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Fluorine in PDB 5tr4: Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243

Enzymatic activity of Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243

All present enzymatic activity of Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243:
6.2.1.45;

Protein crystallography data

The structure of Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243, PDB code: 5tr4 was solved by M.D.Sintchak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 212.485, 172.148, 79.424, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 25.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243 (pdb code 5tr4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243, PDB code: 5tr4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5tr4

Go back to Fluorine Binding Sites List in 5tr4
Fluorine binding site 1 out of 6 in the Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:36.7
occ:1.00
 F2 B:61T101 0.0 36.7 1.0
C16 B:61T101 1.3 42.1 1.0
F1 B:61T101 2.2 44.9 1.0
F B:61T101 2.2 44.0 1.0
S1 B:61T101 2.5 44.1 1.0
C14 B:61T101 2.8 41.3 1.0
C A:ASP547 3.2 27.6 1.0
O A:ASP547 3.2 30.2 1.0
C13 B:61T101 3.2 37.9 1.0
N A:ALA548 3.3 26.4 1.0
CB A:ASP547 3.4 32.3 1.0
O A:HOH1152 3.4 32.9 1.0
CA A:ALA548 3.6 24.1 1.0
C15 B:61T101 3.7 37.3 1.0
CA A:ASP547 3.9 28.6 1.0
CB A:TYR551 4.2 22.8 1.0
C12 B:61T101 4.3 40.1 1.0
CB A:ALA548 4.5 23.4 1.0
C10 B:61T101 4.6 35.7 1.0
CG A:ASP547 4.7 35.2 1.0
OD1 A:ASN545 4.7 32.2 1.0
C A:ALA548 4.8 30.0 1.0
C11 B:61T101 4.9 36.7 1.0
CG A:TYR551 5.0 26.6 1.0

Fluorine binding site 2 out of 6 in 5tr4

Go back to Fluorine Binding Sites List in 5tr4
Fluorine binding site 2 out of 6 in the Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:44.0
occ:1.00
 F B:61T101 0.0 44.0 1.0
C16 B:61T101 1.3 42.1 1.0
F2 B:61T101 2.2 36.7 1.0
F1 B:61T101 2.2 44.9 1.0
S1 B:61T101 2.6 44.1 1.0
O A:HOH1152 3.6 32.9 1.0
CD A:PRO522 3.7 38.3 1.0
CB A:TYR551 3.7 22.8 1.0
CD1 A:TYR551 3.9 26.9 1.0
CG A:TYR551 4.0 26.6 1.0
C14 B:61T101 4.0 41.3 1.0
O A:ASP547 4.4 30.2 1.0
CA A:GLY521 4.6 34.5 1.0
CG A:PRO522 4.6 43.4 1.0
C15 B:61T101 4.8 37.3 1.0
C13 B:61T101 4.8 37.9 1.0
CE1 A:TYR551 4.8 28.2 1.0
N A:PRO522 4.8 41.4 1.0
C A:ASP547 4.9 27.6 1.0

Fluorine binding site 3 out of 6 in 5tr4

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Fluorine binding site 3 out of 6 in the Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:44.9
occ:1.00
 F1 B:61T101 0.0 44.9 1.0
C16 B:61T101 1.3 42.1 1.0
F2 B:61T101 2.2 36.7 1.0
F B:61T101 2.2 44.0 1.0
S1 B:61T101 2.5 44.1 1.0
C14 B:61T101 3.1 41.3 1.0
CB A:TYR551 3.2 22.8 1.0
C15 B:61T101 3.2 37.3 1.0
CG A:TYR551 3.5 26.6 1.0
O A:VAL520 3.6 46.2 1.0
CA A:ALA548 3.8 24.1 1.0
CA A:GLY521 3.9 34.5 1.0
O A:ASP547 4.1 30.2 1.0
CD2 A:TYR551 4.1 27.3 1.0
CD1 A:TYR551 4.1 26.9 1.0
C13 B:61T101 4.2 37.9 1.0
N A:ALA548 4.3 26.4 1.0
C10 B:61T101 4.4 35.7 1.0
C A:VAL520 4.4 35.9 1.0
C A:ASP547 4.4 27.6 1.0
CD A:PRO522 4.5 38.3 1.0
N A:GLY521 4.5 35.6 1.0
O A:ALA548 4.6 29.4 1.0
CB A:ALA548 4.6 23.4 1.0
O A:HOH1152 4.6 32.9 1.0
CA A:TYR551 4.7 23.4 1.0
C A:ALA548 4.7 30.0 1.0
C8 B:61T101 5.0 30.1 1.0
CE2 A:TYR551 5.0 30.5 1.0

Fluorine binding site 4 out of 6 in 5tr4

Go back to Fluorine Binding Sites List in 5tr4
Fluorine binding site 4 out of 6 in the Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F101

b:48.6
occ:1.00
 F2 D:61T101 0.0 48.6 1.0
C16 D:61T101 1.3 56.1 1.0
F D:61T101 2.2 57.8 1.0
F1 D:61T101 2.2 50.7 1.0
S1 D:61T101 2.5 56.7 1.0
C14 D:61T101 3.0 55.7 1.0
C C:ASP547 3.1 31.4 1.0
O C:ASP547 3.2 37.6 1.0
N C:ALA548 3.3 28.2 1.0
CB C:ASP547 3.4 34.2 1.0
C13 D:61T101 3.4 51.7 1.0
CA C:ALA548 3.6 26.6 1.0
CA C:ASP547 3.8 34.8 1.0
C15 D:61T101 3.8 47.0 1.0
CB C:TYR551 4.2 32.2 1.0
CB C:ALA548 4.4 23.5 1.0
C12 D:61T101 4.5 48.4 1.0
OD1 C:ASN545 4.6 45.6 1.0
CG C:ASP547 4.7 42.9 1.0
C C:ALA548 4.8 28.3 1.0
C10 D:61T101 4.8 46.7 1.0

Fluorine binding site 5 out of 6 in 5tr4

Go back to Fluorine Binding Sites List in 5tr4
Fluorine binding site 5 out of 6 in the Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F101

b:57.8
occ:1.00
 F D:61T101 0.0 57.8 1.0
C16 D:61T101 1.3 56.1 1.0
F2 D:61T101 2.2 48.6 1.0
F1 D:61T101 2.2 50.7 1.0
S1 D:61T101 2.6 56.7 1.0
CD C:PRO522 3.6 62.0 1.0
CB C:TYR551 3.8 32.2 1.0
C14 D:61T101 4.0 55.7 1.0
CD1 C:TYR551 4.1 34.9 1.0
CG C:TYR551 4.1 38.3 1.0
CA C:GLY521 4.4 42.8 1.0
O C:ASP547 4.5 37.6 1.0
CG C:PRO522 4.5 63.5 1.0
N C:PRO522 4.7 57.0 1.0
C15 D:61T101 4.8 47.0 1.0
C13 D:61T101 4.9 51.7 1.0
C C:ASP547 4.9 31.4 1.0

Fluorine binding site 6 out of 6 in 5tr4

Go back to Fluorine Binding Sites List in 5tr4
Fluorine binding site 6 out of 6 in the Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Ubiquitin Activating Enzyme (UBA1) in Complex with Ubiquitin and Tak-243 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F101

b:50.7
occ:1.00
 F1 D:61T101 0.0 50.7 1.0
C16 D:61T101 1.3 56.1 1.0
F2 D:61T101 2.2 48.6 1.0
F D:61T101 2.2 57.8 1.0
S1 D:61T101 2.6 56.7 1.0
C14 D:61T101 3.1 55.7 1.0
CB C:TYR551 3.2 32.2 1.0
C15 D:61T101 3.3 47.0 1.0
CG C:TYR551 3.6 38.3 1.0
O C:VAL520 3.6 45.3 1.0
CA C:ALA548 3.7 26.6 1.0
CA C:GLY521 3.8 42.8 1.0
CD2 C:TYR551 4.0 36.5 1.0
O C:ASP547 4.1 37.6 1.0
C13 D:61T101 4.2 51.7 1.0
N C:ALA548 4.2 28.2 1.0
CD1 C:TYR551 4.3 34.9 1.0
C C:VAL520 4.3 44.6 1.0
CB C:ALA548 4.4 23.5 1.0
C C:ASP547 4.4 31.4 1.0
N C:GLY521 4.4 39.4 1.0
C10 D:61T101 4.4 46.7 1.0
O C:ALA548 4.5 31.6 1.0
CD C:PRO522 4.6 62.0 1.0
C C:ALA548 4.6 28.3 1.0
CA C:TYR551 4.7 32.8 1.0
CE2 C:TYR551 5.0 41.2 1.0

Reference:

M.Hyer, M.Milhollen, J.Ciavarri, P.Fleming, T.Traore, D.Sappal, J.Huck, J.Shi, J.Gavin, J.Brownell, Y.Yang, B.Stringer, R.Griffin, F.Bruzzese, T.Soucy, J.Duffy, C.Rabino, J.Riceberg, K.Hoar, A.Lublinsky, S.Menon, M.Sintchak, N.Bump, S.Pulukuri, B.Amidon, S.Langston, S.Tirrell, M.Kuranda, P.Veiby, J.Newcomb, P.Li, J.Wu, L.Dick, P.Greenspan, K.Galvin, M.Manfredi, C.Claibrone, N.Bence. Identification and Characterization of A Small Molecule Inhibitor of the Ubiquitin Activating Enzyme (Tak-243) To Be Published.
Page generated: Tue Jul 15 08:01:43 2025

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