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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

Protein crystallography data

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

Other elements in 5nlj:

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

Fluorine Binding Sites:

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 5nlj

Go back to Fluorine Binding Sites List in 5nlj
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 5nlj

Go back to Fluorine Binding Sites List in 5nlj
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 5nlj

Go back to Fluorine Binding Sites List in 5nlj
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

Reference:

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
Page generated: Sun Dec 13 12:28:53 2020

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