1.0 ND1 A:HIS68 4.1 14.8 1.0 ND1 B:HIS68 4.1 19.2 1.0 CH3 A:ACT107 4.2 27.7 1.0 CG B:HIS68 4.2 15.7 1.0 CG A:HIS68 4.2 13.5 1.0 CG2 A:THR66 5.0 15.4 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/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 6 of Crystal Structure of ZN2-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 35 Mm Zinc Acetate/10% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:11.1 occ:1.00 O B:HOH218 2.0 13.8 1.0 OD1 B:ASP21 2.0 9.8 1.0 CG B:ASP21 2.8 11.1 1.0 OD2 B:ASP21 2.9 13.0 1.0 O B:HOH215 3.9 20.5 1.0 OD1 B:ASN25 3.9 13.3 1.0 CB B:ASP21 4.2 9.6 1.0 NZ B:LYS29 4.2 17.3 1.0 CE B:LYS29 4.3 13.3 1.0 OE1 B:GLU18 4.4 14.4 1.0 CG B:ASN25 4.7 9.6 1.0 CA B:ASP21 4.7 8.5 1.0 CB B:ASN25 4.9 9.6 1.0 N B:GLU18 5.0 9.7 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