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Fluorine in PDB 4l3o: Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5

Protein crystallography data

The structure of Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5, PDB code: 4l3o was solved by K.Yamagata, H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.59 / 2.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.180, 135.613, 148.830, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 26.3

Other elements in 4l3o:

The structure of Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5 (pdb code 4l3o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5, PDB code: 4l3o:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4l3o

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Fluorine binding site 1 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1008

b:30.9
occ:1.00
 FI1 E:FAK1008 0.0 30.9 1.0
CT E:FAK1008 1.3 20.9 1.0
FI3 E:FAK1008 2.2 15.4 1.0
FI2 E:FAK1008 2.2 23.5 1.0
CH E:FAK1008 2.3 20.2 1.0
OH E:FAK1008 2.6 19.6 1.0
O A:GLN167 3.5 21.0 1.0
NZ E:FAK1008 3.6 14.8 1.0
ND1 A:HIS187 3.7 18.1 1.0
O E:HOH1116 3.7 20.2 1.0
CG2 A:ILE169 3.8 20.8 1.0
CB A:HIS187 4.1 15.0 1.0
CD1 A:ILE169 4.2 18.7 1.0
CG A:HIS187 4.2 12.1 1.0
CG1 A:ILE169 4.4 23.7 1.0
O A:HOH641 4.4 15.4 1.0
CE1 A:HIS187 4.6 20.4 1.0
C A:GLN167 4.7 18.2 1.0
CE E:FAK1008 4.7 19.6 1.0
CB A:ILE169 4.7 28.2 1.0

Fluorine binding site 2 out of 12 in 4l3o

Go back to Fluorine Binding Sites List in 4l3o
Fluorine binding site 2 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1008

b:23.5
occ:1.00
 FI2 E:FAK1008 0.0 23.5 1.0
CT E:FAK1008 1.3 20.9 1.0
FI3 E:FAK1008 2.2 15.4 1.0
FI1 E:FAK1008 2.2 30.9 1.0
CH E:FAK1008 2.3 20.2 1.0
OH E:FAK1008 3.0 19.6 1.0
CD1 A:PHE119 3.1 18.1 1.0
NZ E:FAK1008 3.2 14.8 1.0
CE1 A:PHE119 3.5 23.1 1.0
CG A:PHE119 3.7 22.9 1.0
CB A:PHE119 4.1 19.2 1.0
CZ A:PHE119 4.3 26.2 1.0
CD1 A:ILE169 4.4 18.7 1.0
CE E:FAK1008 4.5 19.6 1.0
CD2 A:PHE119 4.5 26.1 1.0
O A:VAL233 4.6 17.6 1.0
CE2 A:PHE119 4.8 24.1 1.0

Fluorine binding site 3 out of 12 in 4l3o

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Fluorine binding site 3 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1008

b:15.4
occ:1.00
 FI3 E:FAK1008 0.0 15.4 1.0
CT E:FAK1008 1.3 20.9 1.0
FI2 E:FAK1008 2.2 23.5 1.0
FI1 E:FAK1008 2.2 30.9 1.0
CH E:FAK1008 2.3 20.2 1.0
NZ E:FAK1008 2.8 14.8 1.0
O A:VAL233 3.2 17.6 1.0
OH E:FAK1008 3.4 19.6 1.0
CG2 A:ILE232 3.6 17.7 1.0
CB A:HIS187 3.8 15.0 1.0
CG2 A:ILE169 3.8 20.8 1.0
O A:HIS187 4.1 19.4 1.0
CE E:FAK1008 4.2 19.6 1.0
C A:VAL233 4.2 14.9 1.0
CD1 A:ILE169 4.2 18.7 1.0
CG A:HIS187 4.3 12.1 1.0
ND1 A:HIS187 4.4 18.1 1.0
N A:VAL233 4.7 17.0 1.0
CD1 A:PHE119 4.8 18.1 1.0
CA A:HIS187 4.9 16.5 1.0
CG1 A:ILE169 4.9 23.7 1.0
C A:HIS187 4.9 16.6 1.0
CB A:ILE169 5.0 28.2 1.0
CA A:VAL233 5.0 13.2 1.0

Fluorine binding site 4 out of 12 in 4l3o

Go back to Fluorine Binding Sites List in 4l3o
Fluorine binding site 4 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1008

b:39.6
occ:1.00
 FI1 F:FAK1008 0.0 39.6 1.0
CT F:FAK1008 1.3 32.6 1.0
FI3 F:FAK1008 2.2 31.1 1.0
FI2 F:FAK1008 2.2 25.6 1.0
CH F:FAK1008 2.3 25.9 1.0
OH F:FAK1008 2.6 30.4 1.0
NZ F:FAK1008 3.6 19.2 1.0
O B:GLN167 3.9 21.3 1.0
CG2 B:ILE169 4.0 23.8 1.0
CD1 B:ILE169 4.2 21.4 1.0
ND1 B:HIS187 4.3 20.7 1.0
CB B:HIS187 4.5 22.9 1.0
CG1 B:ILE169 4.5 30.3 1.0
CG B:HIS187 4.7 21.6 1.0
CE1 B:PHE119 4.7 27.8 1.0
CD1 B:PHE119 4.8 26.2 1.0
CE F:FAK1008 4.8 21.0 1.0
CB B:ILE169 4.9 25.0 1.0

Fluorine binding site 5 out of 12 in 4l3o

Go back to Fluorine Binding Sites List in 4l3o
Fluorine binding site 5 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1008

b:25.6
occ:1.00
 FI2 F:FAK1008 0.0 25.6 1.0
CT F:FAK1008 1.3 32.6 1.0
FI3 F:FAK1008 2.2 31.1 1.0
FI1 F:FAK1008 2.2 39.6 1.0
CH F:FAK1008 2.3 25.9 1.0
NZ F:FAK1008 3.0 19.2 1.0
OH F:FAK1008 3.2 30.4 1.0
CD1 B:PHE119 3.2 26.2 1.0
CG B:PHE119 3.7 30.8 1.0
CE1 B:PHE119 3.7 27.8 1.0
CB B:PHE119 4.0 26.5 1.0
O B:VAL233 4.1 17.0 1.0
CE F:FAK1008 4.3 21.0 1.0
CD2 B:PHE119 4.5 42.0 1.0
CZ B:PHE119 4.5 37.0 1.0
CG2 B:ILE232 4.5 34.8 1.0
CD1 B:ILE169 4.7 21.4 1.0
CE2 B:PHE119 4.8 32.5 1.0

Fluorine binding site 6 out of 12 in 4l3o

Go back to Fluorine Binding Sites List in 4l3o
Fluorine binding site 6 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1008

b:31.1
occ:1.00
 FI3 F:FAK1008 0.0 31.1 1.0
CT F:FAK1008 1.3 32.6 1.0
FI2 F:FAK1008 2.2 25.6 1.0
FI1 F:FAK1008 2.2 39.6 1.0
CH F:FAK1008 2.3 25.9 1.0
NZ F:FAK1008 2.8 19.2 1.0
OH F:FAK1008 3.3 30.4 1.0
CB B:HIS187 3.3 22.9 1.0
O B:VAL233 3.4 17.0 1.0
CG2 B:ILE232 3.5 34.8 1.0
CG2 B:ILE169 3.5 23.8 1.0
O B:HIS187 3.9 21.4 1.0
CG B:HIS187 3.9 21.6 1.0
CE F:FAK1008 4.2 21.0 1.0
ND1 B:HIS187 4.2 20.7 1.0
CD1 B:ILE169 4.3 21.4 1.0
C B:VAL233 4.4 22.4 1.0
CA B:HIS187 4.5 21.7 1.0
C B:HIS187 4.6 29.4 1.0
O B:GLN167 4.6 21.3 1.0
N B:VAL233 4.7 22.0 1.0
CB B:ILE169 4.7 25.0 1.0
CG1 B:ILE169 4.8 30.3 1.0
CD2 B:HIS187 4.9 18.0 1.0
CB B:ILE232 5.0 33.2 1.0

Fluorine binding site 7 out of 12 in 4l3o

Go back to Fluorine Binding Sites List in 4l3o
Fluorine binding site 7 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1008

b:24.4
occ:1.00
 FI1 G:FAK1008 0.0 24.4 1.0
CT G:FAK1008 1.3 21.4 1.0
FI2 G:FAK1008 2.2 27.6 1.0
FI3 G:FAK1008 2.2 25.7 1.0
CH G:FAK1008 2.3 20.9 1.0
OH G:FAK1008 2.6 29.4 1.0
NZ G:FAK1008 3.6 13.3 1.0
O G:HOH1204 3.6 31.6 1.0
CD1 C:ILE169 4.0 31.6 1.0
O C:GLN167 4.0 17.4 1.0
ND1 C:HIS187 4.1 17.7 1.0
CB C:HIS187 4.4 14.7 1.0
CG1 C:ILE169 4.4 32.9 1.0
CG C:HIS187 4.5 15.8 1.0
CG2 C:ILE169 4.6 24.4 1.0
CE G:FAK1008 4.7 15.1 1.0
CE1 C:HIS187 4.9 18.7 1.0
CD1 C:PHE119 5.0 31.1 1.0
CE1 C:PHE119 5.0 34.1 1.0

Fluorine binding site 8 out of 12 in 4l3o

Go back to Fluorine Binding Sites List in 4l3o
Fluorine binding site 8 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1008

b:27.6
occ:1.00
 FI2 G:FAK1008 0.0 27.6 1.0
CT G:FAK1008 1.3 21.4 1.0
FI3 G:FAK1008 2.2 25.7 1.0
FI1 G:FAK1008 2.2 24.4 1.0
CH G:FAK1008 2.3 20.9 1.0
NZ G:FAK1008 3.1 13.3 1.0
OH G:FAK1008 3.1 29.4 1.0
CD1 C:PHE119 3.2 31.1 1.0
CG C:PHE119 3.5 28.7 1.0
CE1 C:PHE119 3.7 34.1 1.0
CB C:PHE119 3.9 26.1 1.0
CD2 C:PHE119 4.2 37.9 1.0
CZ C:PHE119 4.4 39.1 1.0
CE G:FAK1008 4.4 15.1 1.0
CE2 C:PHE119 4.6 35.0 1.0
O C:VAL233 4.7 19.8 1.0
CD1 C:ILE169 4.8 31.6 1.0
CE2 C:PHE235 4.9 19.9 1.0

Fluorine binding site 9 out of 12 in 4l3o

Go back to Fluorine Binding Sites List in 4l3o
Fluorine binding site 9 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1008

b:25.7
occ:1.00
 FI3 G:FAK1008 0.0 25.7 1.0
CT G:FAK1008 1.3 21.4 1.0
FI2 G:FAK1008 2.2 27.6 1.0
FI1 G:FAK1008 2.2 24.4 1.0
CH G:FAK1008 2.3 20.9 1.0
NZ G:FAK1008 2.8 13.3 1.0
O C:VAL233 3.3 19.8 1.0
OH G:FAK1008 3.3 29.4 1.0
CG2 C:ILE232 3.4 19.1 1.0
CB C:HIS187 3.9 14.7 1.0
CD1 C:ILE169 4.0 31.6 1.0
CE G:FAK1008 4.2 15.1 1.0
C C:VAL233 4.2 20.0 1.0
O C:HIS187 4.3 19.3 1.0
CG2 C:ILE169 4.4 24.4 1.0
CG C:HIS187 4.4 15.8 1.0
ND1 C:HIS187 4.6 17.7 1.0
CD1 C:PHE119 4.7 31.1 1.0
N C:VAL233 4.8 20.5 1.0
CG1 C:ILE169 4.9 32.9 1.0
CB C:ILE232 4.9 25.0 1.0
N C:PHE234 4.9 21.8 1.0

Fluorine binding site 10 out of 12 in 4l3o

Go back to Fluorine Binding Sites List in 4l3o
Fluorine binding site 10 out of 12 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F1008

b:37.3
occ:1.00
 FI1 H:FAK1008 0.0 37.3 1.0
CT H:FAK1008 1.3 26.9 1.0
FI3 H:FAK1008 2.2 24.5 1.0
FI2 H:FAK1008 2.2 36.9 1.0
CH H:FAK1008 2.3 25.4 1.0
NZ H:FAK1008 3.0 27.6 1.0
OH H:FAK1008 3.2 23.1 1.0
CB D:HIS187 3.2 16.3 1.0
ND1 D:HIS187 3.4 24.4 1.0
CG2 D:ILE169 3.6 20.7 1.0
CG D:HIS187 3.6 18.5 1.0
O D:GLN167 3.7 26.0 1.0
CD1 D:ILE169 4.3 22.1 1.0
CE H:FAK1008 4.3 16.3 1.0
O D:HIS187 4.4 21.3 1.0
O D:VAL233 4.5 26.0 1.0
CG2 D:ILE232 4.5 28.6 1.0
CE1 D:HIS187 4.5 18.6 1.0
CG1 D:ILE169 4.6 28.4 1.0
CA D:HIS187 4.6 19.8 1.0
CB D:ILE169 4.7 24.4 1.0
CD2 D:HIS187 4.8 20.4 1.0
C D:GLN167 4.9 24.8 1.0
C D:HIS187 4.9 20.0 1.0

Reference:

K.Yamagata, Y.Goto, H.Nishimasu, J.Morimoto, R.Ishitani, N.Dohmae, N.Takeda, R.Nagai, I.Komuro, H.Suga, O.Nureki. Structural Basis For Potent Inhibition of SIRT2 Deacetylase By A Macrocyclic Peptide Inducing Dynamic Structural Change Structure V. 22 345 2013.
ISSN: ISSN 0969-2126
PubMed: 24389023
DOI: 10.1016/J.STR.2013.12.001
Page generated: Thu Aug 1 03:22:00 2024

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