Atomistry » Fluorine » PDB 5fd2-5g3j » 5fyq
Atomistry »
  Fluorine »
    PDB 5fd2-5g3j »
      5fyq »

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: Sun Dec 13 12:22:43 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy