Zinc in PDB 5nlj: Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub

The structure of Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub, PDB code: 5nlj 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)	27.05 / 1.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.360, 49.970, 93.410, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24

The structure of Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub (pdb code 5nlj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub, PDB code: 5nlj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:10.2 occ:0.87 O C:HOH222 1.9 12.8 1.0 OXT A:ACT108 2.0 14.2 1.0 OE1 A:GLU18 2.0 12.6 1.0 OD1 C:ASP21 2.0 9.9 1.0 CD A:GLU18 2.7 12.9 1.0 CG C:ASP21 2.7 10.4 1.0 OE2 A:GLU18 2.8 11.7 1.0 OD2 C:ASP21 2.8 12.0 1.0 C A:ACT108 2.8 22.9 1.0 O A:ACT108 3.1 22.4 1.0 O A:HOH205 3.7 18.0 1.0 ND2 C:ASN25 3.8 8.9 1.0 O A:HOH213 4.1 15.5 1.0 CG A:GLU18 4.1 13.1 1.0 CB C:ASP21 4.2 9.1 1.0 NZ C:LYS29 4.2 18.6 1.0 CE C:LYS29 4.2 15.4 1.0 CH3 A:ACT108 4.3 21.7 1.0 OE1 C:GLU18 4.4 10.5 1.0 CG C:ASN25 4.6 8.3 1.0 CA C:ASP21 4.7 9.9 1.0 CG C:GLU18 4.7 9.8 1.0 CB C:ASN25 4.8 9.5 1.0 CB A:GLU18 4.9 11.2 1.0 N C:GLU18 4.9 10.1 1.0 OXT A:ACT102 4.9 28.1 1.0 CB C:GLU18 5.0 10.8 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:10.4 occ:0.84 O A:HOH213 1.9 15.5 1.0 O A:ACT102 1.9 18.0 1.0 OD1 A:ASP21 2.0 11.5 1.0 CG A:ASP21 2.8 12.7 1.0 OD2 A:ASP21 2.9 12.6 1.0 C A:ACT102 2.9 27.5 1.0 OXT A:ACT102 3.1 28.1 1.0 ND2 A:ASN25 3.9 9.6 1.0 O A:HOH205 3.9 18.0 1.0 CB A:ASP21 4.2 9.8 1.0 CH3 A:ACT102 4.3 25.9 1.0 OE1 A:GLU18 4.3 12.6 1.0 NZ A:LYS29 4.3 23.2 1.0 CE A:LYS29 4.5 17.2 1.0 CA A:ASP21 4.7 8.7 1.0 CG A:GLU18 4.8 13.1 1.0 CG A:ASN25 4.8 9.9 1.0 N A:GLU18 4.9 10.6 1.0 CB A:ASN25 5.0 9.1 1.0 CB A:GLU18 5.0 11.2 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:19.9 occ:0.73 OXT A:ACT103 1.8 29.6 1.0 OD2 A:ASP39 2.0 21.8 1.0 CG A:ASP39 2.8 22.9 1.0 OD1 A:ASP39 2.9 24.0 1.0 C A:ACT103 2.9 29.5 1.0 O A:ACT103 3.3 31.4 1.0 O A:HOH245 4.2 18.2 1.0 CB A:ASP39 4.2 17.3 1.0 CH3 A:ACT103 4.3 28.1 1.0 O A:HOH270 4.4 43.1 1.0 CB A:PRO37 4.8 15.8 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:16.6 occ:0.87 NZ B:LYS6 1.5 25.6 1.0 NE2 B:HIS68 2.0 15.5 1.0 NE2 A:HIS68 2.1 16.2 1.0 OXT A:ACT101 2.2 23.6 1.0 CE B:LYS6 2.9 28.8 1.0 CE1 B:HIS68 2.9 18.4 1.0 C A:ACT101 3.0 25.3 1.0 CE1 A:HIS68 3.0 17.9 1.0 CD2 B:HIS68 3.0 14.2 1.0 CD2 A:HIS68 3.1 16.7 1.0 O A:ACT101 3.2 28.2 1.0 CD B:LYS6 3.5 25.9 1.0 ND1 B:HIS68 4.1 17.6 1.0 CG B:HIS68 4.1 14.1 1.0 ND1 A:HIS68 4.1 17.3 1.0 CG A:HIS68 4.2 15.1 1.0 CH3 A:ACT101 4.4 26.1 1.0 CG2 A:THR66 4.7 16.0 1.0 O B:HOH267 4.8 38.8 1.0 CG B:LYS6 4.9 26.2 1.0 O A:HOH233 4.9 22.4 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn109 b:23.7 occ:0.35 N A:MET1 2.4 17.8 1.0 OD1 C:ASP32 2.5 20.0 1.0 O A:HOH203 3.1 29.6 1.0 O C:HOH235 3.3 34.8 1.0 CG C:ASP32 3.3 19.6 1.0 OD2 C:ASP32 3.3 27.1 1.0 CA A:MET1 3.3 16.2 1.0 C A:MET1 4.3 13.6 1.0 CB A:MET1 4.5 17.0 1.0 CD A:LYS63 4.6 32.3 1.0 CB C:ASP32 4.7 14.8 1.0 N A:GLN2 4.8 12.7 1.0 O A:MET1 4.9 15.9 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:18.8 occ:0.27 N B:MET1 2.1 18.1 1.0 O B:HOH278 2.1 27.0 1.0 O B:HOH228 2.7 21.2 1.0 CA B:MET1 3.1 14.7 1.0 CB B:MET1 3.1 13.8 1.0 O B:VAL17 4.0 11.9 1.0 O B:HOH223 4.1 16.2 1.0 O B:HOH288 4.2 25.1 1.0 C B:MET1 4.3 12.4 1.0 O B:MET1 4.5 13.4 1.0 CG B:MET1 4.6 12.9 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 7 of Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:9.7 occ:0.92 OD1 B:ASP21 2.0 9.4 1.0 O B:ACT101 2.0 12.7 1.0 O B:HOH216 2.0 11.8 1.0 CG B:ASP21 2.7 9.5 1.0 C B:ACT101 2.8 16.5 1.0 OD2 B:ASP21 2.8 13.4 1.0 OXT B:ACT101 2.9 19.4 1.0 ZN B:ZN105 3.3 16.4 0.3 OD1 B:ASN25 4.0 12.1 1.0 O B:HOH202 4.0 21.1 1.0 CB B:ASP21 4.2 8.3 1.0 NZ B:LYS29 4.2 17.4 1.0 CH3 B:ACT101 4.3 18.9 1.0 CE B:LYS29 4.3 13.7 1.0 OE1 B:GLU18 4.4 13.6 1.0 C1 B:PEG102 4.5 20.1 1.0 CA B:ASP21 4.7 8.2 1.0 CG B:ASN25 4.7 11.1 1.0 CB B:ASN25 4.8 10.1 1.0 CG B:GLU18 4.9 11.4 1.0 N B:GLU18 4.9 9.1 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 8 of Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:16.4 occ:0.32 O B:HOH216 2.1 11.8 1.0 OE1 B:GLU18 3.2 13.6 1.0 ZN B:ZN104 3.3 9.7 0.9 C3 B:PEG102 3.6 31.2 1.0 O2 B:PEG102 3.8 34.9 1.0 OXT B:ACT101 3.8 19.4 1.0 O B:HOH202 3.9 21.1 1.0 C2 B:PEG102 3.9 27.2 1.0 C1 B:PEG102 4.1 20.1 1.0 O4 B:PEG102 4.3 28.1 1.0 CD B:GLU18 4.4 12.9 1.0 O B:ACT101 4.5 12.7 1.0 C B:ACT101 4.5 16.5 1.0 C4 B:PEG102 4.6 32.4 1.0 OD1 B:ASP21 4.8 9.4 1.0 O B:HOH215 4.9 30.3 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% 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 9 of Crystal Structure of ZN3-E16V Human Ubiquitin (Hub) Mutant Adduct, From A Solution 70 Mm Zinc Acetate/20% V/V Tfe/1.3 Mm E16V Hub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn106 b:22.5 occ:0.37 NZ B:LYS11 2.0 39.0 1.0 OE1 B:GLU34 2.2 22.2 1.0 O B:HOH269 2.4 32.9 1.0 OE2 B:GLU34 2.5 26.1 1.0 CD B:GLU34 2.7 21.6 1.0 O B:HOH258 2.7 38.5 1.0 CE B:LYS11 3.1 37.0 1.0 O B:HOH252 3.5 30.7 1.0 CD B:LYS11 3.5 38.9 1.0 CG B:GLU34 4.2 17.1 1.0 O B:HOH210 4.3 40.8 1.0 O B:HOH234 4.3 29.8 1.0 O B:LYS33 4.6 12.8 1.0 CA B:GLU34 4.7 14.0 1.0 CB B:GLU34 4.8 16.4 1.0 CG B:LYS11 4.8 32.4 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