Fluorine 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:

Zinc

(Zn)

6 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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 B:F104 b:50.1 occ:0.88 F1 B:ETF104 0.0 50.1 0.9 C1 B:ETF104 1.3 58.5 1.0 F2 B:ETF104 2.1 56.6 0.3 F3 B:ETF104 2.2 56.8 0.8 C2 B:ETF104 2.4 54.5 1.0 O B:ETF104 3.6 61.7 1.0 O B:HOH271 3.8 52.6 1.0 O B:HOH208 4.0 19.0 1.0 OD2 B:ASP52 4.2 24.6 1.0 O B:HOH237 4.2 36.4 1.0 NH2 B:ARG72 4.3 65.9 1.0 O B:HOH228 4.5 36.5 1.0 O B:HOH214 5.0 35.3 1.0 O B:HOH274 5.0 42.0 1.0 CZ B:ARG72 5.0 66.1 1.0

Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F 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 B:F104 b:56.6 occ:0.32 F2 B:ETF104 0.0 56.6 0.3 C1 B:ETF104 1.3 58.5 1.0 O B:HOH208 2.0 19.0 1.0 F1 B:ETF104 2.1 50.1 0.9 F3 B:ETF104 2.1 56.8 0.8 C2 B:ETF104 2.3 54.5 1.0 O B:ETF104 2.9 61.7 1.0 OD2 B:ASP52 3.1 24.6 1.0 CG B:ASP52 3.5 19.6 1.0 O B:HOH237 3.5 36.4 1.0 CB B:ASP52 3.9 14.4 1.0 OD1 B:ASP52 4.0 18.7 1.0 N B:ASP52 4.4 11.1 1.0 O B:HOH228 4.6 36.5 1.0 O B:HOH273 4.8 32.3 1.0 CA B:ASP52 4.8 11.6 1.0 O B:HOH219 4.9 30.8 1.0 O B:HOH214 4.9 35.3 1.0 O B:HOH271 4.9 52.6 1.0

Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F 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 B:F104 b:56.8 occ:0.85 F3 B:ETF104 0.0 56.8 0.8 C1 B:ETF104 1.3 58.5 1.0 F2 B:ETF104 2.1 56.6 0.3 F1 B:ETF104 2.2 50.1 0.9 C2 B:ETF104 2.3 54.5 1.0 O B:ETF104 2.6 61.7 1.0 O B:HOH228 2.6 36.5 1.0 OD2 B:ASP52 3.0 24.6 1.0 O B:HOH208 3.1 19.0 1.0 NH2 B:ARG72 3.4 65.9 1.0 O B:HOH271 3.6 52.6 1.0 CG B:ASP52 3.6 19.6 1.0 O B:HOH214 3.6 35.3 1.0 NH1 B:ARG72 3.8 70.2 1.0 OD1 B:ASP52 3.8 18.7 1.0 CZ B:ARG72 3.9 66.1 1.0 NZ B:LYS27 4.0 20.5 1.0 O B:HOH205 4.5 33.0 1.0 O B:HOH237 4.6 36.4 1.0 CB B:ASP52 4.7 14.4 1.0 NE B:ARG72 5.0 64.2 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