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Fluorine in PDB 6n0m: Crystal Structure of SESTRIN2 in Complex with Nv-0005138

Enzymatic activity of Crystal Structure of SESTRIN2 in Complex with Nv-0005138

All present enzymatic activity of Crystal Structure of SESTRIN2 in Complex with Nv-0005138:
1.11.1.15;

Protein crystallography data

The structure of Crystal Structure of SESTRIN2 in Complex with Nv-0005138, PDB code: 6n0m was solved by D.O'neill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.40 / 3.30
Space group I 2 3 1
Cell size a, b, c (Å), α, β, γ (°) 290.410, 290.410, 290.410, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 25

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138 (pdb code 6n0m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138, PDB code: 6n0m:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 6n0m

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Fluorine binding site 1 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


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 SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:0.1
occ:1.00
 F2 A:K94900 0.0 0.1 1.0
C7 A:K94900 1.4 0.0 1.0
F1 A:K94900 2.3 96.7 1.0
C4 A:K94900 2.3 98.6 1.0
C5 A:K94900 2.7 90.3 1.0
C3 A:K94900 2.8 97.0 1.0
CG A:ARG390 3.1 88.0 1.0
C6 A:K94900 3.6 0.2 1.0
CD A:ARG390 3.8 89.2 1.0
CD1 A:LEU458 3.9 0.0 1.0
CD1 A:ILE393 4.0 0.3 1.0
CB A:ARG390 4.3 94.5 1.0
CA A:ARG390 4.3 98.4 1.0
C1 A:K94900 4.3 93.7 1.0
N A:ARG390 4.5 0.2 1.0
CE1 A:HIS454 4.5 90.7 1.0
CG A:LEU389 4.6 92.7 1.0
CH2 A:TRP444 4.6 0.8 1.0
ND1 A:HIS454 4.6 90.2 1.0
CD2 A:LEU389 4.7 95.2 1.0
O2 A:K94900 4.8 88.7 1.0
NE A:ARG390 4.8 90.1 1.0
NE2 A:HIS454 4.8 94.7 1.0
CG A:HIS454 5.0 79.4 1.0
CZ3 A:TRP444 5.0 0.4 1.0
C A:LEU389 5.0 0.8 1.0

Fluorine binding site 2 out of 10 in 6n0m

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Fluorine binding site 2 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


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 SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F900

b:96.7
occ:1.00
 F1 A:K94900 0.0 96.7 1.0
C7 A:K94900 1.4 0.0 1.0
F2 A:K94900 2.3 0.1 1.0
C4 A:K94900 2.5 98.6 1.0
C6 A:K94900 2.8 0.2 1.0
CG2 A:VAL455 3.1 82.4 1.0
C5 A:K94900 3.2 90.3 1.0
CZ3 A:TRP444 3.2 0.4 1.0
CH2 A:TRP444 3.4 0.8 1.0
C3 A:K94900 3.7 97.0 1.0
CD1 A:ILE393 3.8 0.3 1.0
O A:GLU451 3.9 81.3 1.0
N A:VAL455 4.2 77.2 1.0
CB A:VAL455 4.3 85.5 1.0
CA A:VAL455 4.3 85.7 1.0
CE3 A:TRP444 4.5 95.9 1.0
ND1 A:HIS454 4.6 90.2 1.0
CG A:HIS454 4.6 79.4 1.0
CB A:HIS454 4.6 82.3 1.0
CD1 A:LEU458 4.7 0.0 1.0
CZ2 A:TRP444 4.7 93.1 1.0
C A:HIS454 4.8 82.8 1.0
C A:GLU451 4.9 87.7 1.0
C1 A:K94900 4.9 93.7 1.0

Fluorine binding site 3 out of 10 in 6n0m

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Fluorine binding site 3 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


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 SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F900

b:0.6
occ:1.00
 F2 B:K94900 0.0 0.6 1.0
C7 B:K94900 1.4 0.9 1.0
F1 B:K94900 2.3 0.5 1.0
C4 B:K94900 2.4 96.7 1.0
C3 B:K94900 2.8 93.6 1.0
C6 B:K94900 2.8 96.8 1.0
CG2 B:VAL455 3.3 76.9 1.0
CZ3 B:TRP444 3.5 0.4 1.0
C5 B:K94900 3.6 95.2 1.0
CH2 B:TRP444 3.8 0.3 1.0
O B:GLU451 3.8 86.6 1.0
CB B:HIS454 4.1 82.3 1.0
N B:VAL455 4.1 79.2 1.0
CG B:HIS454 4.1 75.9 1.0
C1 B:K94900 4.3 91.0 1.0
ND1 B:HIS454 4.3 78.2 1.0
CA B:VAL455 4.4 83.8 1.0
C B:HIS454 4.4 79.7 1.0
CD1 B:ILE393 4.4 83.7 1.0
CB B:VAL455 4.5 80.3 1.0
CD2 B:HIS454 4.6 81.8 1.0
C B:GLU451 4.6 88.5 1.0
N1 B:K94900 4.7 91.9 1.0
CB B:GLU451 4.7 95.1 1.0
CE3 B:TRP444 4.8 97.5 1.0
CE1 B:HIS454 4.8 82.6 1.0
O B:HIS454 4.9 80.5 1.0
CA B:HIS454 4.9 80.0 1.0
CA B:GLU451 4.9 89.6 1.0

Fluorine binding site 4 out of 10 in 6n0m

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Fluorine binding site 4 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F900

b:0.5
occ:1.00
 F1 B:K94900 0.0 0.5 1.0
C7 B:K94900 1.4 0.9 1.0
F2 B:K94900 2.3 0.6 1.0
C4 B:K94900 2.3 96.7 1.0
C5 B:K94900 2.7 95.2 1.0
C3 B:K94900 2.8 93.6 1.0
CG B:ARG390 3.2 95.8 1.0
C6 B:K94900 3.7 96.8 1.0
CD B:ARG390 4.0 96.7 1.0
C1 B:K94900 4.2 91.0 1.0
CD1 B:ILE393 4.2 83.7 1.0
O2 B:K94900 4.3 79.7 1.0
CE1 B:HIS454 4.3 82.6 1.0
ND1 B:HIS454 4.3 78.2 1.0
CB B:ARG390 4.4 95.6 1.0
CA B:ARG390 4.4 98.1 1.0
CD2 B:LEU458 4.5 0.5 1.0
NE2 B:HIS454 4.6 91.5 1.0
N B:ARG390 4.6 1.0 1.0
CG B:HIS454 4.6 75.9 1.0
C2 B:K94900 4.7 90.8 1.0
CH2 B:TRP444 4.8 0.3 1.0
CD2 B:HIS454 4.8 81.8 1.0
NE B:ARG390 4.8 96.6 1.0
CG B:LEU458 4.9 96.1 1.0

Fluorine binding site 5 out of 10 in 6n0m

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Fluorine binding site 5 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F900

b:0.7
occ:1.00
 F2 C:K94900 0.0 0.7 1.0
C7 C:K94900 1.4 0.3 1.0
F1 C:K94900 2.2 0.9 1.0
C4 C:K94900 2.4 0.1 1.0
C5 C:K94900 2.8 1.0 1.0
C6 C:K94900 3.2 0.7 1.0
CD1 C:ILE393 3.5 99.2 1.0
C3 C:K94900 3.6 0.7 1.0
CG C:ARG390 3.7 0.7 1.0
CH2 C:TRP444 3.7 88.9 1.0
CD2 C:LEU458 4.0 95.3 1.0
CG2 C:VAL455 4.0 93.2 1.0
CZ3 C:TRP444 4.1 93.3 1.0
CD C:ARG390 4.3 0.2 1.0
CG C:LEU389 4.6 0.4 1.0
CD2 C:LEU389 4.7 0.5 1.0
ND1 C:HIS454 4.7 0.3 1.0
CA C:ARG390 4.7 0.1 1.0
O C:LEU389 4.7 100.0 1.0
CB C:ARG390 4.7 0.5 1.0
CZ2 C:TRP444 4.8 90.5 1.0
CG1 C:ILE393 4.9 96.3 1.0
C1 C:K94900 4.9 99.7 1.0
N C:ARG390 5.0 99.7 1.0
C C:LEU389 5.0 93.7 1.0

Fluorine binding site 6 out of 10 in 6n0m

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Fluorine binding site 6 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F900

b:0.9
occ:1.00
 F1 C:K94900 0.0 0.9 1.0
C7 C:K94900 1.4 0.3 1.0
F2 C:K94900 2.2 0.7 1.0
C4 C:K94900 2.4 0.1 1.0
C6 C:K94900 2.7 0.7 1.0
C3 C:K94900 3.0 0.7 1.0
CG2 C:VAL455 3.3 93.2 1.0
O C:GLU451 3.4 97.0 1.0
CZ3 C:TRP444 3.6 93.3 1.0
C5 C:K94900 3.7 1.0 1.0
CB C:HIS454 3.8 98.2 1.0
N C:VAL455 3.9 97.6 1.0
CG C:HIS454 3.9 99.2 1.0
CH2 C:TRP444 4.0 88.9 1.0
ND1 C:HIS454 4.0 0.3 1.0
C C:GLU451 4.2 0.4 1.0
CA C:VAL455 4.3 95.7 1.0
CB C:GLU451 4.3 0.2 1.0
CB C:VAL455 4.4 94.2 1.0
C1 C:K94900 4.4 99.7 1.0
C C:HIS454 4.5 97.3 1.0
CA C:GLU451 4.5 0.9 1.0
CD2 C:HIS454 4.6 0.7 1.0
CA C:HIS454 4.7 94.5 1.0
CE1 C:HIS454 4.7 0.9 1.0
N1 C:K94900 4.7 90.9 1.0
CE3 C:TRP444 4.7 94.3 1.0
CD2 C:LEU458 4.9 95.3 1.0
CD1 C:ILE393 5.0 99.2 1.0

Fluorine binding site 7 out of 10 in 6n0m

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Fluorine binding site 7 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F900

b:0.3
occ:1.00
 F2 D:K94900 0.0 0.3 1.0
C7 D:K94900 1.3 0.1 1.0
F1 D:K94900 2.2 0.3 1.0
C4 D:K94900 2.4 0.5 1.0
C5 D:K94900 2.9 0.4 1.0
C6 D:K94900 2.9 97.1 1.0
CD1 D:ILE393 3.4 78.6 1.0
CH2 D:TRP444 3.6 97.8 1.0
C3 D:K94900 3.6 0.6 1.0
CG D:ARG390 3.8 0.0 1.0
CG2 D:VAL455 4.0 91.8 1.0
CZ3 D:TRP444 4.1 0.3 1.0
CD2 D:LEU458 4.2 0.1 1.0
CD D:ARG390 4.5 1.0 1.0
CG D:LEU389 4.5 84.6 1.0
CG1 D:ILE393 4.5 85.4 1.0
CD2 D:LEU389 4.6 91.1 1.0
CZ2 D:TRP444 4.7 95.5 1.0
CA D:ARG390 4.9 99.3 1.0
CB D:ARG390 4.9 0.9 1.0
C1 D:K94900 4.9 0.6 1.0
ND1 D:HIS454 5.0 96.5 1.0

Fluorine binding site 8 out of 10 in 6n0m

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Fluorine binding site 8 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F900

b:0.3
occ:1.00
 F1 D:K94900 0.0 0.3 1.0
C7 D:K94900 1.4 0.1 1.0
F2 D:K94900 2.2 0.3 1.0
C4 D:K94900 2.3 0.5 1.0
C3 D:K94900 2.7 0.6 1.0
C6 D:K94900 2.9 97.1 1.0
CG D:HIS454 3.3 89.8 1.0
ND1 D:HIS454 3.4 96.5 1.0
CB D:HIS454 3.4 94.8 1.0
CG2 D:VAL455 3.7 91.8 1.0
C5 D:K94900 3.7 0.4 1.0
N D:VAL455 3.7 88.9 1.0
O D:GLU451 3.8 83.4 1.0
CD2 D:HIS454 3.8 91.3 1.0
CE1 D:HIS454 4.0 95.8 1.0
C D:HIS454 4.1 90.5 1.0
C1 D:K94900 4.2 0.6 1.0
CA D:VAL455 4.2 89.4 1.0
NE2 D:HIS454 4.2 0.4 1.0
CA D:HIS454 4.3 92.4 1.0
CZ3 D:TRP444 4.5 0.3 1.0
CD2 D:LEU458 4.6 0.1 1.0
CB D:VAL455 4.6 90.9 1.0
N1 D:K94900 4.6 0.8 1.0
C D:GLU451 4.6 97.3 1.0
CH2 D:TRP444 4.7 97.8 1.0
CA D:GLU451 4.8 0.4 1.0
CB D:GLU451 4.8 0.8 1.0
CD D:ARG390 4.9 1.0 1.0
O D:HIS454 4.9 81.1 1.0
CG D:ARG390 4.9 0.0 1.0
CD1 D:ILE393 5.0 78.6 1.0

Fluorine binding site 9 out of 10 in 6n0m

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Fluorine binding site 9 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F900

b:0.9
occ:1.00
 F2 E:K94900 0.0 0.9 1.0
C7 E:K94900 1.4 0.5 1.0
F1 E:K94900 2.2 0.9 1.0
C4 E:K94900 2.3 99.1 1.0
C5 E:K94900 2.7 85.4 1.0
C3 E:K94900 2.8 0.3 1.0
CG E:ARG390 3.3 0.6 1.0
CD E:ARG390 3.3 0.2 1.0
ND1 E:HIS454 3.6 0.6 1.0
C6 E:K94900 3.7 0.4 1.0
CE1 E:HIS454 3.7 0.4 1.0
CG E:HIS454 3.8 94.8 1.0
NE2 E:HIS454 3.9 0.0 1.0
CD2 E:LEU458 3.9 0.5 1.0
CD2 E:HIS454 4.0 92.6 1.0
C1 E:K94900 4.2 0.5 1.0
CB E:HIS454 4.5 99.6 1.0
CB E:ARG390 4.5 0.3 1.0
O2 E:K94900 4.6 84.5 1.0
CD1 E:ILE393 4.6 92.5 1.0
NE E:ARG390 4.7 0.4 1.0
N E:VAL455 4.8 89.0 1.0
C2 E:K94900 4.8 98.1 1.0
CG2 E:VAL455 4.9 85.4 1.0

Fluorine binding site 10 out of 10 in 6n0m

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Fluorine binding site 10 out of 10 in the Crystal Structure of SESTRIN2 in Complex with Nv-0005138


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of SESTRIN2 in Complex with Nv-0005138 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F900

b:0.9
occ:1.00
 F1 E:K94900 0.0 0.9 1.0
C7 E:K94900 1.4 0.5 1.0
F2 E:K94900 2.2 0.9 1.0
C4 E:K94900 2.4 99.1 1.0
C6 E:K94900 2.8 0.4 1.0
C5 E:K94900 3.0 85.4 1.0
CH2 E:TRP444 3.1 89.3 1.0
CG2 E:VAL455 3.2 85.4 1.0
CZ3 E:TRP444 3.3 90.6 1.0
C3 E:K94900 3.6 0.3 1.0
CD1 E:ILE393 3.6 92.5 1.0
O E:GLU451 4.2 98.0 1.0
CZ2 E:TRP444 4.4 82.6 1.0
CB E:VAL455 4.5 85.5 1.0
CA E:VAL455 4.5 89.4 1.0
N E:VAL455 4.5 89.0 1.0
CD1 E:LEU389 4.6 0.5 1.0
CE3 E:TRP444 4.6 87.6 1.0
CG E:ARG390 4.8 0.6 1.0
CD2 E:LEU458 4.9 0.5 1.0
C1 E:K94900 4.9 0.5 1.0
CB E:HIS454 5.0 99.6 1.0

Reference:

S.Sengupta, E.Giaime, S.Narayan, S.Hahm, J.Howell, D.O'neill, G.P.Vlasuk, E.Saiah. Discovery of Nv-5138, the First Selective Brain MTORC1 Activator. Sci Rep V. 9 4107 2019.
ISSN: ESSN 2045-2322
PubMed: 30858438
DOI: 10.1038/S41598-019-40693-5
Page generated: Thu Aug 1 22:25:20 2024

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