Fluorine 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:

Zinc

(Zn)

9 atoms

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

Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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 B:F107 b:42.3 occ:0.45 F1 B:ETF107 0.0 42.3 0.5 C1 B:ETF107 1.3 43.2 1.0 F2 B:ETF107 2.1 42.6 0.1 F3 B:ETF107 2.2 41.3 0.4 C2 B:ETF107 2.4 40.6 1.0 OE1 B:GLN40 3.2 39.3 1.0 CB B:GLN40 3.6 21.4 1.0 O B:ETF107 3.6 39.5 1.0 CG B:GLN40 3.8 33.2 1.0 CD B:GLN40 3.8 34.3 1.0 O B:HOH229 3.9 29.6 1.0 O B:GLN40 4.4 17.1 1.0 CG2 B:ILE36 4.6 17.1 1.0 CA B:GLN40 4.7 19.3 1.0 O B:HOH256 4.8 39.4 1.0 C B:GLN40 5.0 18.8 1.0 NE2 B:GLN40 5.0 42.0 1.0

Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F 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 B:F107 b:42.6 occ:0.06 F2 B:ETF107 0.0 42.6 0.1 C1 B:ETF107 1.3 43.2 1.0 F1 B:ETF107 2.1 42.3 0.5 F3 B:ETF107 2.1 41.3 0.4 C2 B:ETF107 2.3 40.6 1.0 O B:ETF107 2.7 39.5 1.0 CD1 B:LEU8 3.6 32.6 1.0 CD2 B:LEU71 4.2 31.9 1.0 O B:HOH229 4.5 29.6 1.0 CD1 A:LEU71 4.9 24.2 1.0

Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F 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 B:F107 b:41.3 occ:0.43 F3 B:ETF107 0.0 41.3 0.4 C1 B:ETF107 1.3 43.2 1.0 F2 B:ETF107 2.1 42.6 0.1 F1 B:ETF107 2.2 42.3 0.5 C2 B:ETF107 2.3 40.6 1.0 O B:ETF107 2.8 39.5 1.0 CD1 B:LEU8 3.5 32.6 1.0 CG2 B:ILE36 3.6 17.1 1.0 O B:GLN40 4.1 17.1 1.0 O B:HOH229 4.1 29.6 1.0 O B:HOH206 4.2 22.3 1.0 CB B:GLN40 4.3 21.4 1.0 CG B:LEU8 4.6 27.4 1.0 OE1 B:GLN40 4.6 39.3 1.0 CG1 B:ILE36 4.7 19.5 1.0 CB B:ILE36 4.8 16.2 1.0 C B:GLN40 4.8 18.8 1.0 CD2 B:LEU71 4.9 31.9 1.0 CD1 B:ILE36 4.9 19.1 1.0 O B:HOH250 4.9 52.7 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