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Fluorine in PDB 5fyq: SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide

Protein crystallography data

The structure of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide, PDB code: 5fyq was solved by P.Knyphausen, S.De Boor, L.Scislowski, A.Extra, L.Baldus, M.Schacherl, U.Baumann, I.Neundorf, M.Lammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.61 / 3.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.948, 114.948, 206.476, 90.00, 90.00, 120.00
R / Rfree (%) 23.2 / 27.1

Other elements in 5fyq:

The structure of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide (pdb code 5fyq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide, PDB code: 5fyq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5fyq

Go back to Fluorine Binding Sites List in 5fyq
Fluorine binding site 1 out of 6 in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1008

b:47.5
occ:1.00
 FI1 C:FAK1008 0.0 47.5 1.0
CT C:FAK1008 1.4 49.3 1.0
FI3 C:FAK1008 2.2 44.8 1.0
FI2 C:FAK1008 2.4 42.2 1.0
CH C:FAK1008 2.4 39.0 1.0
OH C:FAK1008 2.8 28.1 1.0
NZ C:FAK1008 3.5 32.6 1.0
CD1 B:PHE119 3.9 60.2 1.0
CG B:PHE119 4.1 57.7 1.0
CB B:PHE96 4.1 84.6 1.0
CE1 B:PHE119 4.2 58.8 1.0
CD2 B:PHE119 4.5 58.9 1.0
CB B:PHE119 4.6 55.1 1.0
CZ B:PHE119 4.6 58.2 1.0
CG2 B:ILE169 4.7 35.4 1.0
CE C:FAK1008 4.7 32.1 1.0
CG B:PHE96 4.7 91.1 1.0
CE2 B:PHE119 4.8 59.0 1.0
O B:VAL233 4.8 35.5 1.0
CG2 B:ILE232 4.8 52.9 1.0
CD1 B:ILE169 4.8 38.7 1.0
CG B:ARG97 5.0 57.6 1.0

Fluorine binding site 2 out of 6 in 5fyq

Go back to Fluorine Binding Sites List in 5fyq
Fluorine binding site 2 out of 6 in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1008

b:42.2
occ:1.00
 FI2 C:FAK1008 0.0 42.2 1.0
CT C:FAK1008 1.5 49.3 1.0
FI3 C:FAK1008 2.3 44.8 1.0
FI1 C:FAK1008 2.4 47.5 1.0
CH C:FAK1008 2.5 39.0 1.0
O B:VAL233 2.7 35.5 1.0
NZ C:FAK1008 2.7 32.6 1.0
CG2 B:ILE232 3.0 52.9 1.0
OH C:FAK1008 3.7 28.1 1.0
C B:VAL233 3.7 37.4 1.0
CG2 B:ILE169 4.0 35.4 1.0
CE C:FAK1008 4.2 32.1 1.0
CB B:HIS187 4.2 36.7 1.0
O B:HIS187 4.4 40.2 1.0
CB B:ILE232 4.4 45.5 1.0
N B:VAL233 4.4 39.2 1.0
N B:PHE234 4.5 38.7 1.0
CA B:PHE234 4.5 38.7 1.0
CA B:VAL233 4.7 38.3 1.0
CD C:FAK1008 4.7 31.6 1.0
C B:ILE232 4.7 42.2 1.0
CG B:HIS187 4.8 34.7 1.0
CD1 B:ILE169 4.9 38.7 1.0
CD1 B:PHE119 4.9 60.2 1.0

Fluorine binding site 3 out of 6 in 5fyq

Go back to Fluorine Binding Sites List in 5fyq
Fluorine binding site 3 out of 6 in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1008

b:44.8
occ:1.00
 FI3 C:FAK1008 0.0 44.8 1.0
CT C:FAK1008 1.3 49.3 1.0
FI1 C:FAK1008 2.2 47.5 1.0
FI2 C:FAK1008 2.3 42.2 1.0
CH C:FAK1008 2.3 39.0 1.0
OH C:FAK1008 2.9 28.1 1.0
CG2 B:ILE169 3.1 35.4 1.0
NZ C:FAK1008 3.3 32.6 1.0
O B:GLN167 3.6 26.8 1.0
CB B:HIS187 3.8 36.7 1.0
ND1 B:HIS187 3.9 36.4 1.0
CG B:HIS187 4.1 34.7 1.0
CG2 B:ILE232 4.4 52.9 1.0
CB B:ILE169 4.4 35.9 1.0
O B:VAL233 4.5 35.5 1.0
CG1 B:ILE169 4.5 36.5 1.0
CE C:FAK1008 4.6 32.1 1.0
NE B:ARG97 4.6 50.4 1.0
CD1 B:ILE169 4.7 38.7 1.0
C B:GLN167 4.8 26.0 1.0
O B:HIS187 4.9 40.2 1.0
CE1 B:HIS187 4.9 35.3 1.0
N B:ILE169 4.9 32.6 1.0

Fluorine binding site 4 out of 6 in 5fyq

Go back to Fluorine Binding Sites List in 5fyq
Fluorine binding site 4 out of 6 in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1008

b:46.6
occ:1.00
 FI1 D:FAK1008 0.0 46.6 1.0
CT D:FAK1008 1.5 46.3 1.0
FI3 D:FAK1008 2.2 47.0 1.0
FI2 D:FAK1008 2.3 41.1 1.0
CH D:FAK1008 2.4 35.5 1.0
OH D:FAK1008 2.8 24.4 1.0
CE1 A:PHE96 3.2 44.6 1.0
CZ A:PHE96 3.3 47.7 1.0
CD1 A:PHE119 3.4 31.0 1.0
NZ D:FAK1008 3.5 28.3 1.0
CE1 A:PHE119 3.7 31.5 1.0
CG A:PHE119 4.1 31.7 1.0
NH2 A:ARG97 4.4 44.2 1.0
CD1 A:PHE96 4.4 39.0 1.0
CE2 A:PHE96 4.5 46.9 1.0
CZ A:PHE119 4.5 29.7 1.0
CB A:PHE119 4.6 30.9 1.0
CD1 A:ILE169 4.7 27.6 1.0
CE2 A:PHE235 4.7 28.9 1.0
CE D:FAK1008 4.8 29.1 1.0
NE A:ARG97 4.8 42.4 1.0
CD2 A:PHE119 4.8 28.8 1.0
CG2 A:ILE232 4.9 40.1 1.0

Fluorine binding site 5 out of 6 in 5fyq

Go back to Fluorine Binding Sites List in 5fyq
Fluorine binding site 5 out of 6 in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1008

b:41.1
occ:1.00
 FI2 D:FAK1008 0.0 41.1 1.0
CT D:FAK1008 1.4 46.3 1.0
FI3 D:FAK1008 2.1 47.0 1.0
FI1 D:FAK1008 2.3 46.6 1.0
CH D:FAK1008 2.5 35.5 1.0
NZ D:FAK1008 2.7 28.3 1.0
O A:VAL233 2.9 22.9 1.0
CG2 A:ILE232 3.0 40.1 1.0
OH D:FAK1008 3.6 24.4 1.0
C A:VAL233 3.8 23.9 1.0
CE D:FAK1008 4.2 29.1 1.0
CA A:PHE234 4.2 22.5 1.0
N A:PHE234 4.3 23.4 1.0
CD1 A:PHE119 4.4 31.0 1.0
CB A:ILE232 4.4 33.2 1.0
CD D:FAK1008 4.7 31.2 1.0
N A:VAL233 4.9 27.7 1.0
O A:HIS187 5.0 24.4 1.0
CG2 A:ILE169 5.0 29.4 1.0
CA A:VAL233 5.0 25.8 1.0
C A:PHE234 5.0 22.8 1.0
CD1 A:ILE169 5.0 27.6 1.0

Fluorine binding site 6 out of 6 in 5fyq

Go back to Fluorine Binding Sites List in 5fyq
Fluorine binding site 6 out of 6 in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1008

b:47.0
occ:1.00
 FI3 D:FAK1008 0.0 47.0 1.0
CT D:FAK1008 1.2 46.3 1.0
FI2 D:FAK1008 2.1 41.1 1.0
FI1 D:FAK1008 2.2 46.6 1.0
CH D:FAK1008 2.3 35.5 1.0
OH D:FAK1008 3.0 24.4 1.0
NZ D:FAK1008 3.1 28.3 1.0
CG2 A:ILE169 3.6 29.4 1.0
CG2 A:ILE232 3.8 40.1 1.0
CD1 A:ILE169 4.0 27.6 1.0
NH2 A:ARG97 4.0 44.2 1.0
CB A:HIS187 4.1 22.6 1.0
CZ A:PHE96 4.2 47.7 1.0
O A:VAL233 4.2 22.9 1.0
CE D:FAK1008 4.4 29.1 1.0
O A:GLN167 4.4 23.2 1.0
ND1 A:HIS187 4.5 26.0 1.0
CE1 A:PHE96 4.6 44.6 1.0
CG A:HIS187 4.7 24.0 1.0
CG1 A:ILE169 4.7 28.4 1.0
O A:HIS187 4.7 24.4 1.0
CB A:ILE169 4.7 27.9 1.0

Reference:

P.Knyphausen, S.De Boor, N.Kuhlmann, L.Scislowski, A.Extra, L.Baldus, M.Schacherl, U.Baumann, I.Neundorf, M.Lammers. Insights Into Lysine-Deacetylation of Natively Folded Substrate Proteins By Sirtuins. J.Biol.Chem. V. 291 14677 2016.
ISSN: ISSN 0021-9258
PubMed: 27226597
DOI: 10.1074/JBC.M116.726307
Page generated: Thu Aug 1 09:29:53 2024

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