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Fluorine in PDB 5l6j: UBA1 in Complex with Ub-MLN7243 Covalent Adduct

Enzymatic activity of UBA1 in Complex with Ub-MLN7243 Covalent Adduct

All present enzymatic activity of UBA1 in Complex with Ub-MLN7243 Covalent Adduct:
6.2.1.45;

Protein crystallography data

The structure of UBA1 in Complex with Ub-MLN7243 Covalent Adduct, PDB code: 5l6j was solved by M.Misra, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.68
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.476, 193.920, 230.219, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.4

Other elements in 5l6j:

The structure of UBA1 in Complex with Ub-MLN7243 Covalent Adduct also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the UBA1 in Complex with Ub-MLN7243 Covalent Adduct (pdb code 5l6j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the UBA1 in Complex with Ub-MLN7243 Covalent Adduct, PDB code: 5l6j:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5l6j

Go back to Fluorine Binding Sites List in 5l6j
Fluorine binding site 1 out of 6 in the UBA1 in Complex with Ub-MLN7243 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of UBA1 in Complex with Ub-MLN7243 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:57.7
occ:1.00
 F2 B:61T101 0.0 57.7 1.0
C16 B:61T101 1.3 54.8 1.0
F B:61T101 2.1 54.6 1.0
F1 B:61T101 2.2 49.8 1.0
S1 B:61T101 2.6 57.3 1.0
CD A:PRO522 3.5 54.6 1.0
O A:HOH1425 3.7 39.3 1.0
CB A:TYR551 3.9 37.4 1.0
C14 B:61T101 4.0 52.2 1.0
CD2 A:TYR551 4.1 40.0 1.0
CG A:PRO522 4.1 57.3 1.0
CG A:TYR551 4.2 38.2 1.0
CA A:GLY521 4.4 47.0 1.0
N A:PRO522 4.7 54.2 1.0
O A:ASP547 4.7 44.4 1.0
C15 B:61T101 4.7 55.0 1.0
C13 B:61T101 4.9 49.8 1.0

Fluorine binding site 2 out of 6 in 5l6j

Go back to Fluorine Binding Sites List in 5l6j
Fluorine binding site 2 out of 6 in the UBA1 in Complex with Ub-MLN7243 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of UBA1 in Complex with Ub-MLN7243 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:54.6
occ:1.00
 F B:61T101 0.0 54.6 1.0
C16 B:61T101 1.3 54.8 1.0
F2 B:61T101 2.1 57.7 1.0
F1 B:61T101 2.2 49.8 1.0
S1 B:61T101 2.5 57.3 1.0
C14 B:61T101 3.1 52.2 1.0
O A:ASP547 3.1 44.4 1.0
C A:ASP547 3.2 43.4 1.0
O A:HOH1425 3.4 39.3 1.0
CB A:ASP547 3.5 45.7 1.0
N A:ALA548 3.6 40.2 1.0
C13 B:61T101 3.6 49.8 1.0
CA A:ALA548 3.8 39.7 1.0
C15 B:61T101 3.9 55.0 1.0
CA A:ASP547 3.9 44.3 1.0
CB A:TYR551 4.1 37.4 1.0
C12 B:61T101 4.7 47.1 1.0
CB A:ALA548 4.8 38.8 1.0
CG A:ASP547 4.8 46.0 1.0
C A:ALA548 4.9 38.6 1.0
C10 B:61T101 4.9 48.0 1.0
CG A:TYR551 4.9 38.2 1.0

Fluorine binding site 3 out of 6 in 5l6j

Go back to Fluorine Binding Sites List in 5l6j
Fluorine binding site 3 out of 6 in the UBA1 in Complex with Ub-MLN7243 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of UBA1 in Complex with Ub-MLN7243 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:49.8
occ:1.00
 F1 B:61T101 0.0 49.8 1.0
C16 B:61T101 1.3 54.8 1.0
F2 B:61T101 2.2 57.7 1.0
F B:61T101 2.2 54.6 1.0
S1 B:61T101 2.6 57.3 1.0
CB A:TYR551 3.2 37.4 1.0
C14 B:61T101 3.3 52.2 1.0
C15 B:61T101 3.3 55.0 1.0
CG A:TYR551 3.5 38.2 1.0
O A:VAL520 3.7 44.6 1.0
CA A:GLY521 3.8 47.0 1.0
CA A:ALA548 4.0 39.7 1.0
CD1 A:TYR551 4.0 37.7 1.0
CD2 A:TYR551 4.1 40.0 1.0
O A:ASP547 4.2 44.4 1.0
C A:VAL520 4.4 44.2 1.0
N A:GLY521 4.4 45.2 1.0
C13 B:61T101 4.4 49.8 1.0
CD A:PRO522 4.5 54.6 1.0
N A:ALA548 4.5 40.2 1.0
C10 B:61T101 4.5 48.0 1.0
C A:ASP547 4.6 43.4 1.0
O A:HOH1425 4.6 39.3 1.0
CB A:ALA548 4.6 38.8 1.0
O A:ALA548 4.6 41.5 1.0
CA A:TYR551 4.7 38.0 1.0
C A:ALA548 4.8 38.6 1.0
CG2 A:VAL520 4.9 41.5 1.0
CE1 A:TYR551 4.9 39.0 1.0
C A:GLY521 5.0 49.6 1.0

Fluorine binding site 4 out of 6 in 5l6j

Go back to Fluorine Binding Sites List in 5l6j
Fluorine binding site 4 out of 6 in the UBA1 in Complex with Ub-MLN7243 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of UBA1 in Complex with Ub-MLN7243 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F101

b:82.1
occ:1.00
 F2 D:61T101 0.0 82.1 1.0
C16 D:61T101 1.3 79.3 1.0
F D:61T101 2.1 81.5 1.0
F1 D:61T101 2.2 75.4 1.0
S1 D:61T101 2.6 72.2 1.0
CD C:PRO522 3.4 55.4 1.0
O C:HOH1380 3.9 32.1 1.0
C14 D:61T101 4.0 75.0 1.0
CB C:TYR551 4.0 43.3 1.0
CG C:PRO522 4.1 56.0 1.0
CD2 C:TYR551 4.2 44.5 1.0
CG C:TYR551 4.3 43.7 1.0
CA C:GLY521 4.3 52.0 1.0
N C:PRO522 4.6 55.2 1.0
C15 D:61T101 4.6 71.4 1.0
O C:ASP547 4.7 47.2 1.0
C13 D:61T101 4.9 72.7 1.0
C C:GLY521 5.0 53.6 1.0

Fluorine binding site 5 out of 6 in 5l6j

Go back to Fluorine Binding Sites List in 5l6j
Fluorine binding site 5 out of 6 in the UBA1 in Complex with Ub-MLN7243 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of UBA1 in Complex with Ub-MLN7243 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F101

b:81.5
occ:1.00
 F D:61T101 0.0 81.5 1.0
C16 D:61T101 1.3 79.3 1.0
F2 D:61T101 2.1 82.1 1.0
F1 D:61T101 2.2 75.4 1.0
S1 D:61T101 2.6 72.2 1.0
O C:ASP547 3.0 47.2 1.0
C C:ASP547 3.1 45.9 1.0
C14 D:61T101 3.2 75.0 1.0
O C:HOH1380 3.3 32.1 1.0
CB C:ASP547 3.4 48.8 1.0
N C:ALA548 3.5 44.2 1.0
CA C:ALA548 3.7 43.0 1.0
C13 D:61T101 3.8 72.7 1.0
C15 D:61T101 3.8 71.4 1.0
CA C:ASP547 3.8 47.1 1.0
CB C:TYR551 4.0 43.3 1.0
CB C:ALA548 4.6 43.1 1.0
C C:ALA548 4.7 40.4 1.0
CG C:ASP547 4.7 49.5 1.0
C12 D:61T101 4.8 66.4 1.0
C10 D:61T101 4.8 67.0 1.0
CG C:TYR551 4.9 43.7 1.0
N C:TYR551 4.9 42.3 1.0
O C:ALA548 5.0 40.5 1.0

Fluorine binding site 6 out of 6 in 5l6j

Go back to Fluorine Binding Sites List in 5l6j
Fluorine binding site 6 out of 6 in the UBA1 in Complex with Ub-MLN7243 Covalent Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of UBA1 in Complex with Ub-MLN7243 Covalent Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F101

b:75.4
occ:1.00
 F1 D:61T101 0.0 75.4 1.0
C16 D:61T101 1.3 79.3 1.0
F2 D:61T101 2.2 82.1 1.0
F D:61T101 2.2 81.5 1.0
S1 D:61T101 2.5 72.2 1.0
C15 D:61T101 3.1 71.4 1.0
C14 D:61T101 3.1 75.0 1.0
O C:VAL520 3.4 49.3 1.0
CB C:TYR551 3.6 43.3 1.0
CA C:GLY521 3.7 52.0 1.0
CG C:TYR551 3.9 43.7 1.0
CA C:ALA548 4.0 43.0 1.0
C C:VAL520 4.2 50.0 1.0
N C:GLY521 4.3 51.5 1.0
C10 D:61T101 4.3 67.0 1.0
C13 D:61T101 4.3 72.7 1.0
CD1 C:TYR551 4.4 42.2 1.0
O C:ASP547 4.4 47.2 1.0
CD C:PRO522 4.4 55.4 1.0
CD2 C:TYR551 4.5 44.5 1.0
CB C:ALA548 4.6 43.1 1.0
N C:ALA548 4.6 44.2 1.0
C C:ASP547 4.7 45.9 1.0
CG1 C:VAL520 4.8 47.3 1.0
C8 D:61T101 4.9 55.6 1.0
O C:ALA548 4.9 40.5 1.0
C C:GLY521 4.9 53.6 1.0
C9 D:61T101 5.0 61.4 1.0
O C:HOH1380 5.0 32.1 1.0
C C:ALA548 5.0 40.4 1.0

Reference:

M.Misra, M.Kuhn, M.Lobel, H.An, A.V.Statsyuk, C.Sotriffer, H.Schindelin. Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme. Structure V. 25 1120 2017.
ISSN: ISSN 1878-4186
PubMed: 28578874
DOI: 10.1016/J.STR.2017.05.001
Page generated: Thu Aug 1 11:19:21 2024

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